Agenda for Genomics TC
Updates to ChIP-on-chip and DNA methylation – 10 min (Rini)
CGH update – 5 min (Hailing)
miRNA assay – 15 min (Marc, Martin) miRNA launch – 30 min (Steve, Paco) Update from Condie Carmack – 10 min
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ChIP-on-chip and DNA methylation Genomics TC April 2007
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Agenda
Updates to ChIP-on-chip and DNA methylation
Upcoming products and initiatives
Custom design assistance is here!
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244K product and price review
Part number
G4489A G4490A G4491A
Description
Human Promoter 2-set Mouse Promoter 2-set Yeast Whole Genome (Agilent)
Current designs (Unrestricted AMADIDs only)
N/A N/A N/A
G4492A G4493A G4495A
Human CpG Island Yeast Whole Genome 4x44K (Agilent) Unrestricted AMADID 1X244K
G4496A G4497A G4498A G4499A G4810A
Custom AMADID 1X244K Custom AMADID 4X44K Custom AMADID 2X105K Custom AMADID 8X15K Unrestricted AMADID 4x44K
N/A N/A C.elegans, Arabidopsis, Drosophila and ANY Catalog product N/A
N/A N/A N/A S. pombe (Agilent)
G4811A
G4812A
Unrestricted AMADID 2X105K
Unrestricted AMADID 8X15K
Mouse CpG
N/A
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Design and database updates
mm8 and hg18 annotation update completed for promoter sets, CpG Island arrays, whole genome sets eArray will have the new annotations by the end of the month All model organism arrays annotated by May (Drosophila, Arabidopsis, C. elegans) Both mouse and human CpG Island arrays are now gene-annotated Rat database update and promoter array set with newest build Rn 3.4 (May) Agilent zebrafish database completed, uploaded in eArray by June
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More about annotation updates
Mouse mm7 updated to mm8. Human hg17 updated to hg18. Rat Rn3.1 updated to Rn3.4. Data may be different as peaks that were called using the old annotations may not be called with the new annotations Customers who wish to use old annotations from eArray will have to use an external lift over tool available from UCSC – eArray can only support one build per organism. Customers using the catalog sets who do not wish to use the new annotations simply do not need to install the new design files – if they want the new annotations, they will have to remove the older design files and install the newly annotated versions.
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Protocol updates: DNA methylation
Application note released in end of the month Recommends mdip protocol as recommended by Weber et. al and describes complete protocol Shows data from cancer cell lines and X-chromosome Analysis visualizations were done in CGH Analytics TC training will be set up in early May for AEs.
NOTE: Both CoC and DNA methylation have a 20 rpm hyb recommendation – slightly higher S/N
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ChIP-on-chip and DNA methylation marketing news
DNA methylation product note will be released at the end of April – specs and benefits DNA methylation application note to be released at the end of April – describes a protocol for using our CpG Island arrays
DNA methylation and CpG Island array poster at AACR (April), Epigenetics conference (April), ESHG (June)
Complete solution campaign (with release of amplification and labeling kits in Sept) Co-marketing with CSPs
Possible antibody co-marketing/cross-selling with OEM
ChIP guide will be updated with all new announcements by the end of April
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Updates on custom design help
Custom design process:
Customer should try eArray
If eArray is difficult, please contact me (Rini) with the issue We have hired a third party, Genotypic, to do custom designs in eArray for the customer at no charge to the customer. Andy Bhattacharjee handles technical aspects of relationship
All inquiries for this should originate with me
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Future initiatives for ChIP-on-chip
April 2007: Additional format:
8 pack
Summer 2007 : gDNA labeling kit, gDNA amplification, DNA sample QC assays, Beyond Summer 2007
Software robustness, integrated with gene expression analysis Strengthen eArray and usability/hardware Higher feature density Additional organisms and databases as needed Automation Service providers, antibody validation and co-marketing
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Future DNA methylation initiatives
DNA methylation array design (re-design, optimization)
Software and visualization
FFPE samples Amplification methods Compare/optimize other isolation methods
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