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					                                                                                Cornell University
                                                                                Life Sciences Core Laboratories Center
    Grills G, VanEe J, Schweitzer P, Wang W, Li Y, Zhang S, Kinsland C, Williams R, Deng K-
    Grills G, VanEe J, Schweitzer P, Wang W, Li Y, Zhang S, Kinsland C, Williams R, Deng K-Y ,, Pillardy J, Sun Q, Stelick T, Paronett E, Spisak J, Cote L, Cameron R, Zhao J, Hover B, Figueroa M, Shaknovich R,
                                                                                           K-Y Pillardy J, Sun Q, Stelick T, Paronett E, Spisak J, Cote L, Cameron R, Zhao J, Hover B, Figueroa M, Shaknovich R,
               Xin Y, Monni S, Sherwood R, Baumgart S, Mattison J, Mottler C, Bayles C, Xia G, Ponnala L, Stefanov S, Bukowski R, Myers C, Ripoll D, Flaherty J, Manocchia A, Dick J, Dodge E, Smith K,
               Xin Y, Monni S, Sherwood R, Baumgart S, Mattison J, Mottler C, Bayles C, Xia G, Ponnala L, Stefanov S, Bukowski R, Myers C, Ripoll D, Flaherty J, Manocchia A, Dick J, Dodge E, Smith K,
                                                                    Clark A, Lin D, Aquadro C, Zipfel W, Begley T, Rose J, Soloway P, Melnick A
                                                                    Clark A, Lin D, Aquadro C, Zipfel W, Begley T, Rose J, Soloway P, Melnick A
                                                                                                                  Life Sciences Core Laboratories Center, Cornell University, Ithaca, NY
                                                                                                                  Life Sciences Core Laboratories Center, Cornell University, Ithaca, NY
                                                                                                                                                                              Ithaca,


                  ABSTRACT                                                                                                                                           CORE LABORATORIES
The Cornell University Life Sciences Core Laboratories
Center (CLC) provides an array of genomics, proteomics,                                               DNA Sequencing                                                           Proteomics & Mass                                                                                                 Computational Biology
imaging and informatics shared research resources and
services to the university community and to outside
investigators. With a concentration of advanced
                                                                                                      and Genotyping                                                          Spectrometry Facility                                                                                                  Service Unit
instrumentation and expertise in their applications, the CLC
is a key resource for life sciences basic research and
                                                                                                          Facility
medical research investigators at Cornell University and at
other academic institutions and commercial enterprises.


                                                                                                                                                                                                                                                                                               Bioinformatics and computational biology services

        INTRODUCTION
                                                                                                                                                                        Mass Spectrometer             Mass Spectrometer              Mass Spectrometer
                                                                                                                                                                  Dionex MDLC and ABI 4000 Q Trap   ABI 4700 MALDI-TOF/TOF          Bruker Esquire Ion Trap                                • Provide research, software and hardware support for biology
                                                                                             Illumina / Solexa          Sequenom         Applied Biosystems                                                                                                                                  research groups.
                                                                                              Genome Analyzer        Compact MassArray   3730xl DNA Analyzer
                                                                                                                                                                                                                                                                                           • Research: collaborate on research projects that require
                                                                                                                                                                                                                                                                                             expertise in genomics, proteomics, quantitative genetics and
Scope and goals of Center: The Cornell University                                                                                                                                                                                                                                            structural biology.
Core Laboratories Center (CLC) includes fee-for-service
research, technology testing and development, and                                                                                                                                                                                                                                          • Computational resources: developed and maintain an extensive
educational components. The mission of the CLC is to                                                                                                                                                                                                                                         suit of computational biology applications on clusters (BioHPC),
promote research in the life sciences with advanced                                                                                                                      Protein preparation, detection, and identification                                                                  with web interface for easy access.
technologies in a shared resource environment
                                                                                            High throughput DNA sequencing and genotyping
                                                                                                                                                                         •   Protein and Peptide Separation (2D gel and 2D HPLC)                                                           • Software development: develop and modify software tools for
(http://cores.lifesciences.cornell.edu).                                             •   Next generation sequencing (Roche 454 GS FLX, Illumina GA II)                   •   Sample Preparation (digestion, desalt, concentration)                                                           customized solutions; adapt computationally intensive
                                                                                     •   Conventional DNA sequence detection and analysis (ABI 3730xl)                   •   Protein Identification (gel and solution samples)                                                               applications into massively parallel environment.
New Life Sciences Initiative: The CLC was established as                             •   Fragment analysis (microsatellite instability)                                  •   Quantitative Proteomics (2D DIGE, iTRAQ)
                                                                                                                                                                                                                                                                                                                  High-
                                                                                                                                                                                                                                                                                           • One of ten Microsoft High-Performance Computing Institutes
part of the Cornell University New Life Sciences Initiative                          •   SNP genotyping (ABI SNPlex, Illumina, Affymetrix, Sequenom)                     •   Protein Characterization (PTMs)
(www.lifesciences.cornell.edu).                                                                                                                                                                                                                                                              worldwide.
                                                                                     •   Real Time PCR (ABI 7900 HT)                                                     •   Small Molecule Identification and Quantitation

University funded core facilities: The CLC includes all the
university funded core facilities at Cornell University in
Ithaca, NY. University funding is used to allow core facilities
to grow to a mature level of service to the research
community. The Center is currently composed of 9 different
                                                                                                   DNA and Protein                                                       Protein Production and                                                                                                  Information Technology
facilities, with ~10,000 sq. ft. of research and administrative
space. The CLC includes both newly established and pre-
                                                                                                  Microarrays Facility                                                   Characterization Facility                                                                                                   Services Facility
existing facilities. The Center has a review policy that allows                                                                                                                                                                            Biochemical Assays

for the addition of new cores by request of faculty.
                                                                                                                                                                                                                                                     Binding
                                                                                                                                                                                                                                                                  Protein
                                                                                                                                                                                                                                                                         Surface
                                                                                                                                                                                                                                                                         Waveguide
                                                                                                                                                                                                                                                                         Substrat e




Administration: The Center is administered through the                                                                                                                                                                                   Broadband
                                                                                                                                                                                                                                          Source
                                                                                                                                                                                                                                                               Reflec ted
                                                                                                                                                                                                                                                               wavelength



Cornell University Institute for Biotechnology and Life                                                                                                                                                                                      Cell-Based Assays
                                                                                                                                                                                                                                                                 Mass


Science Technologies (www.biotech.cornell.edu).
                                                                                                                                                                                                                                                     Cell        R edist ribut ion


                                                                                                                                                                                                               Calc MW: 61.05 kDa                                         Surface
                                                                                                                                                                                                                                                                          Waveguide



The Cornell University Life Sciences Core Laboratories
                                                                                                                                                                                                                                                                          Substrate


                                                                                          GeneChip Microarrays   BeadChip Microarrays    NimbleGen Microarrays
Center provides resources? The resources and network of
Who can use ouran array of services as part of a services of
                                                                                                                                                                                                                                         Broadband               Reflected
                                                                                               Affymetrix         Illumina BeadStation     Hybridization System                                                                           Source                wavelength




life CLC facilities are open to all at Cornell University. We
the science shared core facilitiesinvestigators at Cornell                                                                                                                                                      Analytical              High Throughput
                                                                                                                                                                       AKTA FPLC         AKTAXpress
                                                                                                                                                                                                            Ultracentrifugation            Screening                                                          Information technology (IT) services
University. The CLC supports research at the Cornell and
serve the Cornell University basic research investigator
medical in Ithaca, NY, the Weill Cornell Graduate School of
campus research community, other academic institutions,                                                                                                             Protein expression, purification, and characterization                                                                 • Create and maintain IT infrastructure that supports research
Medical Sciences in New York City, NY, and the Weill Cornell
and commercial enterprises, with the concentration of                                                                                                             and high throughput biochemical and cell based screening                                                                   and operations within the core laboratories of the Center.
advanced instrumentation and The CLC also within our
Medical College in Doha, Qatar.expertise foundprovides                                             Gene expression and DNA analysis
resources and services to investigators at other academic
laboratories. In association with the New York State Center                                                                                                          • Cloning and Mutagenesis: produce constructs containing
                                                                                                                                                                                   Mutagenesis                                                                                                          • Create and support enterprise LIMS used to place
for Advanced Technology (CAT) commercial enterprises.
institutions and to researchers atin Life Science Enterprise,                              Expression analysis: quantitation (coding level analysis,
                                                                                                       analysis                                                        desired sequence.                                                                                                                  orders and receive results from multiple laboratories,
New York State companies receive a discount on our                                         biomarker signatures, transcription mapping), regulation                                                                                                                                                       to view sample submission history with associated
                                                                                           (DNA methylation, origins of replication, mapping sites of                • Protein Purification: purify proteins from recombinant strains.
                                                                                                                                                                               Purification
CAT: The CLC is part of a New York State designated
services.                                                                                                                                                                                                                                                                                                 data files, to provide data results quickly and securely,
Center for Advanced Technology in Life Science Enterprise.                                 transcription factor binding).                                            • Characterization: study binding interactions, oligomeric state
                                                                                                                                                                       Characterization                                                                                                                   to track financials, and to view order status.
NY State companies receive a discount on CLC services.                                     DNA analysis: whole genome (linkage analysis, association
                                                                                                analysis                                                               and enzyme kinetics.
                                                                                                                                                                                                                                                                                                        • Offer access to commercial software licenses.
                                                                                           studies, population genetics, chromosomal copy number),                     High-            Label-
                                                                                                                                                                     • High-Throughput Label-Free Screening: for biochemical and
                                                                                           targeted genotyping (fine mapping, custom SNPs), sequence                   cell-based assays.                                                                                                  • Provide IT support for academic units on campus outside of
                                                                                           analysis (comparative sequencing, SNP identification,
               RESOURCES
                                                                                                                                                                                                                                                                                             the Center as a fee-for-service.
                                                                                           sequence analysis of small genomes).                                      • Training: train students in methods and techniques.
                                                                                                                                                                       Training



DNA Sequencing and Genotyping: Roche 454 GS FLX, Illumina Genome
                        Genotyping
Analyzer II with Paired End module, two ABI 3730xl DNA Analyzers, Illumina
BeadStation 500GX, Sequenom MassArray, ABI 7900 HT, 3 Tecan Genesis liquid
                                                                                                Epigenomics Facility                                                                 Microscopy and                                                                                                 Advanced Technology
                                                                                                                                                                                     Imaging Facility                                                                                                   Assessment
handling robots (2 RSP200 and a RSP150), Beckman Biomek FX, MD spectraPlus
plate reader, Nanodrop 1000, Sigma 4-15C centrifuge, Fisher Marathon 3200R               Analysis of regulation of gene activity and expression
centrifuge, six PE 9700 thermocyclers, AbGene plate heat sealer, Caliper LC90.
DNA Microarrays: Affymetrix System (including 3000 Scanner with autoloader,
      Microarrays                                                                          Use NimbleGen, Illumina, and Affymetrix microarrays,
three 450 Fluidics Stations, and a 640 Hyb Oven), custom spotted arrayer, Maui                                                                                                                                                                                                        • Identify, test, evaluate, acquire, implement, and optimize newly
4- and 12-bay Hyb Stations, Agilent scanner with autoloader, Axon 4000B                    Sequenom MassArray, ABI 3730xl, Illumina Genome Analyzer
                                                                                                                                                                                                                                                                                        emerging technologies as shared resources in core facilities.
scanner, Agilent 2100 Bioanalyzer, Multimek 96, Tecan HS400 hybridization                  for studies on:
station. Proteomics and Mass Spectrometry: 4 mass specs: an ABI 4700
                                 Spectrometry                                                     • DNA methylation
Analyzer MALDI-TOF/TOF, an ABI 4000 Q Trap electrospray ionization (ESI)-                                                                                                                                                                                                             • Implement the Life Sciences Advanced Technology Seminar series.
based hybrid triple quadrupole/linear ion trap, an Bruker ESI-based 3D ion trap                   • Protein-nucleic acid association
Esquire, and a API 150 ESI. Two HPLC systems: a Dionex MDLC system and an                         • Small RNA, CGH and CNV profiling
Agilent 1100 HPLC, both interfaced with electrospray ionization mass specs for
online LC/MS/MS or offline MALDI-TOF/TOF analysis. One 2D gel electrophoresis
system (GE Healthcare), a gel spot picker robot (ProPic, Genomic Solution), a                                                                                                                                                                                                                                                  Contact Information
                                                                                                                                                                                                                                                                                                                                   http://cores.lifesciences.cornell.edu
gel extraction/liquid handling robot (ProPrep, Genomic Solution), a gel image
scanner (GE Healthcare), and a Typhoon 9410 image system (GE Healthcare) for                                          Animal
                                                                                                                                                                                                                                                                                       Core Laboratories Center                    Proteomics and Mass Spectrometry                       Advanced Technology

                                                                                                   Transgenic Facility
quantitative fluorescence analysis. Protein Production: AKTA FPLC, ITC, French
                                                                                                                                                                                                                                                                                       George Grills                               Sheng Zhang, Director                                  Assessment
Press, sonicator, Stopped Flow Spectrophotometer, shaker, autoclave, Storm
                                                                                                                                                                                                                                                                                       Director of Operations                      LSCLC_proteomics_ms@cornell.edu                        George Grills, Director
Imager, plate reader, Analytical Ultra Centrifuge, Allegra centrifuge, Avanti J-20
                                                                                                                                                                                                                                                                                       LSCLC_director@cornell.edu                                                                         LSCLC_ata@cornell.edu
XPI centrifuge, L100 XP centrifuge, Rapid Quench, Emulsiflex, Basic Z, Corning                                   A                                                                                                                                                                                                   Protein Production and Characterization
Epic. Microscopy and Imaging: three confocal microscopes (Leica TCS SP2 with
spectral capabilities, Zeiss LSM 510 Meta with spectral capabilities, and BioRad
                                                                                                                                                                                  Image data collection and analysis                                                                   DNA Sequencing and Genotyping Cynthia Kinsland, Director
                                                                                                                                                                                                                                                                                                                                                                   Institute for Biotechnology
                                                                                                                                                                                                                                                                                       Peter Schweitzer, Director    LSCLC_protein@cornell.edu
MRC600), a fluorescence microscope (Olympus BX-50 with MetaMorph                                                                                                                                                                                                                                                                                                   and Life Science Technology
                                                                                                                                                                                                                                                                                       LSCLC_dna@cornell.edu
software), two stereo microscopes (Zeiss Stemi 2000C and Leica MZFLIII with                                                                                          Transmitted and fluorescence light microscopy, confocal                                                                                         Computational Biology Service Unit
                                                                                                                                                                                                                                                                                                                                                                   http://www.biotech.cornell.edu
fluorescence capabilities), a spectrofluorometer (SLM 8000c), two whole mouse                                                                                        microscopy, stereo microscopy, spectrofluorometry, molecular                                                      DNA Microarrays               Jaroslaw Pillardy, Director
luminescence / fluorescence imagers (Olympus OV100 and Xenogen IVIS-200), a
high-resolution ultrasound imager (Visual Sonics Vevo 770), and a multiphoton                                                                                        imaging (whole mouse luminescence and fluorescence imaging),                                                      Wei Wang, Director            LSCLC_cbsu@cornell.edu
                                                                                                                                                                                                                                                                                       LSCLC_mircroarray@cornell.edu
microscope (in development). Transgenics: Nikon and Leica microscopes,                                Transgenic organism production                                 and high-resolution ultrasonic imaging.                                                                                                         Information Technology Services
                                                                                                                                                                                                                                                                                                                                                                                    Member of


Eppendorf and Narishige micro-manipulators, an Eppendorf Transjector, Sutter                                                                                                                                                                                                           Epigenomics                   James VanEe, Director
Flaming micropipette puller and FTS bio-cool III freezer. Computational Biology:
a 677 node cluster with 1226 CPUs, including a 425 node Sun Linux cluster with
                                                                                     • Generate gain-of-function and loss-of-function transgenic mice.               Instrument training and application expertise for digital imaging,                                                Yushan Li, Director           LSCLC_its@cornell.edu
                                                                                                                                                                                                                                                                                       LSCLC_epigenomics@cornell.edu
280 GB local HD space, and 3 Windows clusters totaling 252 nodes with 344 GB         •    Provide nuclear injection of DNA into fertilized oocytes.                  image analysis, live cell microscopy, tissue and animal imaging
                                                                                                                                                                                                                                                                                                                     Trangenic Facility
local HD space. 6 web and database servers with 1.1 TB total HD space. Four          •    Provide ES cell injections into blastocysts.                               and fluorescence techniques and measurements.                                                                     Microscopy and Imaging        Ke-Yu Deng, Director                    New York State Office of Science, Technology and Academic Research
file and database servers with 15.5 TB total HD space. Access to large shared-                                                                                                                                                                                                         Rebecca Williams, Director    LSCLC_transgenics@cornell.edu
memory server with 64 GB RAM. Information Technology: 15 servers, >4 TB              •    Provide cryopreservation services.
                                                                                                                                                                                                                                                                                       LSCLC_mif@cornell.edu
RAID storage, 4-core server 8 GB RAM, 12 TB backup capacity.                         •    Generation of transgenic organisms of other species possible.
                           Cornell University
                           Life Sciences
                           Core Laboratories Center                   DNA Sequencing and Genotyping Facility
                                                                                       Schweitzer P, Stelick T, Paronett E, Spisak J, Cote L, Cameron R, Aquadro C
                                                                                       Schweitzer P, Stelick T, Paronett E, Spisak J, Cote L, Cameron R, Aquadro C

                                                                                                                                         Cornell University, Ithaca NY
                                                                                                                                         Cornell University, Ithaca NY


               ABSTRACT                                                                                                                                     SERVICES AND RESULTS
The DNA Sequencing and Genotyping Facility of the Cornell
University Life Sciences Core Laboratories Center (CLC)               New Sequencing Technologies                                                                          Illumina Sequencing                                                                             Facility Users
provides an array of shared research resources and services
to the university community and to outside investigators.              Next Generation Sequencing Platforms                                                    Run Statistics from phiX Controls (n=26)                                                                                                         Facility User
The facility offers a concentration of advanced                                                                                                                                   Average   Std. Dev.   Minimum   Maximum                                                                                    Satisfaction Survey
                                                                                                                                                              Clusters per Tile     28 K      6.2 K       21 K      48 K                                 Numbers of Samples
instrumentation and expertise in their applications. Services                                                                                                Reads per Channel     8.3 M      1.9 M      6.2 M      14 M
                                                                                                                                                                                                                                                       per Institutional Affiliation
include the ABI3730xl platform for Sanger sequencing of                                                                                                      Bases per Channel
                                                                                                                                                             Reads per Full Run
                                                                                                                                                                                   297 M
                                                                                                                                                                                    66 M
                                                                                                                                                                                              67 M
                                                                                                                                                                                              15 M
                                                                                                                                                                                                         223 M
                                                                                                                                                                                                          49 M
                                                                                                                                                                                                                   517 M
                                                                                                                                                                                                                   115 M
plasmid and PCR products. Resources for massively-                                                                                                           Bases per Full Run    2.4 B      0.5 B       1.8 B    4.1 B
                                                                                                                                                              % Pass Filtering      55%        12%        31%       71%
parallel, “next generation” sequencing include the Roche                                                                                                        % Alignment         92%       9.5%        72%       97%
454 GS FLX and the Illumina Genome Analyzer II. The                                                                                                               % Error           1.3%      1.1%        0.5%      4.9%

Sequenom MassArray is available for SNP genotyping,
methylation and gene expression studies. The ABI 7900HT
is available for RT-PCR studies. The facility also provides
                                                                          Roche 454 GS FLX                  Illumina Genome Analyzer II
support for SNP genotyping using automated sample                         • 150 million bases / full run    • 1-3 billion bases (gigabases) per full run
processing pipelines for ABI SNPlex, Illumina GoldenGate                  • 600,000 reads / full run        • >60 million reads per full run
and Infinium, and Affymetrix SNP and Targeted Genotyping                  • 250-500 bases per read          • 35-70 bases per read
                                                                          • 1-16 channels per chip          • 8 channels per chip
projects. The goal of the facility is to meet the increasing              • multiple samples can be run     • single channel can give >8 million reads
need of investigators for rapid and accurate DNA                            per channel                       and >150 million bases per run
sequencing and genotyping.                                                                                  • multiple samples can be run per channel



                                                                           •   whole genome sequencing (de novo assembly or re-sequencing)
                                                                           •   re-sequencing of targeted genomic regions of interest

       INTRODUCTION                                                        •
                                                                           •
                                                                           •
                                                                               SNP genotyping and low frequency mutation detection
                                                                               genome-wide DNA methylation profiling
                                                                               protein-nucleic acid association profiling (ChIP-Seq)
                                                                           •   whole genome gene expression profiling (RNA-Seq)
                                                                           •   small RNA discovery and transcriptome profiling
DNA Sequencing: The facility provides Sanger cycle                         •   degraded RNA gene expression studies (e.g. FFPE clinical samples)
 Conventional sequencing technologies services: The facility
sequencing of plasmids and PCR products and sequence
 provides DNA sequencing of plasmids and PCR products
detection and analysis using two ABI 3730xl instruments.
 with either standard sequencing primers or user provided
We also accept user performed cycle sequencing reactions
 primers, using ABI 3730xl instruments. We also accept user
for sequence analysis. Average data return time on the ABI
 performed cycle sequencing reactions. Average data return
                                                                                                                                                                                  Illumina GoldenGate                                                        Affymetrix Targeted Genotyping
3730xl is less than 30 hours. Sample submission, tracking
 time is less than 48 hours. Sample submission, tracking
and data retrieval are implemented with a web based                                       SNP Genotyping
 and data retrieval are implemented with a web based
laboratory information management system.                                                                                                                                            SNP Genotyping
 laboratory information management system.
New Sequencing Technologies: The facility provides
 New sequencing services: The facility offers the Illumina
massively parallel sequencing on the Roche 454 GS FLX and
 Solexa Genome Analyzer as a standard core genomic
Illumina GA II platforms. Applications includeservice. and
amplicon resequencing projects, ChIP-Seq, Digital Gene
 Genotyping: Genotyping analysis is available using the ABI
Expression, whole transcriptome, and small RNA analysis.
 3730xl, including DNA fragment analysis for microsatellite
 instability (MSI) with up to five-dye detection, and SNPlex
Genotyping: Genotyping analysis is available using the
                                                                      ABI 3730xl                       Sequenom                  ABI 7900 HT
 analysis with 96 samples run in parallel with up to 48 SNPs
ABI 3730xl, including DNA fragment analysis and SNPlex                                                 MassArray                   single-
                                                                                                                                 • single-plex genotyping
 detected per sample. The Illumina BeadStation 500GX                          48-
                                                                      • up to 48-plex genotyping
                                                                                                                                   using Taqman
analysis with up to 48 SNPs detected per sample. The                    using SNPlex technology        • custom panels
 microarray instrument capabilities include a standard
Illumina BeadStation 500GX microarray instrument is                                                            40-
                                                                                                         up to 40-plex using
 human whole genome 650K SNP genotyping array, custom
capable of custom SNP genotyping panels with up to                                                       iPlex Gold technology                                                    Applied Biosystems
 genotyping arrays with multiplexing from 96 to 60,000 SNPs,
60K SNPs or whole genome association studies with up to                                                                                                                                                                                                     Affymetrix Whole Genome Genotyping
 and LOH and copy number analysis. The Affymetrix system,
650K SNPs per sample, with LOH and copy number variation
                                                                                                                                                                                  SNPlex Genotyping
 available in collaboration with the DNA Microarrays Facility,
(CNV) analysis. Affymetrix SNP genotyping is available in
 provides complementary SNP genotyping analysis. The
collaboration with the Microarrays Facility. The
 ABI 7900HT instrument provides Real-Time PCR, DNA/RNA
Sequenom MassArray is available for up to 40-plex SNP
 quantitation and SNP genotyping, with sample processing
genotyping, plus methylation and gene expression studies.
 in 96 or 384 well plates.
The ABI 7900HT instrument provides real-time PCR for
quantitative gene expression and SNP genotyping.                        Illumina BeadStation                        Affymetrix
 Other services: Shotgun library construction, custom                   • custom panels up to 1536-plex
                                                                                              1536-                                       20,000-
                                                                                                                    • custom panels up to 20,000-plex
                                                                          (GoldenGate)                                (Targeted Genotyping)
 robotic liquid handling projects, and consultation for project
Epigenomics: Quantitative DNA methylation analysis is                   • whole genome genotyping panels              whole-
                                                                                                                    • whole-genome genotyping panels
 design and data analysis.                                                                                            (SNP 6.0 Array)
available on the Sequenom MassArray, in collaboration with                 Infinium)
                                                                          (Infinium)
the Epigenomics Facility.
 Administration: The DNA Sequencing and Genotyping
 Facility is a member of the Cornell University Life Sciences
Other services: Shotgun library construction, custom robotic
 Core Laboratories Center, which is administered through
liquid handling projects, and consultation for project design
 the Institute for Biotechnology and Life Science
and data analysis.
 Technologies.                                                        Conventional DNA Sequencing                                                                                   Other Services                                                                             Epigenomics
                                                                         and Fragment Analysis
Administration: The DNA Sequencing and Genotyping
 Who can use our resources? The services of the facility are
Facility is a member of the Cornell University Life Sciences                                                                                                                                                                                                         DNA Methylation Analysis
 open to all investigators at Cornell University, including the
Core Laboratories Center, which is administered through the
 Ithaca campus, the Weill Cornell Graduate School of Medical
Institute for Biotechnology and Life Science Technologies.                                                     DNA Sequence Analysis
 Sciences in New York City, and the Weill Cornell Medical
 College in Qatar. The facility also provides services to
Who can use our resources? The services of the facility are
 investigators at other academic institutions and to
open to all investigators at Cornell University and Cornell
 commercial companies.
affiliated institutions, including the Ithaca, NY campus and               ABI 3730xl
the Weill Cornell Medical Colleges in New York City, NY and
 Advanced Technology (CAT) in Life Science Enterprise, NY                                                                                                                High Throughput Liquid Handling
in Doha, Qatar. The facility also provides services to
 State companies receive a discount on facility services.
investigators at other academic institutions, non-profit                                                                                                                 • Tecan Genesis and Beckman Biomek robots
                                                                                                                                                                                  rearraying, cherry-
                                                                                                                                                                         • Sample rearraying, cherry-picking, concentration adjustment
enterprises and commercial companies.                                                                                                                                    • Large-scale liquid handling for PCR and sequencing projects
                                                                                                                                                                           Large-                                                                                                 Sequenom MassArray
                                                                                                                                                                                                                                                                                     high-
                                                                                                                                                                                                                                                           • epiTYPER technology for high-throughput analysis of methylated DNA
CAT: In association with the New York State Center for                                                                                                                                                                                                 Sample prep and data analysis provided in collaboration with the Epigenomics Facility
Advanced Technology (CAT) in Life Science Enterprise, NY                                                       DNA Fragment Analysis
State companies receive a discount on facility services.
                                                                      The facility has two 96-capillary
                                                                                           96-                                                                                                                    Custom Projects                                              Contact Information
                                                                      array electrophoresis DNA
                                                                      analyzers capable of running                                                                                                                • Primer-walking
                                                                                                                                                                                                                    Primer-                                         DNA Sequencing and Genotyping Facility
             RESOURCES                                                ~120 DNA sequencing plates or
                                                                      ~240 fragment analysis plates
                                                                      per week, with
                                                                                                                                                                                                                  • Shotgun library sequencing
                                                                                                                                                                                                                                                                           Peter Schweitzer, Director
                                                                                                                                                                                                                                                                        E-mail: LSCLC_dna@cornell.edu
                                                                      ~ 24 hour data return time                                                                                                                  • Project design and data analysis                 Web: http://cores.lifesciences.cornell.edu
                                                                                                                                                                                                                    consultation
Facility resources include: Roche 454 GS FLX, Illumina Genome
Analyzer II with Paired End module, two ABI 3730xl DNA Analyzers,
                                                                                                                                                                  ABI 7900 HT                                     • Troubleshooting
                                                                                                                                                                                                                                                                           Member of


                                                                                                                                                                  • Quantitative gene expression
Sequenom MassArray, six PE 9700 thermocyclers, ABI 7900 HT                                                                                                                             Sybr-
                                                                                                                                                                    using Taqman and Sybr-green                                                                                                                      New York State Office of Science, Technology and Academic Research

Sequence Detection System, Illumina Beadstation 500GX with Infinium
upgrade, two Tecan Genesis liquid handling robots (RSP150 and 200),
one Beckman Biomek FX, MD spectraPlus plate reader, Nanodrop1000
spectrophotometer, Sigma 4-15C centrifuge, Fisher Marathon 3200R.
                        Cornell University
                        Life Sciences
                        Core Laboratories Center                                   Microarrays Facility
                                                                                                                     Wang W, Zhao J, Hover B, Kresovich J, Lin D
                                                                                                                     Wang W, Zhao J, Hover B, Kresovich J, Lin D
                                                                                                                                   Cornell University, Ithaca, NY
                                                                                                                                   Cornell University, Ithaca, NY



             ABSTRACT                                         MATERIALS AND METHODS                                                                                            RESULTS

The Microarray Facility of the Cornell University                                   Facility Services                                                  SNP Genotyping Processing                                                                                      Facility Throughput
Life Sciences Core Laboratories Center (CLC)
                                                                                               • Project experimental design consultation
offers a broad range of microarray services and                 Project Design                                                                                                                                                                                                          Microarray Facility Throughput
                                                                                               • RNA quality assessment
shared research resources to the university                   Sample Processing                • Sample processing and data generation
research community and to outside investigators.               Data Generation                       Platforms supported:                                                                                                                          100%




                                                                                                                                                                                                            Arrays Processed (% of total for FY2008-09)
The goal of the facility is to provide life science                                                    - Affymetrix                                                                                                                                       90%
                                                                                                       - NimbleGen




                                                                                                                                                                                      Arrays Processed (% of est for FY2008-09
investigators with services that use advanced                                                          - Illumina                                                                                                                                         80%
microarray instrumentation and extensive                                                               - Agilent                                                                                                                                          70%
expertise in microarray based applications. The                                                        - CombiMatrix
                                                                                                                                                                                                                                                          60%
facility helps researchers with all aspects of                                                         - Custom spotted array printing                                                                                                                                                                                                        NimbleGen
                                                                                                       - Illumina Genome Analyzer                                                                                                                         50%                                                                                 Affymetrix SNP
microarray experiments, including project design,                                                      - Roche 454 GS FLX                                                                                                                                                                                                                     Affymetrix TG
sample processing, and data analysis. Services                                                 • Applications include:
                                                                                                                                                                                                                                                          40%                                                                                 Affymetrix Expression

                                          microRNA,
include support for gene expression, microRNA,                                                      - Gene expression and RNA-Seq                                                                                                                         30%                                                                                 Agilent
                                                                                                    - SNP genotyping                                                                                                                                                                                                                          Spotted Array Printing
SNP genotyping and epigenomics projects using                                                                                                                                                                                                             20%
microarrays, including the Affymetrix, Illumina,                 Data Analysis                      - ArrayCGH and CNV
                                                                                                    - Small RNA profiling                                                                                                                                 10%
NimbleGen,
NimbleGen, and Agilent microarray platforms, and                                                    - ChIP-Chip and ChIP-Seq                                                                                                                              0%
massively-
massively-parallel RNA profiling projects (digital                                                  - DNA methylation                                                                                                                                             FY2004-     FY2005-       FY2006-     FY2007-   FY2008-

gene expression and microRNA) and protein-                                                          - Seq-Capture of targeted genomic regions                                                                                                                       05          06            07          08      09 (est)
                       microRNA)          protein-                                             • Custom array design and evaluation                                                                                                                                                          Year
                                    (ChIP-Seq)
nucleic acid association studies (ChIP-Seq) using                                              • Data preprocessing and normalization
the Roche 454 GS FLX and the Illumina Genome                                                   • High-level data analysis:                                                                                                                                 Data Return Time:
Analyzer II.                                                                                      - Differential gene selection
                                                                                                  - Cluster analysis                                                                                                                                       •   RNA quality assessment by Bioanalyzer: 1 week
                                                                                                  - Prediction model                                                                                                                                       •   Sample labeling and hybridization to array: 2 weeks
                                                                                                  - Pathway and functional analysis                                                                                                                        •   Spotting custom microarrays: 2 weeks
                                                                                                  - ArrayCGH and ChIP-on-chip                                                                                                                              •   Statistical microarray data analysis: 1 week


     INTRODUCTION
                                                                              Instrument Platforms                                                        SNP Genotyping Results                                                                                             Facility Usage
                                                                                                                                                                                                                                                                                                         FY2007-
                                                                                                                                                                                                                                                                            Cornell Ithaca / Weill Usage FY2007-08
                                                                                                                                                                                                                                                                                          per total arrays processed
Administration: The Microarray Facility is a member
of the Cornell University Life Sciences Core Laboratories                                                                                                                                                                                                                                    non-Cornell
                                                                                                                                                                                                                                                                                            investigators
Center, which is administered through the Institute for                                                                                                                                                                                                                                          3%

Biotechnology and Life Science Technologies                                                                                                                                                                                                                                        Cornell Weill only
                                                                                                                                                                                                                                                                                          7%
(www.biotech.cornell.edu).
                                                                                                                                                                                                                                                                          Cornell Ithaca only
                                                                                                                                                                                                                                                                                 21%
Who can use our resources: The shared resources and
                                                                     Affymetrix               Illumina BeadStation               NimbleGen
services of the facility are open to all investigators at     3000 7G Scanner, autoloader,     500GX BeadArray Reader,       Maui 4-bay and 12-bay
Cornell University. The facility supports research at all      three 450 Fluidics Stations,        hybridization oven,       Hybridization Stations,
                                                                                                                                                                                                                                                                                                                       Collaborative Cornell
the University campuses, including the Ithaca campus,            640 hybridization oven,          orbiting plate shaker,         Elution Station,                                                                                                                                                                          Ithaca / Weill
                                                                 liquid handling robotics       liquid handling robotics    liquid handling robotics
the Weill Cornell Graduate School of Medical Sciences in                                                                                                                                                                                                                                                                        69%

New York City, and the Weill Cornell Medical College in
                                                                                                                                                                                     Usage by Colleges per PIs                                                                                               Usage by Departments per PIs
Qatar. The CLC also provides resources and services to                                                                                                                                                                                                         (Cornell Ithaca)                                             (Cornell Ithaca)
investigators at other academic institutions and to                                                                                                                                                                                                                                                                                                 Biomedical Engineering
                                                                                                                                                                                                                                                                                                                                                    Crop and Soil Sciences
                                                                                                                                                                                                   Outside
researchers at commercial enterprises.                                                                                                                                                          Investigators                                                                                                                                       Horticulture
                                                                                                                                                                                                                                                                                                                                                    Natural Resources
                                                                                                                                                                                    Engineering      3%
                                                                                                                                                                                                                                                                                                                                                    NBTC
                                                                                                                                                                                        3%
CAT: In association with the New York State Center for            Custom Spotted                   Tecan HS400                    Sequenom                                          BTI                                                                                                                                                             NYU
                                                                                                                                                                                                                                                                                                                                                    Syracuse
                                                                                                                                                                                    5%
Advanced Technology (CAT) in Life Science Enterprise,             Microarray Printer            Hybridization Station             MassArray                                                                                                                                                                                                         Baker Institute
                                                                                                                                                                                   CALS/Arts                                                                                                                                                        Food Science
New York State companies receive a discount on facility                                                                                                                              10%                                                                                                                                                            Microbiology
                                                                                                                                                                                                                                                                                          Vet School                                                Microbiology and Immunology
services.                                                                                                                                                                                                                                                                                    41%                                                    Plant Breeding and Genetics
                                                                                                                                                                                                                                                                                                                                                    Pop Medicine
                                                                                                                                                                                                                                                                                                                                                    Animal Science
                                                                                                                                                                                                                                                                                                                                                    Clinical Sciences
                                                                                                                                                                                                                                                                                                                                                    Molecular Medicine
                                                                                                                                                                                                                                                                                                                                                    Plant Pathology

                                                                                                           Axon 4000B                 ABI
          RESOURCES
                                                                                                                                                                                                                                                                                                                                                    Molecular Biology and Genetics

                                                                            Agilent Scanner                                                                                                                                                    CALS
                                                                                                                                                                                                                                                                                                                                                    Nutritional Sciences

                                                                         2 μm resolution, autoloader         Scanner                7900 HT                                                                                                     38%
                                                                                                                                                                                                                                                                                                                                                    Plant Biology
                                                                                                                                                                                                                                                                                                                                                    Biomedical Sciences




The infrastructure of the facility includes the following
resources: Affymetrix GeneChip System with both 500K
                                                              New RNA & SNP Profiling Technologies                                                         SNP Genotyping QA/QC                                                                                                                 Value
SNP assay upgrade and 4-color Targeted Genotyping (TG)
upgrade (including a model 3000 Scanner with autoloader,         Next Generation Sequencing Platforms                                                                                                                                                               State- of-the-
                                                                                                                                                                                                                                                                  • State-of-the-art services
three model 450 Fluidics Stations, and a model 640                                                                                                                                                                                                                •   Timely upgrades to cutting edge technology.
hybridization oven), Maui 4-bay and 12-bay Hybridization
                                                                                                                                                                                                                                                                  •   Member of Association of Biomolecular Resource Facilities.
Stations (used for NimbleGen microarray processing),
                                                                                                                                                                                                                                                                  •   Beta-test site for new methods and reagents.
Agilent laser scanner with autoloader, custom-built spotted
arrayer, Axon 4000B array scanner, Agilent 2100                                                                                                                                                                                                                   •   In-house development of novel techniques and protocols.
Bioanalyzer, Multimek 96-channel pipettor, Tecan HS400                                                                                                                                                                                                            • Consistently high quality of results
hybridization station. Access to Roche 454 GS FLX,
Illumina Genome Analyzer II with Paired End module,                                                                                                                                                                                                               • Rapid and reliable return time
Illumina BeadStation 500GX with Infinium upgrade                                                                                                                                                                                                                  • Cost effectiveness
                                                                   Roche 454 GS FLX                    Illumina Genome Analyzer II
(including a BeadArray Reader, hybridization oven, and             • 150 million bases / full run      • 1-3 billion bases (gigabases) per full run
orbiting plate shaker), Sequenom Compact MassArray with            • 600,00 million reads / full run   • >60 million reads per full run                                                                                                                           • Consultation and data analysis services
methylation, expression and SNP genotyping modules, ABI            • 250-500 bases per read            • 35-70 bases per read
                                                                   • 1-16 channels per chip            • 8 channels per chip
7900 HT Sequence Detection System, AbGene plate heat               • multiple samples can be run       • single channel can give >8 million reads
sealer, three Tecan Genesis liquid handling robots (one              per channel                         and >150 million bases per run
RSP150 and two RSP200), one Beckman Biomek FX, MD                                                      • multiple samples can be run per channel

spectraPlus plate reader, Caliper LC-90, Nanodrop 1000                                                                                                                                                                                                                            Contact Information
spectrophotometer, Sigma 4-15C centrifuge, Fisher
Marathon 3200R centrifuge, and a dedicated pre-PCR room,             •   whole genome gene expression profiling (RNA-Seq)                                                                                                                                                  DNA and Protein Microarrays
                                                                     •   small RNA discovery and transcriptome profiling
isolated from the main lab with positive air pressure and            •   degraded RNA gene expression studies (e.g. FFPE clinical samples)                                                                                                                                         Wei Wang, Director
restricted card access.                                              •   protein-nucleic acid association profiling (ChIP-Seq)                                                                                                                                          E-mail: LSCLC_micorarray@cornell.edu
                                                                     •   whole genome sequencing (de novo assembly or re-sequencing)                                                                                                                                    Web: http://cores.lifesciences.cornell.edu
                                                                     •   re-sequencing of targeted genomic regions of interest
                                                                     •   SNP genotyping and low frequency mutation detection                                                                                                                                                Member of

                                                                     •   genome-wide DNA methylation profiling
                                                                                                                                                                                                                                                                                                                                New York State Office of Science, Technology and Academic Research
                                Cornell University

                                                                                                                          Epigenomics Facility
                                                                                                                                                                                                                                                                                                 Weill Cornell
                                Life Sciences
                                                                                                                                                                                                                                                                                                 Medical College
                                Core Laboratories Center



                                       Li Y, Wang W, Schweitzer P, Figueroa M, Shaknovich R, Xin Y, Monni S, Stelick T, Paronett E, Zhao J, Hover B, Grills G, Aquadro C, Lin D, Melnick A
                                       Li Y, Wang W, Schweitzer P, Figueroa M, Shaknovich R, Xin Y, Monni S, Stelick T, Paronett E, Zhao J, Hover B, Grills G, Aquadro C, Lin D, Melnick A

                                                                                                                   Cornell University, Ithaca, NY, and Weill Cornell Medical College, NY, NY
                                                                                                                   Cornell University, Ithaca, NY, and Weill Cornell Medical College, NY, NY
                                                                                                                                                                             College,


                 ABSTRACT                                                                                                      MATERIALS AND METHODS                                                                                                                                RESULTS
The Epigenomics Facility of the Weill Cornell Medical
College and the Cornell University Life Sciences Core
                                                                                               Epigenomics Core Facility                                                                                       Methods                                      Example of Epigenomics Project
Laboratories Center (CLC) provides an array of epigenomics                                                              Services                                                                    DNA Methylation Arrays
research resources and services to the university
community and to outside investigators. The facility offers a
                                                                                               • DNA methylation micoarrays (HELP or MeDIP)                                        HELP assay
concentration of advanced instrumentation and expertise in
                                                                                                                                                                                    HpaII
                                                                                                                                                                                   (HpaII tiny fragment enrichment by ligation mediated PCR)
their applications. This is an inter-campus facility, with                                     • DNA methylation sequencing
resources and services located both on the Cornell                                                                                                                                 •       Dual color assay with internal control for copy number or SNPs
University campus in Ithaca, NY, and the Weill Cornell                                            (Sequenom MassArray, ABI 3730xl, 454, GA II)                                     •       384 K custom array capturing 25,000 HpaII fragments
Medical College in NYC, NY. DNA methylation profiling and                                                                                                                          •       2.1 M custom array capturing 1.3 million HpaII fragments
protein-nucleic acid association analysis (ChIP-Chip and                                         ChIP- on-
                                                                                               • ChIP-on-Chip
                                                                                                                                                                                   •       Long oligo array array with probes specific to this assay
ChIP-Seq) resources include the NimbleGen Illumina,                                              (NimbleGen Illumina, Affymetrix, Agilent )                                        •       Validated statistical analysis methodology available
Affymetrix, and Agilent microarray platforms, the Sequenom                                                                                                                         •       Allows measurement of methylation as a continuous variable
MassArray, the ABI 3730xl, and the Roche 454 GS FLX and                                          ChIP-
                                                                                               • ChIP-Seq (Roche 454 GS FLX, Illumina GA II)                                       •       Enriches for the HYPOmethylated fraction of the genome and
Illumina Genome Analyzer II. The goal of the facility is to                                    • LIMS tracking system                                                                      hence favorable signal to noise ratio
meet the increasing need of investigators for rapid and
accurate epigenomics project design, sample preparation,                                       • High throughput capacity                                                          MeDIP (methylation immunoprecipitation)
data generation, and data analysis.
                                                                                               • Quality control at multiple steps                                                 •       Enriches methylated DNA
                                                                                               • Analytical pipeline for primary analysis                                          •       Dual color assay test vs. input
                                                                                                                                                                                   •       NimbleGen standardized

        INTRODUCTION                                                                           • UCSC Browser Mirror with built in custom
                                                                                                  tracks for interpolating data with genomes
                                                                                                                                                                                   •       384 K and 2.1 array formats


                                                                                               • Miroarray relational database
The Cornell University Core Laboratories Center (CLC): The                                     • Computational biology support
CLC includes fee-for-service research, technology testing                                                                                                                                                     Methods
and development, and educational components. The
mission of the CLC is to promote research in the life                                                                                                                                                Histone Modifications
sciences with advanced technologies in a shared resource
                                                                                                                                                                                       ChIP- on-
                                                                                                                                                                                       ChIP-on-Chip
environment (http://cores.lifesciences.cornell.edu).
                                                                                                  Technology Platforms
Sample preparation services: The Epigenomics Facility                                                                                                                                  •     Whole genome amplification (less false negatives)
provides sample preparation services for DNA methylation                                                         ChIP-
                                                                                    Microarrays for methylation, ChIP-Chip, CGH, and CNV analysis                                      •     Ligation mediated PCR (better signal for certain apps)
profiling and protein-nucleic acid association (ChIP-Chip                                                                                                                              •     QPCR validation
and ChIP-Seq) studies. Sample submission, tracking and                                                                                                                                 •     Flexible array designs for any sequenced genome
data retrieval are implemented with a web based laboratory
                                                                                                                                                                                       ChIP-
                                                                                                                                                                                       ChIP-Seq
information management system.
                                                                                                                                                                                                                                                                         Example of Results
Epigenomics data generation technologies: In collaboration                                                                                                                             •     Unbiased genomic coverage
with the DNA Sequencing and Genotyping Facility and the                                                                                                                                •     Less amplification bias
DNA Microarrys Facility, the Epigenomics Facility offers the                            NimbleGen                 Illumina BeadStation                     Affymetrix
NimbleGen, the Illumina BeadStation 500GX and the                                    Maui 4-bay and 12-bay         500GX BeadArray Reader,        3000 7G Scanner, autoloader,
                                                                                     Hybridization Stations,           hybridization oven,         three 450 Fluidics Stations,
Affymetrix microarray platforms, the Sequenom MassArray,                                 Elution Station,             orbiting plate shaker,         640 hybridization oven,
the ABI 3700xl conventional sequencer and the Illumina                              liquid handling robotics        liquid handling robotics         liquid handling robotics
Genome Analyzer II next generation sequencer as standard
                                                                                    Agilent and CombiMatrix array processing and custom spotted array processing also available.
                                                                                                                                                array
                                                                                                                                                                                                  NimbleGen Platform
core services.
Analysis services: In collaboration with the CLC informatics
                                                                                                                                                                                                                 Features
core, called the Computational Biology Services Unit
(CBSU), the Epigenomics Facility offers informatics                                                                                                                                              • Customization at nominal cost
pipelines for epigenomics analysis.
                                                                                                                                                                                                 • 384 K or 2.1 M features
                                                                                                                                                                                                                                                                                                              Gene expression profiling, genome
Administration: The Epigenomics Facility is a member of the
                                                                                                                                                                                                 • Isothermal, long oligo design                                                                              wide DNA methylation and H3K9
Cornell University Life Sciences Core Laboratories Center,                                                                                                                                                                                                                                                            ChIP-on-
                                                                                                                                                                                                                                                                                                              acetyl ChIP-on-Chip was performed
                                                                                                                                                                                                                                                                                                              in five leukemia clinical trial
administered through the Institute for Biotechnology and                                                                                                                                           Re-
                                                                                                                                                                                                 • Re-usable                                                                                                  specimens. Different sets of genes
Life Science Technologies.                                                                       Sequenom MassArray                                 ABI 3730xl                                                                                                                                                were captured as differentially

                                                                                         Genomic profiling of DNA methylation                                                                      12-
                                                                                                                                                                                                 • 12-plex designs available                                                                                  regulated by the three platforms.
                                                                                                                                              Bisulfite sequencing for                                                                                                                                        The biological difference between
Who can use our resources? The facility services are open                                 using quantitative high-throughput                                                                                                                                                                                  patients was most accurately
                                                                                                                                               methylation analysis
to all investigators at Cornell University, including the Ithaca                                 mass spectrometry                                                                                                                                                                                            captured by integrating the three
                                                                                                                                                                                                                                                                                                              platforms together.
campus, the Weill Cornell Medical College in New York City,
and the Cornell medical school in Doha, Qatar. The facility
also provides services to investigators at other academic
institutions and to commercial companies.                                           New Epigenomics Technologies                                                                            Computational Resources
                                                                                                                                                                                                                                                                                                             An example of coordinately regulated
CAT: The CLC is a New York State designated Center for
Advanced Technology (CAT) in Life Science Enterprise.
                                                                                       Next Generation Sequencing Platforms                                                                                                                                                                                  genes as visualized using the
                                                                                                                                                                                                                                                                                                                          Facility’
                                                                                                                                                                                                                                                                                                             Epigenomics Facility’s UCSC browser
                                                                                                                                                                                                                                                                                                             mirror. Gene expression, DNA
NY State companies receive a discount on facility services.                                                                                                                                                                                                                                                  methylation and H3K9 acetylation is
                                                                                                                                                                                            • LIMS tracking system including QC                                                                              shown.



                                                                                                                                                                                            • 677 node computer cluster with 1226 CPUs
               RESOURCES                                                                                                                                                                       (425-
                                                                                                                                                                                               (425-node Sun Linux cluster with 280 GB local HD space
                                                                                                                                                                                                   252-
                                                                                                                                                                                               and 252-node Windows cluster with 344 GB local HD space)

                                                                                       Roche 454 GS FLX                        Illumina Genome Analyzer II                                                                                                                         Contact Information
The Epigenomics Facility resources includes: DNA Sequencing and Genotyping             • 150 million bases / full run          • 1-3 billion bases (gigabases) per full run                 • Primary data analysis pipeline
                                                                                       • 600,00 million reads / full run       • >60 million reads per full run
Facility: Sequenom Compact MassArray, Illumina Genome Analyzer II, Roche
454 GS FLX, two ABI 3730xl DNA Analyzers, six PE 9700 thermocyclers,                   • 250-500 bases per read                • 35-70 bases per read
                                                                                                                                                                                                                                                                                      Epigenomics Facility
Eppendorf real-time Master Cycler, ABI 7900 HT Sequence Detection System,              • 1-16 channels per chip                • 8 channels per chip                                        • Analytical package for methylation arrays                                                 Yushan Li, Director
Illumina BeadStation 500GX with Infinium upgrade (including a BeadArray
Reader, hybridization oven, and orbiting plate shaker), AbGene plate heat sealer,
                                                                                       • multiple samples can be run           • single channel can give >8 million reads                                                                                                          Ari Melnick, Faculty Advisor
                                                                                         per channel                             and >150 million bases per run
three Tecan Genesis liquid handling robots (one RSP150 and two RSP200), one
                                                                                                                               • multiple samples can be run per channel                                              ChIP-on-
                                                                                                                                                                                            • Analytical packages for ChIP-on-Chip                                          Stefano Monni, Data Analysis Supervisor
Beckman Biomek FX, MD spectraPlus plate reader, Caliper LC-90, Nanodrop
1000 spectrophotometer, Sigma 4-15C centrifuge, Fisher Marathon 3200R                                                                                                                                                                                             Maria (Ken) Figueroa and Rita Shaknovich, Research Support
centrifuge. DNA Microarrays Facility: Maui 4-bay and 12-bay Hybridization
                                                                                                                                                                                            • ChIP-Seq packages (in development)
                                                                                                                                                                                              ChIP-                                                         Peter Schweitzer, Director of the DNA Sequencing and Genotyping Facility
Stations (used for NimbleGen microarray processing), Agilent laser scanner with
autoloader, Axon 4000B laser scanner, Affymetrix GeneChip System with both                 •   genome-wide DNA methylation profiling                                                                                                                                      Wei Wang, Director of the Microarrays Facility
500K SNP assay upgrade and 4-color Targeted Genotyping (TG) upgrade                        •   protein-nucleic acid association profiling (ChIP-Seq)                                                                                                                       E-mail: LSCLC_epigenomics@cornell.edu
(including a model 3000 Scanner with autoloader, three model 450 Fluidics                  •   whole genome gene expression profiling (RNA-Seq)                                             • UCSC browser with stable custom tracks
Stations, and a model 640 hybridization oven), custom-built spotted arrayer,               •   small RNA discovery and transcriptome profiling                                                                                                                              Web: http://cores.lifesciences.cornell.edu
Agilent 2100 Bioanalyzer, Multimek 96-channel pipettor, Tecan HS400                        •   degraded RNA gene expression studies (e.g. FFPE clinical samples)
hybridization station, and access to Illumina BeadStation 500GX. Computational             •   whole genome sequencing (de novo assembly or re-sequencing)                                  • Array relational database                                                        Member of
Biology Service Unit (CBSU): A 677-node cluster with 1226 CPUs, including a
                                                                                           •   re-sequencing of targeted genomic regions of interest
425-node Sun Linux cluster with 280 GB local HD space, and 3 Microsoft
Windows clusters totaling 252 nodes and 504 CPU with 344 GB local HD space.                •   SNP genotyping and low frequency mutation detection                                                                                                                                                            New York State Office of Science, Technology and Academic Research


Access to Dell PowerEdge Rack 900 with 64 GB RAM. Six web and general
purpose servers with 1.1 TB total HD space. Four file and database servers with
15.5 TB total HD space.
                                    Cornell University
                                    Life Sciences
                                    Core Laboratories Center                                   Proteomics and Mass Spectrometry Facility
                                                                                                                                           Zhang S, Sherwood R, Baumgart S, Ptak C, Rose JKC
                                                                                                                                           Zhang S, Sherwood R, Baumgart S, Ptak C, Rose JKC

                                                                                                                                                                               Cornell University, Ithaca NY
                                                                                                                                                                               Cornell University, Ithaca NY




                    ABSTRACT                                                             MATERIALS AND METHODS                                                                                                                                                                                                                                                                                                                                                                                                                                RESULTS
  The Proteomics and Mass Spectrometry Facility of the
  Cornell University Life Sciences Core Laboratories Center
                                                                                                    Gel-
                                                                                               1D Gel-based Protein                                                                                                                                                                             Samples Processed                                                                                                                                                                                                                                                                          Major Scientific Contributions
  (CLC) provides an array of shared research resources and
  services to the university community and to outside
                                                                                           Identification/Characterization
                                                                                                                                                                                                                                                                                                                     Comparison of Sample Throughput
  investigators. The mission of the facility is to provide                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Provide consultation services for
  faculty, students and researchers with cutting edge                                                                                                                                                                           300                                                                                                                                                                                                                                                                               282                            284                                           researchers across the world
  technologies in mass spectrometry and proteomics, high
  quality services and innovative solutions that will                                                                                                                                                                                                                                                                                                                                                                                                                                    252
  significantly contribute to life sciences research, training                                                                                                                                                                  250                                                                                                                                                                     229
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Train Ph.D. students and postdocs
                                                                                                                                             C18 RP                                                                                                                                                                                                                                                                                  221
  and education programs. The facility has mass                                                     In-gel                                 Nano column                                                                                                                                                                                                                                                                                                        198
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Support grant proposals from PIs




                                                                                                                                                                                                      % Analyzed Samples
  spectrometers for both proteomics and metabolomics                                              digestion                                                                                                                     200
  analyses. Services include 2D gel and 2D LC separation for                                                                                                                                                                                                                                                                                                                    170
  macromolecules, robotic and manual sample preparation for
  proteomics samples, protein identification, quantitative                                                                                                                                                                      150                                                                                                                                                                                                                                                                                                                                                            Publish scientific papers
                                                                                                                                                                                                                                                                                                                                                          122
  proteomics by 2D DIGE analysis or shotgun-based iTRAQ,                                                                                                                                                                                                                                                                     110
                                                                                                                                                        nanoLC-MS/MS                                                                                                            100
  and characterization of post-translational modifications
                                                                                                                                                                                                                                100                                                                                                                                                                                                                                                                                                                                                            Present scientific posters in
  through both non-targeted discovery and targeted discovery
  approaches. Informatics analysis services include mass
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               conferences
  spectrometry data interpretation and small molecule                                                                                                                               TIC                                              50
  identification and quantitation.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  proteomics-
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Host proteomics-oriented workshops
                                                                                                                                                                                          ER
                                                                                                                                                                   EMS                                                                0
                                                                                                                                                                                                                                                                        Q1                                           Q2                                   Q3                    Q4                   Q1                          Q2                       Q3                           Q4                     Q1                              Q2                                               Co-
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Co-organize monthly campus-wide
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   campus-
          INTRODUCTION                                                                                                                                                              EPI: MS/MS                                                                                                                           FY 05-06                                                                                                    FY 06-07                                                                           FY 07-08                                                               Cornell Proteomics Program meetings

                                                                                         Mascot / ProteinPilot database search                                        IDA analysis

  Services provided: MS-based consultation services, sample
  analysis (individually submitted and project-based samples),                                                                                                                                                                         Samples Analyzed per                                                                                                                                                                                                                                                                                                                                              Services and
  data processing and interpretation, and technique training.
                                                                                                                                                                                                                                      Application/PI Affiliation                                                                                                                                                                                                                                                                                                                                      Sample Return Time
  Administration: The Proteomics and Mass Spectrometry                                           Gel-
                                                                                              2D Gel-based Comparative
  Facility is a member of the Cornell University Life Sciences
                                                                                                                                                                                                                                                                                                                                                                                                                             Data Interpretation
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         We have performed the following services
                                                                                                Proteomics Workflow
                                                                                                                                                                                                                                                                                                                     Sm all Molecule
                                                                                                                                                                                                                                                                                                                           3.8%                                                                                                      4.9%
  Core Laboratories Center, which is administered through the
                                                                                                                                                                                                                                                    MW Determ ination
  Institute for Biotechnology and Life Science Technologies                                                                                                                                                                                               2.4%                                                                                                                                                                                                                                                                                                                           • HPLC (SCX, RP, IP) and gel separation for proteins,
  (www.biotech.cornell.edu).                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Protein IDs
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            44.2%                                                                          peptides, nucleotides and small molecules
  Who can use our resources? The shared resources and
  services of the facility are open to all investigators at Cornell                                                                                             Spot picking
                                                                                                                                                                                                                                Sam ple Prep                                                                                                                                                                                                                                                                                                                                             • Sample preparation: protein affinity depletion, sample
                                                                                                                                                                                                                                   17.4%
  University. The facility also provides resources and services                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            cleanup, in-gel/solution digestion, concentration
  to investigators at other academic institutions and to                                                                                                   In-gel digestion
  researchers at commercial enterprises.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 • Protein Identification for 1D gel, 2D gel/solution samples
                                                                                                       Image analysis

  CAT: In association with the New York State Center for
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         • Quantitative proteomics:
  Advanced Technology (CAT) in Life Science Enterprise,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         2D gel-based analysis: DIGE, SYPRO Ruby, CCB,
  NY State companies receive a discount on facility services.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Pro-Q Diamond, Image analysis
                                                                                                                                                                                                                                                                                    PTMs
                                                                                           MALDI-TOF/TOF                                      No Hit                                                                                                                                12.8%                                                                                                                                                                                                                                                                                                       iTRAQ labeling and subsequent shotgun analysis
                                                                                                                                                                           nanoLC/MS/MS
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         • Protein characterizations:
                 RESOURCES                                                                                                  Hit                                                                                                                                                                                                                            Quantitative
                                                                                                                                                                                                                                                                                                                                                           Proteom ics
                                                                                                                                                                                                                                                                                                                                                              14.5%
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 PTMs: phosphorylation, methylation, deamidation
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 oxidation, nitration, acetylation, N-glycosylation
                                                                                                                             Mascot 2.2
                                                                                                                                                                                 • NCBI                                                                                                                                                                                                                                                                                                                                                                                                          Others: AA mutation, chemical modifications,
                                                                                                                                                                                 • SwissProt
 Infrastructure includes: Four mass spectrometers: a 4700 Analyzer MALDI-
                                      spectrometers                                                                          Protein Pilot 2.0
                                                                                                                             MS-ProBlast
                                                                                                                                                          Database Search
                                                                                                                                                                                 • Genbank
                                                                                                                                                                                                                                                                                                                                                                                 External                                                                                                     College of                                                                                         unnatural amino acid, N/C-terminal mapping
 TOF/TOF, a 4000 Q Trap triple quadrupole/linear ion trap, a 3D ion trap                                                                                                                                                                                     USDA/BTI                                                                                                             13.6%                                                                                                     Agriculture LS
                                                                                                                             BioAnalyst 1.4                                      • MSDB
 Esquire-LC, and an API 150EX. Three HPLC systems: a Dionex MDLC
 system, an Agilent 1100, and a Perkin Elmer 200 series. One 2D gel
                                                                                                                                                         Bioinformatics                                                                                       11.4%                                                                                                                                                                                                                             36.3%                                                                                    • Small molecule identification and quantitation
 electrophoresis system: Multiphor II, a gel spot picker robot (ProPic), a gel
 extraction/liquid handling robot (ProPrep) and a Typhoon 9410 image                                                                                                                                          Weill Medical                                                                                                                                                                                                                                                                                                                                                              Sample return time:
 system for quantitative fluorescence analysis. Bioinformatics software:                                                                                                                                        School
 DeCyder 6.5, ImageMaster 6.0, Mascot 2.2, and ProteinPilot 2.0.                                                                                                                                                  3.0%
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         • 5-8 days for individually submitted samples
                                                                                               iTRAQ-
                                                                                               iTRAQ-based Quantitative                                                                                                College of Vet.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         • 1-6 months for project-based samples

 Instrumentation & Services                                                                        Shotgun Analysis                                                                                                      Medicine
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           College of A&S
                                                                                                                                                                                                                           10.9%       College of Human
                                                                                                                                                                                                                                            Ecology
                                                                                                                                                                                                                                                                                                                                                                                                             College of
                                                                                                                                                                                                                                                                                                                                                                                                            Engineering
                                                                                                                                                                                                                                                                                                                                                                                                               7.1%
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                15.3%
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Value
                                                                                                                                                                                                                                             2.5%
                                                                                                           Treated                                                Control                                                                                                                                                                                                                                                                                                                                                                                                                State-of-the-
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         State-of-the-art services
                                                                                                                               Reduce,                                                                                                                                                                                                                                                                                                                                                                                                                                                         •   Timely upgrades to cutting edge technology
                                                                                                                        Cysteine Block & Digest
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               •   Member of Association of Biomolecular Resource Facilities
                                                                                                      Tryptic Digest                                     Tryptic Digest                                                                                                                                                                                                                                                                                                                                                                                                                        •   Beta-test site for new methods and reagents
                                                                                                                    Reporter mass 114/117
                                                                                                                                                                                                       New Techniques Implemented                                                                                                                                                                                                                                                                                                                                                              •   In-house development of novel techniques and protocols
                                                                                                                                                    H
                                                                                                                                                    N
                                                                                                                                  N                       PEPTIDE                                                                                                                                                                                                                                                                                                                                                                                                                        Quality of results
       MDLC & Mass Spectrometer                   HPLC/Mass Spectrometer
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       MS Survey Scan            Precursor Ion Scan
                                                                                                                                                                                                                                                                                                                                                                                                     Reporter mass 114/117                                                                                                           Target MRM Scan




                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Rapid and reliable turnaround time
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              QqQ mode
                                                                                                                        N                      O                                                                                                                                                                                                                                                                                                 H
   Dionex CapLC & ABI Hybrid 4000 Q Trap     Agilent 1100 & Bruker Esquire-LC Ion Trap                                                                                                                                                                                                                                                                                                                                       N
                                                                                                                                                                                                                                                                                                                                                                                                                                                 N
                                                                                                                                                                                                                                                                                                                                                                                                                                                             PEPTIDE
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              LIT mode
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Enhanced Resolution


                                                                                                                                           Balance mass 31/28
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Add to
                                                                                                                                                                                                                                                                                                                                                                                                               N                                                                                                                                                    Exclusion List



                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Cost effectiveness
                                                                                                                                                                                                                                                                                                                                                                                                                                           O
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 IDA Criteria
                                                                                                                                                                                                                                                                                                                                                                                                                                     Balance mass 31/28

                                                                                                    Tag 1 Peptides                                        Tag 2 Peptides                                                         DIGE                                                                                                                                       iTRAQ
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Consultation services
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Acquire MS/MS Spectra


                                                                                                                                                           117 reagent
                                                                                                                                                                                                                                                                                                                                                                                                                                     114




                                                                                                     114 reagent
                                                                                                                                                                                                                                                                                                                                                                                                                                                 116
                                                                                                                                                                                                                                                                                                                                                                                                                                           115


                                                                                                                                                                                                                                                                                                                                                                                                                                                       117




                                                                                                                                           Mix                                                                                                                                                                                                                                                                                                                                                                  Targeted-
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  PTMs

                                                                                                                             Treated/Control                                                                                                                                                                                                                                                                         111.0   112.8      114.6    116.4
                                                                                                                                                                                                                                                                                                                                                                                                                                            Mass (m/z)
                                                                                                                                                                                                                                                                                                                                                                                                                                                              118.2        120.0
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Contact Information
Gel Imaging Laser Scanner       Sample Preparation Robot        Mass Spectrometer
GE Typhoon 9400 & DeCyder 6.5    Genomic Solution ProPrep     ABI 4700 MALDI-TOF/TOF
                                                                                                                             Peptide Mixture                                                                                                                                                                                                                                                                                                                                                                                                                                                          Proteomics and Mass Spectrometry Facility
                                                                                                                                                                                                     Cho
                                                                                                                                                                                                                           SM
                                                                                                                                                                                                                                PC
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                emPAI                                                                                            Sheng Zhang, Director
   •   Biomolecular Separation (2D gel and 2D HPLC)                                                                                        2D-LC/MS/MS                                                                                                                                      MRM-quan                                                                              ProQ stain
                                                                                                                                                                                                                                                                                                                                                                                                                                                         LC-MALDI                                                               100.000
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       E-mail: LSCLC_proteomics_ms@cornell.edu
                                                                                                                                                                                                                                        Affiliation of Principal
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Top hit only




   •   Sample Preparation (digestion, desalt, affinity depletion)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Web: http://cores.lifesciences.cornell.edu
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Combined

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 10.000
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        emPAI




   •   Protein Identification (gel-based and solution-based)                                                                                                                                                                                                                                                                                                                    Pro Q                                                      C18 RP              10      30         50                                              1.000




                                                                                                                                                                                                                                     Investigators Using Facility
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Time (min)
                                                                                                                              Time (min)                                                                                                                    9.8e4
                                                                                                                                                                                                                                                            9.5e4
                                                                                                                                                                                                                                                                                                                                                                                                                                           Nano column


                                                                                                                                                                                                 a
   •   Quantitative Proteomics (2D DIGE, iTRAQ)
                                                                                                                                                                                                                                                            9.0e4                                                                                                                    116 Kd



                                                                                                                                              C18 RP
                                                                                                                                                                                                                                                            8.5e4
                                                                                                                                                                                                                                                            8.0e4
                                                                                                                                                                                                                                                                                                                                                                                     BSA 66Kd


                                                                                                    SCX column
                                                                                                                                                                                                                                                            7.5e4
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      50% split                                                   0.100
                                                                                                                                                                                                                                                            7.0e4
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        4000 Q Trap                                    0.01                        0.1               1
                                                                                                                                                                                                                                                            6.5e4




                                                                                                                                              Nano column
                                                                                                                                                                                                                                                            6.0e4                                                                                                                    OVA                                                                                                                                                               Normalized Spot Intensities
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Member of
   •   MS-based Protein Characterization (PTMs)
                                                                                                                                                                                                                                          Intensity, cps




                                                                                                                                                                                                                                                            5.5e4
                                                                                                                                                                                                                                                            5.0e4
                                                                                                                                                                                                                                                            4.5e4
                                                                                                                                                                                                                                                            4.0e4
                                                                                                                                                                                                                                                            3.5e4                                                                                                                    Casein
                                                                                                                                                                                                                                                            3.0e4




   •   Small Molecule Identification and Quantitation
                                                                                                                                                                                                                                                            2.5e4
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       MALDI-TOF/TOF
                                                                                                                                                                                                                                                            2.0e4
                                                                                                                                                                                                                                                            1.5e4


                                                                                                                                  X 10
                                                                                                                                                                                                                                                                                                                                                                                     18 Kd
                                                                                                                                                                                                                                                            1.0e4


                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   New York State Office of Science, Technology and Academic Research
                                                                                                                                                                                                                                                           5000.0
                                                                                                                                                                                                                                                                                                                                                                                     14 Kd
                                                                                                                                                                                                                                                              0.0
                                                                                                                                                                                                                                                                    1   2   3   4   5   6   7   8   9   10 11 12     13 14   15   16 17 18   19 20   21                                                                                                  Probot



   •   MS Data Processing and Interpretation
                                                                                                                                                                                                                                                                                                         Time, min

                                                                                                                                                                                                                                                                                                                                                           Sypro Ruby Stained                 ProQ Diamond Stained
                            Cornell University
                            Life Sciences 
                            Core Laboratories Center 
                                                                            Protein Production and Characterization Facility 
                                                                                                                                                            Kinsland C, Mattison J, Mottler C, Begley T
                                                                                                                                                            Kinsland C, Mattison J, Mottler C, Begley T

                                                                                                                                                                           Cornell University, Ithaca, NY
                                                                                                                                                                           Cornell University, Ithaca, NY


               ABSTRACT                                                                                                                                                                 RESOURCES AND SERVICES
The Protein Production and Characterization Facility                         Molecular Biology Services                                                                                                                                           Rapid Kinetics                                                                                                                                                          High-
                                                                                                                                                                                                                                                                                                                                                                                                                          High-Throughput
of the Cornell University Life Sciences Core
Laboratories Center (CLC) provides an array of
shared research resources and services to the
                                                                          The facility offers a full range of molecular biology services:
                                                                                                                                                                                            SF-2004 Stopped Flow
                                                                                                                                                                                             Spectrophotometer
                                                                                                                                                                                                                                                         • dead time <1 msec
                                                                                                                                                                                                                                                         • 10 µL sample volume
                                                                                                                                                                                                                                                                                                                                                                                                                        Label-Free Screening
                                                                                                                                                                                                                                                                                                                                                                                                                        Label-
                                                                          • cloning                                                                                                                                                                      • reaction times from 5 msec to several minutes
university community and to outside investigators.                               • any vector                                                                                                                                                                                                                                                                                                   Biochemical Assays
The facility provides a concentration of advanced                                                                                                                                                                                                        • double mixing experiments possible                                                                                                             Binding                             Corning Epic System
                                                                                 • any method                                                                                                                                                            • fluorescence or absorbance measurements
                                                                                                                                                                                                                                                                                                                                                                                                                       Protein
                                                                                                                                                                                                                                                                                                                                                                                                                             Surface

instrumentation and expertise in their applications.                      • mutagenesis of cloned genes                                                                                                                                                                                                                                                                                                                      Waveguide
                                                                                                                                                                                                                                                                                                                                                             [Substrate] (μM)                                                Substrate
                                                                                                                                                                                                                                                                                                                                                                                                                                               • optical biosensor technology
Instrumentation includes a stopped-flow                                          • point mutations                                                                                                                                                                                           1
                                                                                                                                                                                                                                                                                                                                                                      1
                                                                                                                                                                                                                                                                                                                                                                       2                                                                       • biochemical and cell-based assays




                                                                                                                                                                                                                                                                 Normalized Fluorescence
                                                                                                                                                                                                                                                                                           0.98

spectrophotometer, rapid quench flow instrument,                                 • deletions                                                                                                                                                                                               0.96                                                                        5
                                                                                                                                                                                                                                                                                                                                                                                             Broadband
                                                                                                                                                                                                                                                                                                                                                                                              Source
                                                                                                                                                                                                                                                                                                                                                                                                                     Reflected
                                                                                                                                                                                                                                                                                                                                                                                                                    wavelength
                                                                                                                                                                                                                                                                                                                                                                                                                                               • SBS-standard 384-well microplate format
isothermal titration calorimeter, multi-detection                                • insertions                                                                                                                                                                                              0.94                                                                        10
                                                                                                                                                                                                                                                                                           0.92
                                                                                                                                                                                                                                                                                                                                                                       20                        Cell-Based Assays                             • evaluation of drug targets
                                                                                 • chimera generation                                                                                                                                                                                       0.9

plate reader, analytical ultracentrifuge, large                           • other services by request
                                                                                                                                                                                                                                                                                           0.88
                                                                                                                                                                                                                                                                                           0.86
                                                                                                                                                                                                                                                                                                                                                                       40
                                                                                                                                                                                                                                                                                                                                                                       80
                                                                                                                                                                                                                                                                                                                                                                                                          Cell
                                                                                                                                                                                                                                                                                                                                                                                                                      Mass
                                                                                                                                                                                                                                                                                                                                                                                                                      Redistribution           • detection of binding of a 300 Da compound
capacity shakers, cell disruptors, FPLC, low-flow                                                                                                                                                                                                                                                                                                                      160
                                                                                                                                                                                                                                                                                                                                                                                                                              Surface
                                                                                                                                                                                                                                                                                                                                                                                                                              Waveguide          to a 70 kDa protein with CVs of <10%
                                                                                 • gene synthesis                                                                                                                                                                                          0.84
                                                                                                                                                                                                                                                                                           0.82                                                                        320
                                                                                                                                                                                                                                                                                                                                                                                                                              Substrate
                                                                                                                                                                                                                                                                                                                                                                                                                                               • 5000-10,000 data points per day
chromatography systems, phosphoimagers, and the                                  • novel vector generation                                                                                                                                                                                        0        0.1                               0.2       0.3

                                                                                                                                                                                            RQF-3 Rapid Quench Flow                                                                                              Time (s)                                                                    Broadband                Reflected
Corning Epic. The facility can support bacterial,                                • in vivo mutagenesis                                                                                                                                                                                     200
                                                                                                                                                                                                                                                                                                                                                                                               Source                wavelength

                                                                                                                                                                                                                                                                                                                                                                    Fast Phase
yeast, insect and mammalian tissue culture. The
                                                                                                                                                                                                                                                                                           180
                                                                                                                                                                                                                                                                                           160                                                                      Slow Phase

goal of the facility is to meet the increasing need of                                                                                                                                                                                                                                     140




                                                                                                                                                                                                                                                                      Rate (s-1)
                                                                                                                                                                                                                                                                                           120

investigators for purified proteins, molecular                                                                                                                                                                                                                                             100
                                                                                                                                                                                                                                                                                            80

biology services, and instrumentation for kinetic
                                                                                                                                                                                                                                                                                                                                                                                                              Multi-
                                                                                                                                                                                                                                                                                                                                                                                                              Multi-Mode Plate Reader
                                                                                                                                                                                                                                                                                            60
                                                                                                                                                                                                                                                                                            40

studies, protein interaction characterization, and                                                                                                                                                                                                                                          20
                                                                                                                                                                                                                                                                                             0
                                                                                                                                                                                                                                                                                                  0                200                                 400
high throughput screening.                                                                                                                                                                                                                                                                                 [Substrate] (μM)                                                                                                               BioTek Synergy HT
                                                                         Investigators provide a template for PCR (if necessary) and a                                                                                                                   • reaction times from 2 msec to 10 sec                                                                    4                                                                                   • fluorescence
                                                                         description of the final construct desired. The facility                                                                                                                        • 15 µL sample volume                                                                                                                                                                         • time-resolved fluorescence
                                                                         performs all necessary steps to return a sequence-verified                                                                  Data provided by                                    • capture 20 time points from 300 µL of reactant                                                                                                                                              • luminescence

       INTRODUCTION                                                      construct.                                                                                                             J. Hanes, Cornell University                             • freeze quench adaptor                                                                                                                                                                       • absorbance (200-999 nm, 1 nm increment)
                                                                                                                                                                                                                                                                                                                                                                                                                                                       • 1 to 384 well plates
                                                                                                                                                                                                                                                                                                                                                                                                                                                       • ambient + 4°C to 50°C, shaking optional
                                                                                                                                                                                                                                                                                                                                                                                                                                                       • 2 syringe pumps (5-1000 µl, 1 µl increment)

Services provided: The Protein Production and                            Protein Expression Optimization                                                                                         Protein-
                                                                                                                                                                                                 Protein-Ligand Interactions                                                                                                                                                                 Example Uses
                                                                                                                                                                                                                                                                                                                                                                                                         • growth curves
Characterization Facility provides standard molecular
                                                                          Scouting to find optimal conditions for protein production                                                                                                                                                                                                                                                                     • kinetics
biology services, including clone construction,                                                                                                                                                                                                     1
                                                                                                                                                                                                                                                                                                                                                                                                         • concentration measurements




                                                                                                                                                                                                                        Normalized Fluorescence
mutagenesis, subcloning and related techniques. The
                                                                            • >20 E. coli host strains                                                                                                                                                                                                                                                                                                   • apoptosis experiments




                                                                                                                                                                                                                                                                                                                         [Thiamin-P] (μM )
                                                                                                                                                                                                                                                                                                                                              40
facility performs expression optimization trials to maximize                                                                                                  Rare tRNAs
                                                                            • temperature at induction                                                                                                                                            0.95

the yield of produced protein and can purify proteins either
by affinity methods or by more classical purification
                                                                            • inducing agent concentration                                                    (-)             (+)                                                                                                                                                             20

                                                                            • coexpression plasmids                                                                                                                                                0.9
schemes. The facility maintains a large inventory of
instrumentation for studying the kinetics of enzymatic
                                                                                   • rare tRNAs
                                                                                   • chaperones
                                                                                                                                                       U            I     U         I
                                                                                                                                                                                                                                                         0       5                                    10            15
                                                                                                                                                                                                                                                                                                                                               0
                                                                                                                                                                                                                                                                                                                                                   0     20                 40    60
                                                                                                                                                                                                                                                                                                                                                                                                                                                       Training
reactions, including instrumentation for pre-steady state                                                                                                                                                                                                                           [PPi] (μM)
                                                                                                                                                                                                                                                                                                                                                                 Time (s)
                                                                                   • binding partners                                                                                                                                                                                                  Kd•PPi = 360 ± 10 nM
studies. The facility has an isothermal titration calorimeter                                                                                                                                                                                                                                                                                                                                   • training available in all techniques performed by the facility
                                                                            • media components
for studying binding reactions. The facility includes an                                                                                                                                                                                                                                                                                                                                        • dedicated bench space for investigators receiving training
                                                                                                                                                                                               Titration Module on SF-2004 Stopped Flow Spectrophotometer
analytical ultracentrifuge for the study of protein molecular                                                                                                                                                                                                                                                                                                                                   • one-on-one training
                                                                                                                                                                                                      • continuous, slow addition of titrant
weights, oligomerization states and binding kinetics. The                                                                                                                                                                                                                                                                                                                                       • lab specific projects
                                                                                                                                                                                                      • continuously stirred 200 µL sample cell
facility has a high throughput screening platform. The                                                                                                                                                                                                                                                                                                                                          • unlimited future consultation
                                                                         Different N-terminal Fusions
                                                                                   N-                                                                                                                 • 30 million readings in 300 seconds
facility provides training in all these techniques.                                                                                                                                                                                                                                                                                                                                             • access to lab space and equipment for future projects
                                                                                                                                                                                                      • averaging leaves 1000 data points
History: The facility was founded in 2000 with funds from the
Tri-Institutional research program provided by The Atlantic                                                                                                                                                                                                  CSC Nano-ITC III
Philanthropies and with funding from NIH.                                                                                                     A                                 B                                                                                 • 1 mL 24 K gold cell

Administration: The Protein Production and Characterization                              *
                                                                                                     X                                     1 2 3 4                        1 2 3 4 5                                                                               • high sensitivity (0.1 µJ)
                                                                                                                                                                                                                                                                  • rapid response (15 sec)                                                                                                                                                       RESULTS
Facility is a member of the Cornell University Life Sciences                         X                                                                                                                                                                            • low noise (± 0.004 µwatt)
Core Laboratories Center, which is administered through the                                                                           Western blot of soluble protein                                                                                             • wide temperature range (0-80°C)
                                                                             *                X
Institute for Biotechnology and Life Science Technologies
(www.biotech.cornell.edu).
                                                                                 *
                                                                                                                                      (A or B), different expression                                                                                                                                                                                                                                                                                       Value
                                                                                                                                                conditions.                                                                                                                                                                                                        Data provided by
                                                                                                                                                                                                                                                                                                                                                                                             • State-of-the-art instrumentation and services
                                                                                                                                                                                                                                                                                                                                                              J. Hanes, Cornell University
Who can use our resources? The shared resources and                                                                                                                                                                                                                                                                                                                                                      • timely upgrades to cutting edge technology
services of the facility are open to all investigators at Cornell                                                                                                                                                                                                                                                                                                                                        • member of Association of Biomolecular Resource Facilities
University, including the Ithaca campus, the Weill Cornell                                                                                                                                                                                                                                                                                                                                               • in-house development of novel techniques and protocols
Graduate School of Medical Sciences in New York City, and
the Weill Cornell Medical College in Qatar. The facility also                         Protein Purification                                                                                     Analytical Ultracentrifugation                                                                                                                                                                • High quality results
provides resources and services to investigators at other                        AKTAXpress                                                                                AKTA FPLC
academic institutions and to researchers at commercial                                                                                                                                                                                                                                                                                                                                       • Rapid and reliable return time
enterprises.                                                                                                                                                                                  Beckman Coulter Proteomelab XL-I                                                                                                                                                                             • Most clones completed in under 18 days
                                                                                                     Proteins purified from
                                                                                                                                                                                                   • absorbance and interference optics                                                                                                                                                                    • Most mutants completed in under 14 days
                                                                                                     any source material by
CAT: In association with the New York State Center for                                                                                                                                             • sedimentation equilibrium                                                                                                                                                                             • Time readily available on all instruments
                                                                                                     affinity or classical
Advanced Technology (CAT) in Life Science Enterprise,                                                                                                                                              • sedimentation velocity
                                                                                                     methods.                                                                                                                                                                                                                                                                                • Cost effective
NY State companies receive a discount on facility services.

                                                                                                                                                                                                                                                                                                                                                                                             • Consultation services

                                                                         AKTAxpress                                                                                                                                                                                                                                                                                                          • Access to a large library of plasmids and cell strains
             RESOURCES                                                        • purification of 8 affinity tagged proteins per day
                                                                                                                                                                                                                                                                                                                                                                                             • Individualized training and support
                                                                         AKTA FPLC (2)
                                                                               • gel filtration                                                                                                                                                                                                                                              Calc MW: 61.05 kDa
The infrastructure of the facility includes the following resources:           • ion exchange
KinTek SF-2004 stopped-flow spectrophotometer with titration module,           • hydroxyapatite                                                                                                                                                                                                                                                                                                                                                Contact Information
KinTek RQF-3 rapid quench flow instrument with freeze quench adaptor,
CSC Nano-ITC III isothermal titration calorimeter, BioTek Synergy HT
                                                                               • hydrophobic interaction                                                                                                                                                                                                                                                                                                                          Protein Production and Characterization
multi-detection plate reader, Beckman Coulter XL-I analytical                  • other chromatography methods.                                                                                                                                                                                                                                                                                                                            Cynthia Kinsland, Director
ultracentrifuge, three large capacity shakers, Beckman Coulter Avanti
                                                                                                                                                                                                                                                                                                                                                                                                                                     E-mail: LSCLC_protein@cornell.edu
J20-XPi, Allegra 25R and Optima LX-100 centrifuges, Constant Systems     Proteolytic removal of fusion tags available.                                                                        Determination of:
Basic Z and Avestin Emulsiflex C3 cell disruptors, GE Healthcare AKTA                                    Hsp MonoQ 111606:1COPY_UV          Hsp MonoQ 111606:1COPY_Cond                             • molar mass of a protein or tight protein complex                                                                                                                                                                             Web: http://cores.lifesciences.cornell.edu
FPLC (2), AKTAxpress Twin and Storm 860 Phosphoimager, Eppendorf
and Bio-Rad thermocyclers, low-flow chromatography systems,
                                                                                              mAU

                                                                                              1000
                                                                                                                                                                                                    • sample purity, detection of aggregates
NanoDrop ND-1000 spectrophotometer, Corning Epic, and a variety of
                                                                                              800

                                                                                              600
                                                                                                                                                                                                    • presence of self-association                                                                                                                                                                                                         Member of



instrumentation for gel electrophoresis and for small to medium scale                         400                                                                                                   • association constant of heterogeneous complex
                                                                                              200                                                                                                                                                                                                                                                                                                                                                                              New York State Office of Science, Technology and Academic Research
bacterial and yeast growth. For insect and tissue culture, segregated                          0                                                                                                    • hydrodynamic shapes of complexes
space with a 6 ft biosafety hood and dual CO2 incubators is available.                               0               50              100         150                ml
                                 Cornell University
                                 Life Sciences
                                 Core Laboratories Center                              Microscopy and Imaging Facility
                                                                                                                           Williams R, Bayles C, Xia G, Doran R, Zipfel W
                                                                                                                           Williams R, Bayles C, Xia G, Doran R, Zipfel W

                                                                                                                                         Cornell University, Ithaca, NY
                                                                                                                                         Cornell University, Ithaca, NY


                   ABSTRACT                                                                                                                                                          RESULTS
                                                                                                                                                                                                                                      Zeiss 510 Meta Spectral
 The Microscopy and Imaging Facility of the Cornell
 University Life Sciences Core Laboratories Center (CLC)                                    Leica SP2 Spectral Scanning                                                             Olympus OV100
                                                                                                                                                                                 Whole Mouse Imaging                               Scanning Confocal Microscope
                                                                                                Confocal Microscope
 provides an array of shared research resources and services
 relating to optical microscopy, including confocal
 microscopy, fluorescence imaging, spectrofluorimetry,                                                                                                                              •   Single Cell Resolution
 ultrasound, image processing and analysis. The mission of
 the facility is to provide cutting edge technologies and high                                                                                                                      •   Fluorescence
 quality services that will significantly contribute to life                                                                                                                        •   150W Xe lamp
 sciences research, training and education programs.                                                                                                                                •   8 EX/Em filters
                                                                                                                                                                                    •   5 objectives
                                                                                                                                                                                    •   0.69-78.5 mm field of view
         INTRODUCTION                                                                                                                                                               •
                                                                                                                                                                                    •
                                                                                                                                                                                        0.7 µm resolution
                                                                                                                                                                                        CCD camera
                                                                                                                                                                                    •   Motorized XY stage                          Optical grating projects entire emission
                                                                                      Glass prism separates emission                                                                                                                spectrum onto a 32 channel META detector
 Services provided: Transmitted and fluorescence light                                light into its components.
 microscopy, confocal microscopy, stereo microscopy,                                  Wavelength selection is by a
 spectrofluorometry, molecular imaging (whole mouse                                   series of movable slits
 luminescence and fluorescence imaging), and
 high-resolution ultrasonic imaging. Instrument training and
 consultation services for digital imaging, image analysis,
 live cell microscopy, tissue and animal imaging and
 fluorescence techniques and measurements.

 Location: Facility resources are located in the
 Biotechnology Building and in the Veterinary School
 on the Cornell University campus in Ithaca, NY.

 Administration: The Microscopy and Imaging Facility (MIF)                                                                                                                                                                                             RBL-
                                                                                                                                                                                                                                   Calcium dynamics in RBL-2H3 cells. Brighter color indicates
 is a member of the Cornell University Life Sciences Core                                                                                                                                                                          higher calcium concentration (R. Cohen, B. Baird, Cornell Univ).
 Laboratories Center, which is administered through the
 Institute for Biotechnology and Life Science Technologies
 (www.biotech.cornell.edu).

 Who can use our resources? The shared resources and                                                                                                                                                                                            Xenogen IVIS 200
 services of the facility are open to all investigators at Cornell
 University, including the Ithaca campus, the Weill Cornell                           Wild type Drosophila eye disc stained        RBL-2H3 Mast cells stained with a Golgi
                                                                                                                                                                                  (Right) CHAT transgenic mouse embryo,                 Whole Animal Imaging System
 Graduate School of Medical Sciences in New York City, and                                                                                                                        targeting limbs, brain and spine. (Left)
                                                                                      using anti-cut (green), and anti-De-         marker in red and a type 1
 the Weill Cornell Medical College in Qatar. The facility also                        cadherin (red). (R. Booker, Cornell Univ.)   phosphatidylinositol kinase in green.
                                                                                                                                                                                  Control embryo (Y. Tallini, M. Kotlikoff,                                        •   Fluorescence
 provides resources and services to investigators at other                                                                         (L. Vasudevan, B. Baird, Cornell Univ.)        Cornell University).
                                                                                                                                                                                                                                                                   •   Bioluminescence
 academic institutions and to researchers at commercial
 enterprises.                                                                                                                                                                                                                                                      •   150W Quartz Halogen Lamp
                                                                                                                                                                                                                                                                   •   12 EX/Em filters
 CAT: In association with the New York State Center for                                                                                                         Volocity Volumetric Software                                                                           4-26 cm field of view
 Advanced Technology (CAT) in Life Science Enterprise,                                        Bio-Rad MRC600                                                      • 3D interactive rendering, Movie making
                                                                                                                                                                                                                                                                   •
                                                                                                                                                                                                                                                                   •   60 µm resolution
 NY State companies receive a discount on facility services.                                Confocal Microscope                                                   • Quantitation and analysis                                                                      •   Cooled BT-CCD camera
                                                                                                                                                                                                                                                                   •   Heated imaging chamber
                                                                                                                                                                                                                                                                   •   Gas anesthesia manifold
                RESOURCES                                                                                                                                                                                                                                          •   Laser scanning 3D surface
                                                                                                                                                                                                                                                                       topography
 The infrastructureof the facility includes the following resources: three confocal
 microscopes (Leica TCS SP2 with spectral capabilities, Zeiss LSM 510 Meta with
 spectral capabilities, and BioRad MRC600), a fluorescence microscope
 (Olympus BX-50 with MetaMorph software and QImaging Retiga EXi cooled CCD                Chloroplasts and stromules surrounding a
 camera), two stereo microscopes (Zeiss Stemi 2000C and Leica MZFLIII with
 fluorescence capabilities), a spectrofluorometer (SLM 8000c), two whole mouse
                                                                                          nucleus. Red chlorophyll autofluorescence,
                                                                                          merged image, green GFP fluorescence                                                                                           cell.
                                                                                                                                                             Microvilli on the apical membrane of a polarized epithelial cell.
 luminescence / fluorescence imagers (Olympus OV100 and Xenogen IVIS-200), a
 high-resolution ultrasound imager (Visual Sonics Vevo 770), and a multiphoton            (M. Hanson, Cornell University).                                   Lengths in three dimensions were measured over time
 microscope (under development).                                                                                                                             (D. Garbett, A. Bretscher, Cornell University).




    Metamorph Microscope System
                                                                                                                Leica MZ FLIII                                                        Visual Sonics
                                                                                                        Fluorescence Stereo Microscope                                              Vevo 770 Micro-
Wide field Fluorescence Microscope - Olympus BX50
    • DIC (Nomarski), Phase Contrast, Dark field Optics                                                                                                                            Ultrasound System                                     In vivo bioluminescence for transcription factors
    • Q-Imaging Retiga Exi cooled CCD Camera                                                                                                                                        •   Non-invasive                                                                    M.
                                                                                                                                                                                                                                         expression: AP-1 in the brain (M. Burmeister,
    • Electronic shutters                                                                                                                                                           •   30 µm resolution                                 R. Davisson, Cornell University).
                                                                                                                                                                                    •   20 mm field of view
    • Metamorph Premier acquisition / analysis software                                                                                                                             •   Image-guided needle injection
Zeiss Stemi 3000 Stereo Microscope                                                                                                                                                  •   In vivo anatomical structures
    • Dage color camera / Metamorph acquisition software                                                                                                                                                                                                   Contact Information
                                                                                                                                                                                    •   Hemodynamic function
                                                                                                                             3-CKIT transgenic testis                                                                                                 Microscopy and Imaging Facility
                                                                                                                   (Y. Tallini, M. Kotlikoff, Cornell University)                                                                                          Rebecca Williams, Director
                                                                                                                                                                                                                                                            Carol Bayles, Manager
                                                                                                                                                                                                                                                           Guowei “Will” Xia, Manager

                                                                                                          SLM 8000C Spectrofluorimeter                                                                                                               E-mail: LSCLC_mif@cornell.edu
                                                                                                                                                                                                                                                   Web: http://cores.lifesciences.cornell.edu
                                                                                                            •   Dual Excitation Monochrometers
                                                                                                            •   Single Emission Monochrometer
                                                                                                            •   Polarizers                                                                                                                             Member of


                                                                                                            •   Cooled PMT                                                              Mouse heart showing measurement of                                                     New York State Office of Science, Technology and Academic Research

      Mitosis in Drosophila larval neuroblasts showing CID, a kinetochore marker, in                                                                                                    endocardial borders to determine cardiac
      red: NudE, a protein potentially related to the spindle checkpoint mechanism, in                      •   Stirring                                                                performance (D. Infanger, R. Davisson,
      green, and chromosomes in blue (J. Creque, M. Goldberg, Cornell University).
                                                                                                            •   Heating, cooling                                                        Cornell University).
                          Cornell University
                          Life Sciences
                          Core Laboratories Center                     Animal Transgenic Facility
                                                                                                                        Deng KY, Soloway P
                                                                                                                        Deng KY, Soloway P

                                                                                                                   Cornell University, Ithaca NY
                                                                                                                   Cornell University, Ithaca NY


              ABSTRACT                                                     MATERIALS AND METHODS                                                                                                                                                                SERVICES
The Animal Transgenic Facility (ATF) of the Cornell                                                      E                                                                                                                                          Pronuclear microinjection
University Life Sciences Core Laboratories Center                                                                                     Synchronized mouse embryos
                                                                                                         E                            (superovulation with administration of PMS
(CLC) provides shared research resources and
services to the university community and to outside                                                      S                            followed by HCG 48 hours later) are                                                           The facility will inject a minimum of 150 eggs with the goal of at least
                                                                                                                                      collected at day 1 for fertilized eggs to be                                                  2 founder lines from each submitted transgene (FVB/N or B6D2F2).
investigators. Facility services include pronuclear                                                                                   used in pronuclear microinjection, at day 4
and ES cell blastocyst microinjection and                                                                                             for blastocysts to be used in ES cell                                                          Investigator responsibilities:
cryopreservation resources. The goal of the facility                                                                                  microinjection.
is to meet the increasing need of Cornell                                                                                                                                                                                            - Prepare transgene (DNA) for injection (25 - 50 ng/ul in 0.1x TE, pH 7.5).
                                                                                                                                      A few picoliters of DNA are injected per                                                       - Screen the potential transgenic animals and be responsible for weaned mice.
investigators for rapid and accurate production and
                                                                                                                                      fertilized egg at 1-2 ng/ul.
study of gain-of-function and loss-of-function                                                                                        20-25 survived eggs are transferred to each
transgenic organisms.                                                                                                                 recipient. Generally, 10-15 ES cells are
                                                                                                                                      injected per blastocyst. Successfully
                                                                                                                                      injected 10-15 blastocysts are transferred
                                                                                                                                      per pseudopregnant recipient.
                                                                                                                                                                                                                                                  ES cell blastocyst injection
      INTRODUCTION                                                                                                                                                                                                                  The facility will inject 50 blastocysts with the goal of at least 2 chimera mice
                                                                                                                                                                                                                                    for each submitted ES cell line (germ line transmission is not guaranteed).

                                                                                                                                                                                                                                    Investigator responsibilities:
Services provided: The facility offers pronuclear injection of                                                                                                                                                                      - Provide mycoplasma-free ES cells (Mycoplasma test).
DNA into fertilized oocytes and embryonic stem (ES) cell                                                                                                                                                                            - Be responsible for weaned chimera mice and mating for germ line transmission.
injections into blastocysts. The facility also offers
embryonic cryopreservation and embryo reconstitution
services.

Our goal is to generate at least two transgenic founder mice
from each transgene and two chimera mice from each
                                                                                                                                                                                                                                                               Cryopreservation
injected ES cell line. To date, we have produced over 273
transgenic and 80 chimeric founder lines.                                                                                                                                                                                           The facility will cryopreserve 300 to 600 mouse embryos per mouse line at the
                                                                                                                                                                                                                                    1 cell stage by slow controlled-rate freezing and store in liquid nitrogen.
Location: The facility is located in C1033 in the Veterinary                                                                                                                                                                        30 to 40 embryos from each round will be thawed and cultured for quality
Medical Center and contains an isolated colony, a                                                                                                                                                                                   evaluation.
cryopreservation laboratory and a microinjection laboratory.
                                                                                                                                                                                                                                     Investigator responsibilities:
Administration: The Transgenic Facility is a member of the
Cornell University Life Sciences Core Laboratories Center,                                                                                                                                                                           1. Provide 15 - 20 breeding-proved male and 30 - 45 young female animals.
which is administered through the Institute for                                                                                                                                                                                      2. Superovulate female animals and transfer copulatory plugged mice to the facility
Biotechnology and Life Science Technologies.                                                                                                Microinjection station                                                                       before 10:00 am on the date of cryopreservation
Who can use our resources? The services of the facility are
open to all investigators at Cornell University, including the
Ithaca campus, the Weill Cornell Graduate School of Medical
Sciences in New York City, and the Weill Cornell Medical
College in Qatar. The facility also provides services to                                                                                                                                                                                                  Summary of Services
investigators at other academic institutions and to
commercial companies.                                                                                                                                                                                                               • Generate gain-of-function and loss-of-function transgenic mice.
CAT: In association with the New York State Center for
                                                                                                                                                                                                                                    • Maintain an SPF colony.
Advanced Technology (CAT) in Life Science Enterprise,
NY State companies receive a discount on facility services.
                                                                                                                                                                                                                                    • Provide nuclear injection of DNA into fertilized oocytes.

                                                                                                                                                                                                                                    • Provide ES cell injections into blastocysts.

        BACKGROUND                                                                                                                                                                                                                  • Provide cryopreservation.

                                                                         Preimplanted                                       Pronuclear                    ES cell blastocyst                                                        • Generation of transgenic organisms of other species possible
                                                                         mouse embryos                                      microinjection                microinjection                                                              upon request and consultation.
                       Definitions
Transgene: a construct (foreign sequences) that is inserted
Transgene

                                                                                                                                                     RESULTS
into mouse genome.

Transgenic mouse: an organism in which a foreign gene has
            mouse
been experimentally integrated into the genome.

Mouse Embryonic Stem cells (ES cells): undifferentiated
                                       cells)
                                                                          Research Highlights                                                                                      Research Highlights
pluripotent cells derived from the inner cell mass of a mouse
blastocyst, with the potential to develop into whole embryos.
                                                                     Cre/R26R                        Cre/R26R
Gene targeting: modification of endogenous genes through
     targeting                                                   A
homologous recombination.


                                                                                                                C            A
                                                                                                                                                                                                                                                                                    Contact Information
            RESOURCES                                                                                                                                                                                                                                                                   Transgenic Facility
                                                                                                                                                                                                                                                                                        Ke-Yu Deng, Director
                                                                                                                                                                                                                                                                              E-mail: LSCLC_transgenics@cornell.edu
The facility infrastructure resources include: Nikon ECLIPSE     B                                   D
                                                                                            BTransgenic mice:                                                                                                                                                                 Web: http://cores.lifesciences.cornell.edu
TE 200 and Leica DMIRE2 and DMIRB microscopes,                                  β-galactosidase expression under
Eppendorf (5171) and NARISHIGE (MN-188NE) micro-                                maternal Cre recombinase excision                                                                                                                                                                                                      Member of

manipulators, an Eppendorf Transjector (5246), Sutter
Flaming micropipette puller (Model P-97) and FTS bio-cool                        (Panel A) β-galactosidase stained
III controlled Rate Freezer.                                                     E12.5 embryos. (Panel B) Cre genotyping.                                                     Transgenic mice:
                                                                                 K.Y. Deng, H.B. Xin and K. Kotlikoff, Cornell University
                                                                                                                                                             Smooth muscle expression of Cre recombinase and eGFP                                                                          New York State Office of Science, Technology and Academic Research




                                                                                                                                                               H.B. Xin, K.Y. Deng, G. Ji, M. Rishniw and M.I. Kotlikoff, Physiol. Genomics 10:211-215, 2002
                            Cornell University
                            Life Sciences
                            Core Laboratories Center
                                                                          Computational Biology Service Unit
                                                                                    High-
                                                                          Microsoft High-Performance Computing Institute
                                                                                        Pillardy J, Sun Q, Ponnala L, Stefanov S, Bukowski R, Myers C, Ripoll D, Clark A
                                                                                        Pillardy J, Sun Q, Ponnala L, Stefanov S, Bukowski R, Myers C, Ripoll D, Clark A
                                                                                                                      Cornell University, Ithaca, NY
                                                                                                                      Cornell University, Ithaca, NY



               ABSTRACT                                                                                                                                     RESULTS

The Computational Biology Service Unit (CBSU) of                              Bioinformatics and                                                    Research Highlights                                          Research Algorithms
the Cornell University Life Sciences Core
Laboratories Center (CLC) provides informatics                            Computational Biology Services                              Integrated Database and Analysis Pipeline                                    Made Accessible
resources and services to the university community                                                                                         for Integration of Phenotyping, Genotyping,                                            via BioHPC
and to outside investigators. The CBSU is a                               • Provide research, software and hardware support for              Gene Expression and Proteomics Studies
Microsoft designated High Performance Computing                             biology research groups.                                                                                                        •   The CBSU helps investigators
Institute. Facility resources include a cluster with                                                                                                                                                            make their algorithms available to
1200 CPUs. The goal of the facility is to meet the                        • Research: collaborate on research projects that require    •   Developed as a flexible data management and data analysis
                                                                                                                                           pipeline for plant projects and extended to human clinical           their research community through
increasing need of Cornell investigators for broad                          expertise in genomics, proteomics, quantitative                studies.
support in computational biology and                                        genetics and structural biology.                                                                                                    our web interface to BioHPC
bioinformatics.                                                           • Computational resources: developed and maintain an
                                                                                                                                       •   Patient or plant and animal sample information is encrypted
                                                                                                                                                                                                            •   Establishes a web presence for
                                                                                                                                           and is only accessible to authorized personnel.
                                                                            extensive suit of computational biology applications on                                                                             new algorithms and facilitates wide
                                                                            clusters (BioHPC), with web interface for easy access.     •   Data access to the relational database is possible through           use of these new tools in research
                                                                                                                                           either a web browser or flat file spreadsheets.
       INTRODUCTION                                                       • Software development: develop and modify software
                                                                            tools for customized solutions; adapt computationally      •   Database schema is designed to accommodate both basic
                                                                                                                                                                                                                    long-
                                                                                                                                                                                                                Two long-running examples:

                                                                            intensive applications into massively parallel                 research projects and clinical study protocols.                           LOOPP
                                                                            environment.                                                                                                                                        10,000 submissions in 3 years
Services provided: Research, software and hardware                                                                                     •   Analysis of the resulting large scale data sets done on
support for life sciences research groups, including                                                                                       massively parallel computer clusters.                                     MDIV
research collaboration, software development, and
maintenance of computational resources for bioinformatics.                                      BioHPC                                 •   Implemented in the Cornell University Ithaca/Weill
                                                                                                                                           Collaborative Program in Personalized Medicine.
                                                                                                                                                                                                                                9,800 submissions in 3 years

History: The Computational Biology Service Unit (CBSU)                               Computational Biology                                 Projects include Chronic Obstructive Pulmonary Disease           •   Other programs include MKPRF,
was founded in 2001 as a computational resource for the                                                                                    and Neural Tube Defect studies.                                      InStruct and iDeCal
Tri-institutional Collaboration of Cornell University,                            High Performance Computing
Rockefeller University and Memorial Sloan-Kettering Cancer
Center. In 2006, the facility become part of the Cornell
                                                                                     Made Easily Accessible
University Life Sciences Core Laboratories Center. Also in
2006, the CBSU was chosen to become one of ten Microsoft
                                                                                          cbsuapps.tc.cornell.edu
                                                                                                                                                    Research Highlights                                     Education and Consulting
High-Performance Computing Institutes worldwide.
                                                                          • BioHPC is a suit of computational biology tools on                        Comparative genomics
Administration: The CBSU is a member of the Cornell                                                                     easy-
                                                                            MS Windows clusters accessible through an easy-                                                                               • The CBSU provides consulting for
University Life Sciences Core Laboratories Center (CLC)                     to-
                                                                            to-use web interface                                                      and proteomics studies
                                                                                                                                                                                                            research in areas such as computational
and is hosted in the Cornell University Center for Advanced                                                                                          of plant C3/C4 pathways                                biology algorithms, software and
Computing (CAC). The CLC is administered through the                      • Designed and developed at the CBSU
Institute for Biotechnology and Life Science Technologies
                                                                          • Covers various aspects of bioinformatics:                                                                                       computational needs
(www.biotech.cornell.edu).                                                                                                             •       Collaborative studies for comparative analysis
                                                                              • data mining                • sequence analysis                 of C3 and C4 photosynthesis pathways,
Who can use our resources? The shared resources and                           • population genetics        • phylogenetics                     using rice, maize and sorghum as model                     • The CBSU organizes a workshops
services of the facility are open to all investigators at Cornell
University. The facility supports research at all the                         • protein structure                                              systems.                                                     covering a broad range of bioinformatics
University campuses, including the Ithaca campus, the Weill               • Interface written in   C++   using ASP.NET and                                                                                  for researchers on the Cornell University
Cornell Graduate School of Medical Sciences in New York
                                                                            MS SQL Server                                              •       Collaboration includes the CBSU and                          campuses in both Ithaca and New York
City, and the Weill Cornell Medical College in Qatar. Some                                                                                     5 investigator groups from Cornell University,               City.
of the computational resources of the CBSU are available to               • Provides an interface for job, cluster, data and                   Yale University and Iowa State University.
and used by investigators worldwide through a web                           users administration
interface. The facility also provides resources and services                                                                                                                                              • Participated in the Bridging the Rift
to investigators at other academic institutions and to                    • Easily customized with new applications                                                                                         Foundation School of Bioinformatics
researchers at commercial enterprises.
                                                                                                                                                                                                            in collaboration with scientists from both
                                                                                                                                                                                                            Israel and Jordan.
                                                                                   Research Highlights
             RESOURCES
                                                                                     Support for Multiple
                                                                                  Next Generation Sequencing                                                                                                Partnership with Microsoft
                                                                                                                                                  Research Highlights
The infrastructure of the facility includes the following resources:
A total 677-node cluster with 1354 CPUs, including a 425-node Sun Linux            and Genotyping Platforms                                                                                              MS High Performance Computing Institute
cluster (AMD Opteron 2GHz) with 280 GB local HD space, and 3
Microsoft Windows clusters totaling 252 nodes and 504 CPU (192 2-CPU
nodes 256 Pentium 4 Xeon 2.4GHz, 40 Pentium 4 x64 Xeon 3.4GHz, 20         •     CBSU developed data analysis pipelines for                                 Structural Biology
Pentium 4 x64 Xeon 3.4GHz) with 344 GB local HD space. 6 web and                next generation sequencing and genotyping                                                                                 • The CBSU is one of ten Microsoft
general purpose servers with 1.1 TB total HD space. 4 file and database
                                                                                platforms from Roche (454 GS FLX), Illumina            •      The CBSU provides software and expertise in                   designated HPC Institutes worldwide
servers with 15.5 TB total HD space. Access to a large shared-memory
machine with 64 GB RAM.                                                         (Genome Analyzer II) and Affymetrix.                          proteins structure prediction and molecular
                                                                                                                                              modeling.                                                   • Facility is a beta test site for Microsoft
                                                                          •     Sequencing and genotyping data analysis
                                                                                                                                       •      The group collaborates with Cornell research                  software tools in computational biology
                                                                                tools have been implemented on our HPC
                                                                                                                                              groups in various projects requiring structural
     Expertise and Infrastructure                                               clusters. We have access to a large memory
                                                                                                                                              protein models and analysis of their                        • Facility is developing new bioinformatics
                                                                                system for genotyping, CNV and genome
                                                                                                                                                              physio-
                                                                                                                                              mechanical and physio-chemical properties.                    tools on the Microsoft platform
                                                                                assembly projects.
 •      Six Ph.D. level scientists with research                                                                                              Two examples:
        expertise in diverse areas of                                     •     Collaborating with multiple investigator                                  Studies on the selection on Glycine β-1,3-
        computation biology                                                     groups to develop novel applications using                                endoglucanase genes differentially inhibited
                                                                                next generation sequencing technologies.                                  by Phytophthora glucanase inhibitor protein.
                                                                                                                                                                                                                          Contact Information
                                                                                                                                                                                                                     Computational Biology Service Unit
 •      Massively parallel computational                                                                                                                  J.K.C. Rose, et. al
        resources:                                                                                                                                        (Plant Biology Dept., Cornell University)                          Jaroslaw Pillardy, Director
                                                                                                                                                                                                                                 Qi Sun, Co-Director
        4 clusters totaling                                                                                                            Studies on the effect of localized                                                    LSCLC_cbsu@cornell.edu
                                                                                                                                                                                                                        http://cores.lifesciences.cornell.edu
        677 compute nodes                                                                                                              π-non-aromatic interaction on the unfolding
        with 1,354 processors                                                                                                          pathways of structural homologues of                                         Member of

                                                                                                                                       ribonuclease.
 •      Multiple web, database, storage                                                                                                A. H.A. Scheraga, et. al                                                                                                 New York State Office of Science, Technology and Academic Research


                                                                                                                                       (Chemistry and Chemical Biology Dept., Cornell University)
        (13 TB total) and computational servers
                      Cornell University
                      Life Sciences
                      Core Laboratories Center
                                                                        Information Technology Services Facility 
                                                                                   VanEe J, Flaherty J, Manocchia A, Dick J, Dodge E, Smith K.
                                                                                   VanEe J, Flaherty J, Manocchia A, Dick J, Dodge E, Smith K.
                                                                                                  Cornell University, Ithaca, NY
                                                                                                  Cornell University, Ithaca, NY


              ABSTRACT                                                    LABORATORY INFORMATION MANAGEMENT SYSTEMS (LIMS)
                                                                Next Generation Sequencing
The Information Technology Services Facility                                                                            Online Ordering                    Reporting                                   Scheduling
of the Cornell University Life Sciences Core                           IT Pipelines
Laboratories Center (CLC) provides desktop
and network support, software license
management, and custom IT services to a
diverse array of Cornell University life
sciences investigators and academic units.




     INTRODUCTION

Services provided: The Information Technology
Services Facility provides production and
management of Laboratory Information
Management Systems (LIMS), software licensing
management, desktop and network support, and
specialized IT services.                                                 Process Tracking and Management                                         Invoices and Billing                 Equipment Interlock
Administration: The Information Technology
Services Facility is a member of the Cornell
University Life Sciences Core Laboratories Center,
which is administered through the Institute for
Biotechnology and Life Science Technologies
(www.biotech.cornell.edu).
                                                                                        Instrument Systems
Who can use our resources? The shared resources
                                                                       Reagents
                                                                                                                   Protocols and
and services of the facility are open to all                                                                       Process Status
investigators at Cornell University, including the
Ithaca campus, the Weill Cornell Graduate School of
Medical Sciences in New York City, and the Weill
Cornell Medical College in Qatar. The facility also
provides resources and services to investigators at
other academic institutions and to researchers at                      Robotics           Data Processing           Data Return
commercial enterprises.                                                                     and Backup

CAT: In association with the New York State Center
for Advanced Technology (CAT) in Life Science
Enterprise, NY State companies receive a discount
on facility services.
                                                                 SOFTWARE LICENSING                                          DESKTOP/NETWORK                                         CUSTOMERS

                                                              • Concurrent use licensing managed by                         • Network procurement and                   Groups using the resources of the Information
                                                                                                                                                                        Technology Services Facility include:
           RESOURCES                                            Sassafras Keyserver                                           management                                • Life Sciences Core Laboratories Center (CLC)

                                                               >120 research laboratories subscribe                         • University policy and security               •
                                                                                                                                                                           •
                                                                                                                                                                               DNA Sequencing and Genotyping
                                                                                                                                                                               DNA and Protein Microarrays
                                                                                                                              compliance and communication                 •
                                                                                                                                                                           •
                                                                                                                                                                               Epigenomics
                                                                                                                                                                               Proteomics and Mass Spectrometry
The infrastructure of the Information Technology Services         •   DNASTAR Lasergene                                                                                    •   Protein Production and Characterization
Facility includes the following resources:                                                                                                                                 •   Microscopy and Imaging
                                                                  •   GeneCodes Sequencher                                  • Support Windows, MacOS, Linux                •   Animal Transgenics
15 Linux and Windows-based file, database and application         •   Codoncode Aligner                                       desktops and file or application          • Institute for Biotechnology
servers and compute clusters totaling >20TB RAID storage          •   PAUP
dedicated to CLC operations, Firewall and Intrusion                                                                           servers                                     and Life Science Technologies
Detection Systems plus centrally managed Access Control           •   MacClade                                                                                          • Nanobiotechnology Center (NBTC)
Lists for data security, on-site secure, environmentally          •   Gene Construction Kit 2                               • Full service, personalized, consulting    • Computational Biology and Biological Statistics
controlled machine room (~150 sq ft), access to central           •   Adobe Photoshop
campus machine room, ~20 TB of backup/archive capacity                                                                                                                  • USDA-ARS Functional & Comparative Proteomics
located in central facility, Gigabit wired network and            •   Adobe Illustrator                                                                                   Center (FCPC)
extensive wireless coverage provided by the university tied
                                                                                                                                                                        • Dept. of Biomedical Engineering
to redundant GB/10GB campus backbone, campus
connectivity to National Lambda Rail, Internet 2, NYSGrid.    • Provide directory of other free and                       SPECIALIZED SERVICES                          • Weill Institute for Cell and Molecular Biology
                                                                commercial software that support
                                                                                                                                                                        • Cornell Center for a Sustainable Future
                                                                core facility data
                                                                                                                          • LAMP web hosting environment                • USDA-ARS Maize Genetics Research
        DATA ANALYSIS                                         • Support scheduling and access to                          • Custom web applications
                                                                analysis software and hardware via                                                                                     Contact Information
  • Work with laboratories and vendors to                       terminal services or in-lab                               • Cluster configuration and management
                                                                                                                                                                                   Information Technology Services Facility
    implement data pipelines for quality control
                                                                                                                          • Applications that require life sciences                           James VanEe, Director
  • Assist customers with standard and                        • Manage software and hardware                                laboratory technology expertise                                   LSCLC_its@cornell.edu
                                                                                                                                                                                       http://cores.lifesciences.cornell.edu
    customized analysis tools and techniques                    procurement and license tracking
                                                                                                                          • Large storage subsystems
                                                                                                                                                                                         Member of


                                                                                                                          • Desktop and server backup                                                                      New York State Office of Science, Technology and Academic Research
                                                                                                                                                                                           Member of

				
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