bb676ae0-9012-47d9-a432-e1d5444febca.xls Notes 1
A B C D E F G H I J
1 Experiment Groups Inventory for Affymetrix microarray Inventory for the Group STAT Project.xls
2
3 Revised: 12/24/2009
4 Version: V.5.12.7
5 Editor: P. Lemkin lemkinp@niddk.nih.gov [C] (NIDDK/NIH)
Principal Lothar
6 Investigator Hennighausen lotharh@niddk.nih.gov [E] (NIDDK/NIH)
7
8 This inventory database consists of microarray data monitoring various Stat genes for the Group STAT Project (GSP).
9 Each group has give us microarray data they are contributing to the group database.
10
11 This is a revised draft based on some of GSP members feedback and observations describing their data.
12 Please let me know if there are fields we left out, fields you think we should drop, corrections, reorder fields, and
13 any changes the order of any fields.
14
15 If some fields can by other samples, but can't be filled out by one group or for particular samples, we leave the
16 fields blank and we will try to add them later if possible.
17
18 Data Sharing Agreement
19 The microarray gene expression profiling experiments that are available in the "JAK-STAT Prospector" have been generated by researchers
20 from the National Institutes of Health (NIDDK, NIAMS, NHLBI and NIAID) using Federal funds. The mouse data are freely available to
21 researchers inside and outside the United States to foster their scientific endeavors. This Web site only contains the mouse data.
22 For any Human data mentioned in the GSP Inventory, contact the respective PIs for availability. If information from this database
23 is to be included in scientific publications or presentations, the National Institutes of Health and the "JAK-STAT Prospector"
24 (http://jak-stat.nih.gov/) should be acknowledged. If the data are also available through GEO, the respective accession number
25 should be acknowledged.
26
27
28
29 Thanks again to the GSP members for your help.
30
31 Notes:
32 (1) The Experiment Group consists of one or more file folders of .CEL files (and possibly additional analysis data).
33 This means that several sets of .CEL files may be part of the same experiment group.
34 Each experiment group is assigned an identifier with a EG prefix such as EG003. If a group of related
35 experiments should be split into several subgroups, then it is split into EG003.1, EG003.2, etc.
36 (2) The following annotation fields are entered once per experiment group of data
37 Summary of experiment
38 Purpose of the experiment
39 Experimental design
bb676ae0-9012-47d9-a432-e1d5444febca.xls Notes 2
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40 (3) The Sample identifier is entered if it is different from the .CEL file name
41 (4) Some sample names have a date inconsistent with the directory it is in. The sample date is the one used.
42 (5) We list all of stimulation agents in the Experiment Group.
43 better document the experiment.
44 (6) [TODO] normalize the english and other descriptions so the database can be more easily searched.
45 (7) For details on each of the following Experiment Groups below, see the Experiment Groups sheet.
46 (8) If a paper reference is available then list it. Can be modified by in-press or in-prep or not-yet.
47 (9) Each sample gets a unique sample GSP ID defined using the following rule:
48 {Simple GSP ID}.{Tissue}.{GeneWT/KO}.{opt. Sample ID or 'br#' or "tr#"}.{Stimulation}.{opt. A or B}
49 Where: the {Simple GSP ID} is defined below in (10).
50 If there is no Sample ID, then the ".{Sample ID}" is just left off.
51 If there is no Sample ID and the sample is a replicate, to identify it we add "br1", "br2", etc. for
52 biological replicates and "tr1", "tr2" etc. for technical replicates.
53 If a multichip platform is used, then the optional .A and .B are added.
54 Example: EG003.1-05.Muscle.Stat5MKO.48.GH
55 (10) Each sample gets a unique sample Simple GSP ID (SGID) using the following normalization rule. A SGID is:
56 EGx.y-n where x.y is the Experiment group (4 digit number for x, 1 digit for y if present), and n is the sequential 2 digit index of the
57 sample starting at 1 in the experiment group. All numbers have leading 0's if needed to bring them out to the required number of digits.
58 Examples: EG006-03, EG003.1-01, EG006-12, EG012-10, etc.
59 (11) "Stim." is the stimulation if any.
60 (12) "Dur. Stim" is the duration of the stimulation
61 (13) "Rep." means is it a replicate. Put nothing, "biological", or "technical".
62 (14) "AffyPlat" is the Affy chip(s) platform.
63 (15) "Date" is the date the sample was run.
64 (16) "Affy .CEL file" nameis required with the ".CEL" file extension.
65 (17) "Folder" is the project or file folder source of the .CEL files.
Experiment In Number of is A+B
66 P.I. Group ID Experiment Group mAdb Species samples array
67 L.Hennighausen EG001 Ter119+ erythroid cells from mouse fetal liver cells of control and Stat5-null mice yes Mouse 6
68 L.Hennighausen EG002 Liver tissue from control and Stat5-null mice +/- acute GH injection yes Mouse 7
69 L.Hennighausen EG003.1 Muscle cells from control and Stat5-null 12-week mice with GH treatment yes Mouse 6
70 L.Hennighausen EG003.2 Muscle cells from control and Stat5-null 15-week mice without GH treatment yes Mouse 7
71 L.Hennighausen EG004 Mouse embryonic fibroblasts (MEFs) from control & Stat5-null mice (+/- GH, +/- IFN treatment) yes Mouse 18
72 L.Hennighausen EG005.1 Fetal liver-KSL HSC cells (enriched hematopoietic stem cells) from control and Stat5-null mice yes Mouse 18
73 L.Hennighausen EG005.2 Bone marrow-KSL cells (enriched hematopoietic stem cells) from Mxr-Cre:Stat5 fl/fl adult mice yes Mouse 6
74 L.Hennighausen EG006 Granulocyte Macrophage Progenitor (GMPs) from control and Stat5-null mice yes Mouse 20
75 L.Hennighausen EG007 Common Myeloid Progenitor (CMPs) from control and Stat5-null mice yes Mouse 11
76 J.O'Shea EG008.1 Mouse CD8+ IL-7 yes Mouse 4
77 J.O'Shea EG008.2 Mouse DC LPS Stat5 yes Mouse 3
78 J.O'Shea EG008.3 Mouse CD4+ Stat5 proliferation yes Mouse 6
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79 J.O'Shea EG008.4 Mouse CD4+ Th17 Stat3 yes Mouse 6
80 J.O'Shea EG008.5 Mouse CD4+ Th1 Stat4 yes Mouse 6
81 J.O'Shea EG009.1 Human PBMC T-cells Stimulated with IFN-alpha and paired controls no Human 8 A+B
82 J.O'Shea EG009.2 Human PBMC T-cells Stimulated with IL-2 and paired controls no Human 10 A+B
83 J.O'Shea EG009.3 Human PBMC T-cells Stimulated with IL-2+IL-12 and paired controls no Human 10 A+B
84 J.O'Shea EG009.4 Human PBMC T-cells Stimulated with IL-12+IL-18 and paired controls no Human 12 A+B
85 J.O'Shea EG009.5 Human PBMC T-cells Stimulated with IL-18 and paired controls no Human 14 A+B
86 J.O'Shea EG009.6 Human PBMC T-cells Stimulated with IL-12 and paired controls GEO no Human 14 A+B
87 W.Leonard EG010 Human T-cells subjected to IL-2 yes Human 10 A+B
88 W.Paul EG011 Mouse Th2 cells deficient for Gfi1 or GATA3, stimulated with PMA/ionomycin, use Th1 cells as control Mouse 5 A+B
89 L.Hennighausen EG012 Mouse hematop. stem cells from bone marrow of Stat5 f/f (control) & Stat5 f/f; Mx1-Cre (STAT5-ko) Mouse 16
90 L.Hennighausen EG013 Fat pads carrying RBPJCreA and WT transplants +/- E/P stimulation no Mouse 8
91 L.Hennighausen EG014 pregnant
Mammary tissue from Stat5a/5b floxed/floxed mice (WT) and Stat5a/5b floxed/floxed; MMTV-CreA mice (KO) Mouse day 6.
no 4
92
93
94
95 Note: don't double count the controls used in EG009.1 through EG009.6. We subtract these from the total -25
Total
96 samples= 210
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 4
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Principal Experiment
1 Investigator Investigators Group ID (1) Experiment Group Summary of experiment (2) Purpose of experiment (2)
Lothar Hennighausen Bing-Mei Zhu, EG001 Ter119+ erythroid Determine some of the major up and down Determine Stat5-dependent genes
Weiping Chen cells from mouse regulated genes dependent on Stat5. in the Erythropoietic cells in Stat5-
fetal liver cells of Especially iron metabolism-related genes KO or WT mice.
control and Stat5- were down regulated and resulted in impaired
null mice iron uptake into erythropoietic cells and then
microcytic anemia.
2
Lothar Hennighausen Atsushi Hosui, Peter EG002 Liver tissue from Identify STAT5 target genes in mouse liver Identify genes that are activated by
Klover, Ji Hoon Yu, control and Stat5-null tissue. Control mice and mice from which the growth hormone (GH) through
Weiping Chen mice +/- acute GH Stat5 locus had been deleted using an Alb- STAT5
injection Cre transgene were injected with GH or PBS
and RNA was isolated after three hours.
3
Lothar Hennighausen Peter Klover, EG003.1 Muscle cells from With GT treatment: three Stat5 fl/fl controls Determine Stat5-dependent genes
Weiping Chen control and Stat5- (#44, #47, and #50) and three Stat5 muscle- in the skeletal muscle with and
null 12-week mice ko 12-week mice (Stat5MKO, #42, #43, and without exogenous GH stimulation.
with GH treatment #48).
4
Lothar Hennighausen Peter Klover, EG003.2 Muscle cells from Without GH treatment: experiment three Stat5 Determine Stat5-dependent genes
Weiping Chen control and Stat5- fl/fl controls (#4035, #4036, and #4042) and in the skeletal muscle with and
null 15-week mice three Stat5MKO (#4038, #4060, and #4063) without exogenous GH stimulation.
without GH 15 week mice .
treatment
5
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 5
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Lothar Hennighausen Atsushi Hosui, Bing- EG004 Mouse embryonic Activation of STATs by cytokines: Growth Determine and compare the
Mei Zhu, Weiping fibroblasts (MEFs) hormone (GH) preferentially activates STAT5 expression levels of target genes of
Chen from control and and to a lesser extent STAT1 and STAT3. In Stat5, Stat3, Stat1 under
Stat5-null mice (+/- contrast, IFN gamma (IFNg) preferentially stimulation of cytokines and
GH treatment; +/- activates STAT1 and to a lesser extent hormones.
IFN treatment) STAT3 and STAT5. The relative level of
activation of different STATs by GH and IFNg
is likely dependent on the cell type analyzed.
6
Lothar Hennighausen Akiko Kimura, Cyril EG005.1 Fetal liver-KSL cells The engraftment potential, reconstruction Determine the essential genes for
Martin, Weiping (enriched ability and survival of hematopoietic stem self renewal, proliferation,
Chen hematopoietic stem cells from STAT5-KO are impaired. Since differentiation and survival of
cells) from control hematopoietic stem cells are quiescent, hematopoietic stem cells which
and Stat5-null mice isolated KSL cells are stimulated with cytokine work downstream of STAT5.
coocktail. To address which kinds of genes
are associated with this issue, adult-KSL cells
7 are analyzed.
Lothar Hennighausen Akiko Kimura, Cyril EG005.2 Bone marrow-KSL The engraftment potential, reconstruction Determine the essential genes for
Martin, Weiping cells (enriched ability and survival of hematopoietic stem self renewal and survival of
Chen hematopoietic stem cells from STAT5-KO are impaired. To hematopoietic stem cells which
cells) from Mxr- address which kinds of genes are associated work downstream of STAT5.
Cre:Stat5 fl/fl adult with this issue, adult-KSL cells are analyzed.
mice
8
Lothar Hennighausen Akiko Kimura, EG006 Granulocyte Granulocyte macrophage colony stimulating Identify genes in GMPs that are
Weiping Chen Macrophage factor (GM-CSF) activates biological activated by STAT5.
Progenitor (GMPs) programs that lead to the formation of
from control and granulocytes (host defense against invaders).
Stat5-null mice STAT5 is the key mediator of this signaling
cascade. We investigate CMP and GMP cell
types that respond to GM-CSF.
9
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Lothar Hennighausen Akiko Kimura, EG007 Common Myeloid Granulocyte macrophage colony stimulating Identify genes in CMPs that are
Weiping Chen Progenitor (CMPs) factor (GM-CSF) activates biological activated by STAT5.
from control and programs that lead to the formation of
Stat5-null mice granulocytes (host defense against invaders).
STAT5 is the key mediator of this signaling
cascade. We investigate CMP cell types that
respond to GM-CSF.
10
John O'Shea Lai Wei EG008.1 Mouse CD8 IL-7 To identify IL-7 induced genes in CD8+ T Identification of IL-7 induced genes
cells, we isolated naïve and memory CD8+ T in CD8+ T cells
cells from B6 mice and cultured under either
no cytokine or IL-7 treatment conditions.
11
John O'Shea Lai Wei, Hydae EG008.2 Mouse DC LPS Freshly isolated DCs from wild type and Stat5 Identification of Stat5 dependent
Ramos Stat5 deficient mice were treated with LPS to LPS induced genes in DCs
identify Stat5 dependent genes in DCs.
12
John O'Shea Lai Wei, Arian EG008.3 Mouse CD4 Stat5 To identify Stat5 dependent Identification of Stat5 dependent
Laurence proliferation proliferative/proapoptotic/ antiapoptotic genes, proliferative/apoptosis genes in
CD4+ T cells with or without Stat5 expression cultured CD4+ T cells
were stimulated with anti-CD3/CD28 for 1, 3,
and 5 days, respectively.
13
John O'Shea Lai Wei, Arian EG008.4 Mouse CD4 Th17 To identify Stat3 regulated gene programs Identification of Stat3 dependent
Laurence Stat3 that balance Th17 and iTreg differentiation, and independent genes involved in
CD4+ T cells from wild type or Stat3 deficient Th17 and iTreg differentiation
mice were cultured for 3 days under either
14 Th17 or iTreg conditions.
John O'Shea Lai Wei, Yuka EG008.5 Mouse CD4 Th1 To identify Stat4 dependent and independent Identification of Stat4 dependent
Kanno, Wendy Stat4 genes that contribute Th1 differentiation, and independent genes involved in
Watford, Hiroaki naïve CD4+ T cells were isolated from B6 and Th1 differentiation
Takatori Stat4 deficient mice and cultured under Th0
and Th1 conditions for 3 days.
15
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John O'Shea Linda Muul, Alan EG009.1 Human PBMCs T- Expression data from human PBMC samples We employed microarray analysis
Berger, Hong-Wei cells Stimulated exposed to IL-2, IL-18, IL-2+IL-12, IL-12+IL- of IL-2, IL-18, IL-2+IL-12, IL-12+IL-
Sun with IFN-alpha and 18, IFN-alpha and paired controls. The same 18, IFN-alpha induced gene
paired controls controls samples were used in EG009.1 thru expression to provide further
EG009.6. insights into its effects on immune
response.
16
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John O'Shea Linda Muul, Alan EG009.2 Human PBMCs T- Expression data from human PBMC samples We employed microarray analysis
Berger, Hong-Wei cells Stimulated exposed to IL-2, IL-18, IL-2+IL-12, IL-12+IL- of IL-2, IL-18, IL-2+IL-12, IL-12+IL-
Sun with IL-2 and paired 18, IFN-alpha and paired controls. The same 18, IFN-alpha induced gene
controls controls samples were used in EG009.1 thru expression to provide further
EG009.6. insights into its effects on immune
response.
17
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 9
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John O'Shea Linda Muul, Alan EG009.3 Human PBMCs T- Expression data from human PBMC samples We employed microarray analysis
Berger, Hong-Wei cells Stimulated exposed to IL-2, IL-18, IL-2+IL-12, IL-12+IL- of IL-2, IL-18, IL-2+IL-12, IL-12+IL-
Sun with IL-2+IL-12 and 18, IFN-alpha and paired controls. The same 18, IFN-alpha induced gene
paired controls controls samples were used in EG009.1 thru expression to provide further
EG009.6. insights into its effects on immune
response.
18
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 10
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John O'Shea Linda Muul, Alan EG009.4 Human PBMCs T- Expression data from human PBMC samples We employed microarray analysis
Berger, Hong-Wei cells Stimulated exposed to IL-2, IL-18, IL-2+IL-12, IL-12+IL- of IL-2, IL-18, IL-2+IL-12, IL-12+IL-
Sun with IL-12+IL-18 18, IFN-alpha and paired controls. The same 18, IFN-alpha induced gene
and paired controls controls samples were used in EG009.1 thru expression to provide further
EG009.6. insights into its effects on immune
response.
19
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John O'Shea Linda Muul, Alan EG009.5 Human PBMCs T- Expression data from human PBMC samples We employed microarray analysis
Berger, Hong-Wei cells Stimulated exposed to IL-2, IL-18, IL-2+IL-12, IL-12+IL- of IL-2, IL-18, IL-2+IL-12, IL-12+IL-
Sun with IL-18 and 18, IFN-alpha and paired controls. The same 18, IFN-alpha induced gene
paired controls controls samples were used in EG009.1 thru expression to provide further
EG009.6. insights into its effects on immune
response.
20
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John O'Shea Wendy Watford, EG009.6 Human PBMCs Expression data from human PBMC samples We employed microarray analysis
Linda Muul, Alan Stimulated with IL- exposed to IL-12 and paired controls. The of IL-12 induced gene expression to
Berger, et.al. 12 and paired same controls samples were used in EG009.1 provide further insights into its
controls GEO thru EG009.6. effects on immune response.
21
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Warren Leonard Panu Kovanen, EG010 Human T-cells T lymphocytes play a central role in controlling Find genes expressed in T cells
Peter Munson subjected to IL-2 adaptive immune responses. IL-2 critically and of those, the ones regulated by
regulates both T cell growth and death and is IL-2.
involved in maintaining peripheral tolerance,
but the molecules involved in these and other
IL-2 actions are only partially known. We now
provide a comprehensive compendium of the
genes expressed in T cells and of those
regulatedby IL-2 based on a combination of
DNA microarrays and SAGE. The newly
identified IL-2 target genes include many
genes previously linked to apoptosis in other
cellular systems that may contribute to IL-2-
dependent survival functions. We also studied
the mRNA expression of known regulators of
signaling pathways for their inductionin
response to IL-2 in order to identify potential
novel positive and/or negative feedback
regulators of IL-2 signaling. We show that IL-2
regulates only a limited number of these
genes (see paper for details).
22
William Paul Jeff Zhu EG011 Mouse CD4 Th2 CD4 T cells were purified from wild type, To search for genes that are
cells deficient for Gfi1fl/fl or Gata3fl/fl mice. Cells were regulated by Gfi-1 and GATA-3 in
Gfi1 or GATA3, stimulated under Th2 conditions for 1 rounds. Th2 cells. (Note: Gfi-1 and GATA-
stimulated with During the second round of stimulation under 3 are highly expressed in Th2 cells.
PMA/ionomycin, Th2 conditions, Cre-GFP was introduced. Both of them play important roles in
use Th1 cells as GFP+ or GFPneg cells were sorted and the Th2 cell expansion driven by IL-
control further expanded for 2 rounds under Th2 2.)
conditions. Cells were stimulated with
PMA/ionomycin for 2 hr before RNA isolation.
23
Lothar Hennighausen Lothar EG012 Mouse hematopoietic Mouse hematopoietic stem cells were isolated Determine Stat5-dependent genes
Hennighausen, stem cells isolated from bone marrow of Stat5 f/f (control) and Stat5 inMouse hematopoietic stem cells
Michael Rieger from bone marrow of f/f; Mx1-Cre (Stat5-KO) mice using FACS sorting. with and without exogenous TPO
Stat5 f/f (control) and Cells were starved for 5 hours and subsequently stimulation.
Stat5 f/f; Mx1-Cre stimulated with thrombopoietin (TPO) for 2 hours.
(STAT5-ko) stim. RNA was isolated and used for Affy analysis.
with TPO
24
Lothar Hennighausen Lothar EG013 Mouse mammary fat Mice carrying WT (l) and RBPJCreA (r) mammary Determine genes that are differentially
Hennighausen, pads transplanted transplants were untreated or treated with regulated in E/P treated WT and RBPJ
Gertraud Robinson, with WT and RBPJ estrogen/progesterone injections and harvested 48 KO cells
Weiping Chen epithelia hrs later.
25
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Lothar Hennighausen Daisuke Yamaji, EG014 Mammary tissue from Pregnant day 6: two Stat5a/5b floxed/floxed mice To search for genes that are regulated
Lothar Stat5a/5b (WT, #1047 and #1048) and two Stat5a/5b by STAT5 in the mammary gland at
Hennighausen, floxed/floxed mice floxed/floxed; MMTV-CreA mice (KO, #1040 and day 6 of pregnancy
Weiping Chen (WT) and Stat5a/5b #1043).
floxed/floxed;
MMTV-CreA mice
(KO) pregnant at day
6.
26
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G H I J K L M N
Mouse (strain) Cell lines / Affy chip(s) Dates samples
1 Experimental design (2) Stimulation (6) or Human tissue sample Genes WT Genes KO platform were run
Isolated Ter119-positive fetal liver cells from three mouse Erythroid STAT5 STAT5-null MOE430_2 6/8/2004
to five E14.5 embryos of the same genotype were
combined, and total RNA was extracted using
TRIzol reagent (Life Technologies) with two
additional ethanol precipitations. Microarray
analyses were performed using Affymetrix Mouse
Genome 430 2.0 array GeneChips (Affymetrix). Up-
and down-regulated genes were selected based on
P values of 1.5 or -1.5
as assessed by ANOVA using Partek Pro software
(Partek). To determine specific pathways, gene
pathway analysis was obtained using the
statistically significant gene list (P<0.05)
2 represented on the chip.
??WHAT?? GH mouse Liver STAT5 STAT5-null MOE430_2 3/11/2008
3
The treated mice were given growth hormone (GH) GH mouse Muscle STAT5 STAT5-null MOE430_2 2/9/2007
midday for 3 hours and quadriceps muscle was
isolated RNA and frozen in dry ice. RNA was
isolated using TriZol reagent (Invitrogen) followed
by RNeasy column purification(Qiagen). The
untreated mice quadriceps muscle was isolated
midday and frozen in dry ice. RNA was prepared
4 as before.
The treated mice were given growth hormone (GH) GH mouse Muscle STAT5 STAT5-null MOE430_2 6/10/2008
midday for 3 hours and quadriceps muscle was
isolated RNA and frozen in dry ice. RNA was
isolated using TriZol reagent (Invitrogen) followed
by RNeasy column purification(Qiagen). The
untreated mice quadriceps muscle was isolated
midday and frozen in dry ice. RNA was prepared
5 as before.
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1. MEFs were isolated from control and STAT5-null GH, IFN mouse MEF STAT5 STAT5-null MOE430_2 07/22/08
fetuses. 2. Control and STAT5-null MEFs were
cultured and subsequently starved for 12 hours.
This should result in the loss of STAT activation
and thus the termination of any transcription
induced by STATs. 3. The starved control and
STAT5-null MEFs were acutely stimulated with GH
for 60 minutes and RNA was isolated. RNA was
also prepared from starved MEFs that had not
been stimulated. 4. Affy chips were hybridized with
the RNA (Weiping and George have the info about
the quality of the RNA and whether an amplification
6 was necessary)
KSL cells were stimulated +/- (100 ng/mL each of 100 ng/mL each mouse BM-KSL STAT5 STAT5-null MOE430_2 1/3/08, 1/9/08 in
TPO, IL3, Flt3 ligabnd, GM-CSF, IL-6) of TPO, IL3, Flt3 1/3/08, 2/8/08 in
ligabnd, GM- 1/3/08, 6/21/07 in
CSF, IL-6 3/21/07
7
KSL cells are harvested from adult bone marrow of without mouse BM-KSL STAT5 Mx1-Cre:STAT5 MOE430_2 5/9/07 & 7/10/07
STAT5 fl/fl (control) and Mx1-Cre:STAT5 fl/fl (KO). stimulation KO in 3/21/07
Isolated total RNA were used for microarray
analysis.
8
1. GMPs were isolated from bone marrow from GM-CSF mouse GMP STAT5 fl/fl Mx1-Cre:STAT5 MOE430_2 3/25/08 in
mice STAT5 fl/fl (control) and Mx1-Cre:STAT5 fl/fl (CTL) KO 3/25/08, 8/18/08
(KO) of hematopoietic stem cells. 2. Control and in 8/18/08,
STAT5-null GMPs were cultured and subsequently 6/10/08 in
starved for 12 hours. This should result in the loss 3/25/08
of STAT activation and thus the termination of any
transcription induced by STATs. 3. The starved
control and STAT5-null GMPs were acutely
stimulated with GM-CSF for 60 minutes and RNA
was isolated. RNA was also prepared from starved
GMPs that had not been stimulated. 4. Affy chips
were hybridized with the RNA (Weiping and
George have the info about the quality of the RNA
and whether an amplification was necessary).
9
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1. CMPs were isolated from bone marrow from GM-CSF mouse CMP STAT5 fl/fl Mx1-Cre:STAT5 MOE430_2 3/25/08 in
mice STAT5 fl/fl (control) and Mx1-Cre:STAT5 fl/fl (CTL) KO 3/25/08, 8/18/08
(KO) of hematopoietic stem cells. 2. Control and in 8/18/08
STAT5-null CMPs were cultured and subsequently
starved for 12 hours. This should result in the loss
of STAT activation and thus the termination of any
transcription induced by STATs. 3. The starved
control and STAT5-null CMPs were acutely
stimulated with GM-CSF for 60 minutes and RNA
was isolated. RNA was also prepared from starved
CMPs that had not been stimulated. 4. Affy chips
were hybridized with the RNA (Weiping and
George have the info about the quality of the RNA
and whether an amplification was necessary).
10
CD8+ T cells, treated vs untreated IL-7 mouse primary T cell WT B6 MOE430_2 3/7/2007,
4/18/2008
11
Dentritic cells, treated vs untreated, WT vs KO LPS mouse primary T cell Stat5 WT Stat5-null MOE430_2 4/1/2008
12
CD4+ T cells, cultured for 1,3,5 days, WT vs KO anti-CD3/CD28, mouse primary T cell Stat5 WT Stat5-null MOE430_2 7/3/2008
IL-2
13
CD4+ T cells, cultured for 3 days, WT vs KO, Th0 anti-CD3/CD28, mouse primary T cell Stat3 WT Stat3-null MOE430_2 12/5/2006
vs Th17 vs iTreg Th17, iTreg
14
CD4+ T cells, naïve or cultured for 3 days, WT vs anti-CD3/CD28, mouse primary T cell Stat4 WT Stat4-null MOE430_2 7/3/2008
KO, Th0 vs Th1 Th1
15
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PBMC's were isolated from 7 healthly NIH blood IFN-alpha human PBMC HG-U133A+B 2002 through
bank donors. For each donor, expression levels 2004
were measured for PBMCs stimulated with IL-2, IL-
18, IL-2+IL-12, IL-12+IL-18, IFN-alpha and
unstimulated controls. Cytokines added at 10ng/ml.
16
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 19
G H I J K L M N
PBMC's were isolated from 7 healthly NIH blood IL-2 human PBMC HG-U133A+B 2002 through
bank donors. For each donor, expression levels 2004
were measured for PBMCs stimulated with IL-2, IL-
18, IL-2+IL-12, IL-12+IL-18, IFN-alpha and
unstimulated controls. Cytokines added at 10ng/ml.
17
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 20
G H I J K L M N
PBMC's were isolated from 7 healthly NIH blood IL-2+IL-12 human PBMC HG-U133A+B 2002 through
bank donors. For each donor, expression levels 2004
were measured for PBMCs stimulated with IL-2, IL-
18, IL-2+IL-12, IL-12+IL-18, IFN-alpha and
unstimulated controls. Cytokines added at 10ng/ml
for each cytokine.
18
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 21
G H I J K L M N
PBMC's were isolated from 7 healthly NIH blood IL-12+IL-18 human PBMC HG-U133A+B 2002 through
bank donors. For each donor, expression levels 2004
were measured for PBMCs stimulated with IL-2, IL-
18, IL-2+IL-12, IL-12+IL-18, IFN-alpha and
unstimulated controls. Cytokines added at 10ng/ml
for each cytokine.
19
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 22
G H I J K L M N
PBMC's were isolated from 7 healthly NIH blood IL-18 human PBMC HG-U133A+B 2002 through
bank donors. For each donor, expression levels 2004
were measured for PBMCs stimulated with IL-2, IL-
18, IL-2+IL-12, IL-12+IL-18, IFN-alpha and
unstimulated controls. Cytokines added at 10ng/ml.
20
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 23
G H I J K L M N
PBMC's were isolated from 7 healthly NIH blood IL-12 human PBMC HG-U133A+B 2002
bank donors. For each donor, expression levels
were measured for PBMCs stimulated with IL-12
and unstimulated controls. Cytokines added at
10ng/ml.
21
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 24
G H I J K L M N
RNA was processed to cRNA probes for Gene IL-2 human PBMC HG_U95Av2 5/1/2001
Chip analysis (Affymetrix).The probes were
hybridized to U95A GeneChips (Affymetrix),
washed and scanned (Hewlett Packard, GeneArray
scanner G2500A) according to procedures outlined
by the manufacturer (Affymetrix). Scanned images
were processed using the MAS4 (Affymetrix). Four
similar experiments were performed, each of which
consisted of one control and one IL-2-treated
sample. A transcript was considered to be ‘present’
when the corresponding probe set gave a ‘present
call’ in at least three of four experiments for either
control or IL-2-treated T cells.
22
To compare WT Th2 with Gfi1KO or GATA3KO IL-2, IL-4 and anti- C57BL/6 Primary CD4 T Gfi1 or Gata3 MOE430A+B 9/13/2005,
Th2 using Th1 cells as another control CD3/CD28, anti- cells that were 8/18/05
IL-12, anti-IFNg activated in vitro
during priming, under Th2
2hr stimulation of conditions
PMA/ionomycin
at the end.
23
??WHAT?? TPO mouse Mouse stem cells STAT5 fl/fl Mx1-Cre:STAT5 MOE430_2 12/30/2008
(CTL) KO
24
Mice carrying WT (l) and RBPJCreA (r) mammary Stimulation with mouse Mouse mammary WT RBPJ KO MOE430_2 1/29/2009
transplants were untreated (407 and 408) or estrogen/progest transplanted fat
treated (410 and 411) with estrogen/progesterone erone injection pads
injections and harvested 48 hrs later.
25
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 25
G H I J K L M N
The mice were mated just before evening and the n/a mouse mammary tissue Stat5a/5b Stat5a/5b MOE430_2 1/28/2009
next day was counted as day 0.5. At day 6.5, after floxed/floxed floxed/floxed;
removing the lymph node, the mammary gland was MMTV-CreA
collected and kept in RNAlater at 4 degree. RNA
was isolated using TriZol reagent (Invitrogen)
followed by RNeasy Plus Mini Kit (Qiagen).
26
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 26
O P Q R S T U V
Data location
Purification Journal ref. if (mAdb, Geo,
procedure (e.g., published (ref. In mAdb DB DVD, FTP Additional
FACS, Ab, etc.) PubMed ID) or (user, project In GEO DB (ID if In caArray DB server, Web documentation
1 Sample Preparation (Lit. ref. is ok) (8) (8) "not yet" name if yes) (8) yes) (ID if yes) site, etc.) (file(s), etc.)
B-M Zhu et.al. Blood, 2008 112: 2071- B-M Zhu et.al. B-M Zhu et.al. GSE11777 No EDGE server
2080 Blood, 2008 112: Blood, 2008 112:
2071-2081 2071-2080
2
??WHAT?? ??WHAT?? ??WHAT?? No No EDGE server
3
see Exper. Design see Exper. not yet GSE14710 No EDGE server
Design
4
see Exper. Design see Exper. not yet GSE14710 No EDGE server
Design
5
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 27
O P Q R S T U V
The embryos at E12.5-13.5 were ??WHAT?? ??WHAT?? No No EDGE server
used. The head and internal organs
were removed, and the torso was
minced and dispersed in
trypsin/EDTA I mL for 30 min at
37°C. Pipet up and down the tissue
to be smaller pieces and culture on
the 10 mm dishes in DMEM with
15% of FBS O/N. MEFs were
maintained in DMEM containing
15% FBS and subcultured 1:3
upon reaching confluence.
6
Nakauchi H, Takano H, Ema H, Osawa Lineage negative not yet AK, CM No No EDGE server
M, Ann N Y Acad Sci. 1999 872:57-66; selection by
discussion 66-70. magnetic beads
and sorting
7
Nakauchi H, Takano H, Ema H, Osawa Lineage negative not yet AK, CM No No EDGE server
M, Ann N Y Acad Sci. 1999 872:57-66; selection by
discussion 66-70. magnetic beads
and sorting
8
Akashi K, Traver D, Miyamoto T, Lineage negative not yet AK No EDGE server
Weissman IL, Nature. 2000 selection by
404(6774):193-197 magnetic beads
and sorting
9
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 28
O P Q R S T U V
Akashi K, Traver D, Miyamoto T, Lineage negative not yet AK No EDGE server
Weissman IL., Nature. 2000 selection by
404(6774):193-197. magnetic beads
and sorting
10
Wei et.al., J Biol Chem. 2007 282:48 Wei et.al., J Biol not yet No No No Files from Lai
34605-34610 Chem. 2007 Wei
282:48 34605-
34610
11
Wei et.al., J Biol Chem. 2007 282:48 Wei et.al., J Biol not yet No No No Files from Lai
34605-34610 Chem. 2007 Wei
282:48 34605-
12 34610
Wei et.al., J Biol Chem. 2007 282:48 Wei et.al., J Biol not yet No No No Files from Lai
34605-34610 Chem. 2007 Wei
282:48 34605-
34610
13
Wei et.al., J Biol Chem. 2007 282:48 Wei et.al., J Biol not yet No No No Files from Lai
34605-34610 Chem. 2007 Wei
282:48 34605-
34610
14
Wei et.al., J Biol Chem. 2007 282:48 Wei et.al., J Biol not yet No No No Files from Lai
34605-34610 Chem. 2007 Wei
282:48 34605-
34610
15
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 29
O P Q R S T U V
Growth protocol as described in Wendy Wendy T. not yet No No Files from L. All EG009.x
T. Watford, et al., Tpl2 kinase regulates Watford, et al., J Muul & A. Berger series share the
T cell interferon gamma production and Exp Med. 2008, same controls.
host resistance to Toxoplasma gondii. PMID:19001140.
Treatment protocol as described in
Wendy T. Watford, et al., Tpl2 kinase
regulates T cell interferon gamma
production and host resistance to
Toxoplasma gondii. Extract protocol
Cytokine-stimulated cells were lysed in
RNeasy lysis buffer (Qiagen, Valencia,
CA) and total RNA was isolated with the
Qiagen RNeasy Midi kit using the
standard protocol. RNA was purified
using Trizol (Invitrogen Life
Technologies, Carlsbad, CA) and
chloroform, followed by ethanol
precipitation. Label protocol Biotin-
labeled cRNA was synthesized using the
BioArray High Yield RNA transcript
labeling kit (Enzo Life Sciences, Inc.,
Farmingdale, NY) Affymetrix). Hyb
protocol cRNA was hybridized to
Affymetrix Human Genome-U133A and
HG-U133B microarray chips according
to the manufacturer’s instructions.
GeneChips were washed and stained in
the Affymetrix GeneChip Fluidics Station
Model 400. Scan protocol GeneChips
were scanned by the HP-Affymetrix
16 GeneArray Scanner using the
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 30
O P Q R S T U V
Growth protocol as described in Wendy Wendy T. not yet No No Files from L. All EG009.x
T. Watford, et al., Tpl2 kinase regulates Watford, et al., J Muul & A. Berger series share the
T cell interferon gamma production and Exp Med. 2008, same controls.
host resistance to Toxoplasma gondii. PMID:19001140.
Treatment protocol as described in
Wendy T. Watford, et al., Tpl2 kinase
regulates T cell interferon gamma
production and host resistance to
Toxoplasma gondii. Extract protocol
Cytokine-stimulated cells were lysed in
RNeasy lysis buffer (Qiagen, Valencia,
CA) and total RNA was isolated with the
Qiagen RNeasy Midi kit using the
standard protocol. RNA was purified
using Trizol (Invitrogen Life
Technologies, Carlsbad, CA) and
chloroform, followed by ethanol
precipitation. Label protocol Biotin-
labeled cRNA was synthesized using the
BioArray High Yield RNA transcript
labeling kit (Enzo Life Sciences, Inc.,
Farmingdale, NY) Affymetrix). Hyb
protocol cRNA was hybridized to
Affymetrix Human Genome-U133A and
HG-U133B microarray chips according
to the manufacturer’s instructions.
GeneChips were washed and stained in
the Affymetrix GeneChip Fluidics Station
Model 400. Scan protocol GeneChips
were scanned by the HP-Affymetrix
17 GeneArray Scanner using the
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 31
O P Q R S T U V
Growth protocol as described in Wendy Wendy T. not yet GSE12839 No Files from L. All EG009.x
T. Watford, et al., Tpl2 kinase regulates Watford, et al., J Muul & A. Berger series share the
T cell interferon gamma production and Exp Med. 2008, same controls.
host resistance to Toxoplasma gondii. PMID:19001140.
Treatment protocol as described in
Wendy T. Watford, et al., Tpl2 kinase
regulates T cell interferon gamma
production and host resistance to
Toxoplasma gondii. Extract protocol
Cytokine-stimulated cells were lysed in
RNeasy lysis buffer (Qiagen, Valencia,
CA) and total RNA was isolated with the
Qiagen RNeasy Midi kit using the
standard protocol. RNA was purified
using Trizol (Invitrogen Life
Technologies, Carlsbad, CA) and
chloroform, followed by ethanol
precipitation. Label protocol Biotin-
labeled cRNA was synthesized using the
BioArray High Yield RNA transcript
labeling kit (Enzo Life Sciences, Inc.,
Farmingdale, NY) Affymetrix). Hyb
protocol cRNA was hybridized to
Affymetrix Human Genome-U133A and
HG-U133B microarray chips according
to the manufacturer’s instructions.
GeneChips were washed and stained in
the Affymetrix GeneChip Fluidics Station
Model 400. Scan protocol GeneChips
were scanned by the HP-Affymetrix
18 GeneArray Scanner using the
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 32
O P Q R S T U V
Growth protocol as described in Wendy Wendy T. not yet No No Files from L. All EG009.x
T. Watford, et al., Tpl2 kinase regulates Watford, et al., J Muul & A. Berger series share the
T cell interferon gamma production and Exp Med. 2008, same controls.
host resistance to Toxoplasma gondii. PMID:19001140.
Treatment protocol as described in
Wendy T. Watford, et al., Tpl2 kinase
regulates T cell interferon gamma
production and host resistance to
Toxoplasma gondii. Extract protocol
Cytokine-stimulated cells were lysed in
RNeasy lysis buffer (Qiagen, Valencia,
CA) and total RNA was isolated with the
Qiagen RNeasy Midi kit using the
standard protocol. RNA was purified
using Trizol (Invitrogen Life
Technologies, Carlsbad, CA) and
chloroform, followed by ethanol
precipitation. Label protocol Biotin-
labeled cRNA was synthesized using the
BioArray High Yield RNA transcript
labeling kit (Enzo Life Sciences, Inc.,
Farmingdale, NY) Affymetrix). Hyb
protocol cRNA was hybridized to
Affymetrix Human Genome-U133A and
HG-U133B microarray chips according
to the manufacturer’s instructions.
GeneChips were washed and stained in
the Affymetrix GeneChip Fluidics Station
Model 400. Scan protocol GeneChips
were scanned by the HP-Affymetrix
19 GeneArray Scanner using the
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 33
O P Q R S T U V
Growth protocol as described in Wendy Wendy T. not yet No No Files from L. All EG009.x
T. Watford, et al., Tpl2 kinase regulates Watford, et al., J Muul & A. Berger series share the
T cell interferon gamma production and Exp Med. 2008, same controls.
host resistance to Toxoplasma gondii. PMID:19001140.
Treatment protocol as described in
Wendy T. Watford, et al., Tpl2 kinase
regulates T cell interferon gamma
production and host resistance to
Toxoplasma gondii. Extract protocol
Cytokine-stimulated cells were lysed in
RNeasy lysis buffer (Qiagen, Valencia,
CA) and total RNA was isolated with the
Qiagen RNeasy Midi kit using the
standard protocol. RNA was purified
using Trizol (Invitrogen Life
Technologies, Carlsbad, CA) and
chloroform, followed by ethanol
precipitation. Label protocol Biotin-
labeled cRNA was synthesized using the
BioArray High Yield RNA transcript
labeling kit (Enzo Life Sciences, Inc.,
Farmingdale, NY) Affymetrix). Hyb
protocol cRNA was hybridized to
Affymetrix Human Genome-U133A and
HG-U133B microarray chips according
to the manufacturer’s instructions.
GeneChips were washed and stained in
the Affymetrix GeneChip Fluidics Station
Model 400. Scan protocol GeneChips
were scanned by the HP-Affymetrix
20 GeneArray Scanner using the
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 34
O P Q R S T U V
Growth protocol as described in Wendy Wendy T. Wendy T. GSE12839 No Files from L. All EG009.x
T. Watford, et al., Tpl2 kinase regulates Watford, et al., J Watford, et al., J Muul & A. Berger series share the
T cell interferon gamma production and Exp Med. 2008, Exp Med. 2008, same controls.
host resistance to Toxoplasma gondii. PMID:19001140. PMID:19001140.
Treatment protocol as described in
Wendy T. Watford, et al., Tpl2 kinase
regulates T cell interferon gamma
production and host resistance to
Toxoplasma gondii. Extract protocol
Cytokine-stimulated cells were lysed in
RNeasy lysis buffer (Qiagen, Valencia,
CA) and total RNA was isolated with the
Qiagen RNeasy Midi kit using the
standard protocol. RNA was purified
using Trizol (Invitrogen Life
Technologies, Carlsbad, CA) and
chloroform, followed by ethanol
precipitation. Label protocol Biotin-
labeled cRNA was synthesized using the
BioArray High Yield RNA transcript
labeling kit (Enzo Life Sciences, Inc.,
Farmingdale, NY) Affymetrix). Hyb
protocol cRNA was hybridized to
Affymetrix Human Genome-U133A and
HG-U133B microarray chips according
to the manufacturer’s instructions.
GeneChips were washed and stained in
the Affymetrix GeneChip Fluidics Station
Model 400. Scan protocol GeneChips
were scanned by the HP-Affymetrix
21 GeneArray Scanner using the
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 35
O P Q R S T U V
PE Kovanen et.al., Intl. Immun. 2005 PE Kovanen PE Kovanen No Files from Peter Note(P.M.): the
17:8 1009-1020 et.al., Intl. et.al., Intl. Munson J14 data pair had
Immun. 2005 Immun. 2005 its labels
17:8 1009-1019 17:8 1009-1020 reversed,
meaning the "+"
was the control
and the "-" had
the IL-2
stimulation. This
is corrected in
this Inventory
DB.
22
Cells were sorted by FACS. cell sorting Ref. to the Gata3 No No NO Files from Jeff
and Gfi1 Zhu
conditional mice.
Zhu et al. Nature
Immunology,
5:1157-1165
(2004). Zhu et al.
PNAS,
103:18214-18219
(2006).
23
Mouse hematopoietic stem cells were cell sorting not yet No No EDGE server
isolated from bone marrow of Stat5 f/f
(control) and Stat5 f/f; Mx1-Cre (STAT5-
ko) mice using FACS sorting. Cells were
starved for 5 hours and subsequently
stimulated with thrombopoietin (TPO) for 3
hours. RNA was isolated and used for Affy
analysis.
24
Total fat pads with transplant were Trisol not yet No No EDGE server
harvested for RNA isolation
25
bb676ae0-9012-47d9-a432-e1d5444febca.xls ExperimentGroups 36
O P Q R S T U V
see Exper. Design see Exper. not yet No No EDGE server
Design
26
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM CellTypeTissue37
A B C D
Affy chip(s)
1 CellTypeTissue platform ExpressionGroups Introduction
BM-KSL MOE430_2 EG005.2 **EDIT *** This experiment determined gene changes in mouse bone marrow-KSL
cells (enriched hematopoietic stem cells) from Mxr-Cre:Stat5 fl/fl adult mice. The
engraftment potential, reconstruction ability and survival of hematopoietic stem
cells from STAT5-KO are impaired. To address which kinds of genes are
associated with this issue, adult-KSL cells are analyzed. (Investigators: Akiko
Kimura, Lothar Hennighausen, Weiping Chen).
2
CD4 MOE430_2 EG008.3 EG008.4 ***EDIT *** Three sets of mouse experiments were used to determine the
EG008.5 expression of CD4 cells with various cytokines. The first was to identify Stat5
dependent proliferative/proapoptotic/ antiapoptotic genes, CD4+ T cells with or
without Stat5 expression were stimulated with anti-CD3/CD28 for 1, 3, and 5 days,
respectively. The second was to identify Stat3 regulated gene programs that
balance Th17 and iTreg differentiation, CD4+ T cells from wild type or Stat3
deficient mice were cultured for 3 days under either Th17 or iTreg conditions. And
the third was to identify Stat4 dependent and independent genes that contribute
Th1 differentiation, naïve CD4+ T cells were isolated from B6 and Stat4 deficient
mice and cultured under Th0 and Th1 conditions for 3 days. (Investigators: Lai
Wei, Arian Laurence, Yuka Kanno, Wendy Watford, Hiroaki Takatori, John
O'Shea).
3
CD8 MOE430_2 EG008.1 ***EDIT *** This experiment identified mouse IL-7 induced genes in CD8+ T cells,
we isolated naïve and memory CD8+ T cells from B6 mice and cultured under
either no cytokine or IL-7 treatment conditions. (Investigators: Lai Wei, John
4 O'Shea).
DC MOE430_2 EG008.2 ***EDIT *** This experiment looked at freshly isolated mouse dendritic cells (DC)
from wild type and Stat5 deficient mice were treated with LPS to identify Stat5
dependent genes in DCs. (Investigators: Lai Wei, Hydae Ramos, John O'Shea).
5
CMP MOE430_2 EG007 ***EDIT *** This experiment investigated genes in mouse Granulocyte Macrophage
Progenitor (GMPs) from control and Stat5-null mice that responded to granulocyte
macrophage colony stimulating factor (GM-CSF). GSF activates biological
programs that lead to the formation of granulocytes (host defense against
invaders). STAT5 is the key mediator of this signaling cascade. (Investigators:
Akiko Kimura, Lothar Hennighausen, Weiping Chen).
6
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM CellTypeTissue38
A B C D
Erythroid MOE430_2 EG001 ***EDIT *** Control and fetal mouse liver Ter119+ erythroid Stat5-null mice were
used to determine some of the major up and down regulated genes dependent on
Stat5. Especially iron metabolism-related genes were down regulated and resulted
in impaired iron uptake into erythropoietic cells and then microcytic anemia.
(Investigators: Bing-Mei Zhu, Lothar Hennighausen, Weiping Chen).
7
GMP MOE430_2 EG006 ***EDIT *** This experiment investigated genes in mouse Common Myeloid
Progenitor (CMPs) from control and Stat5-null mice that responded to granulocyte
macrophage colony stimulating factor (GM-CSF). GSF activates biological
programs that lead to the formation of granulocytes (host defense against
invaders). STAT5 is the key mediator of this signaling cascade. (Investigators:
Akiko Kimura, Lothar Hennighausen, Weiping Chen).
8
HSC MOE430_2 EG005.1 EG012 **EDIT *** Several mouse hematopoietic stem stem systems were investigatd. The
first was mouse bone marrow-KSL cells (enriched hematopoietic stem cells) from
Mxr-Cre:Stat5 fl/fl adult mice. The second was mouse hematopoietic stem cells
isolated from bone marrow of Stat5 f/f (control) and Stat5 f/f; Mx1-Cre (STAT5-ko)
stim. with TPO. (Investigators: Akiko Kimura, Michael Rieger, Lothar
Hennighausen, Weiping Chen).
9
Liver MOE430_2 EG002 **EDIT *** This experiment identified some of the STAT5 target genes in mouse
liver tissue. Control mice and mice from which the Stat5 locus had been deleted
using an Alb-Cre transgene were injected with GH or PBS and RNA was isolated
after three hours. . (Investigators: Atsushi Hosui, Peter Klover, Ji Hoon Yu, Lothar
10 Hennighausen, Weiping Chen).
MEF MOE430_2 EG004 **EDIT *** This experiment looked at gene changes in mouse embryonic fibroblasts
(MEFs) from control and Stat5-null mice (+/- GH treatment; +/- IFN treatment).
Activation of STATs by cytokines: Growth hormone (GH) preferentially activates
STAT5 and to a lesser extent STAT1 and STAT3. In contrast, IFN gamma (IFNg)
preferentially activates STAT1 and to a lesser extent STAT3 and STAT5. The
relative level of activation of different STATs by GH and IFNg is likely dependent on
the cell type analyzed. (Investigators: Atsushi Hosui, Lothar Hennighausen,
Weiping Chen).
11
Muscle MOE430_2 EG003.1 EG003.2 Control and muscle-specific Stat5-null mice (Stat5-MKO) were injected with growth
hormone (GH) and muscle (which) tissue was isolated after 15 minutes. Tissue was
also harvested from non-injected mice. (Investigators: Peter Klover, Lothar
12 Hennighausen, Weiping Chen).
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM CellTypeTissue39
A B C D
PBMC-HGU133 HG- EG009.1 EG009.2 ***EDIT *** Human PBMC's were isolated from 7 healthly NIH blood bank donors.
U133A+B EG009.3 EG009.4 For each donor, expression levels were measured for PBMCs stimulated with IL-2,
EG009.5 EG009.6 IL-18, IL-2+IL-12, IL-12+IL-18, IFN-alpha and unstimulated controls. Cytokines
added at 10ng/ml.. (Investigators: Linda Muul, Alan Berger, John O'Shea).
13
PBMC-HGU95 HG_U95Av2 EG010 ***EDIT *** This experiment looked for gene changes in human T-cells subjected to
IL-2. T lymphocytes play a central role in controlling adaptive immune responses. IL-
2 critically regulates both T cell growth and death and is involved in maintaining
peripheral tolerance, but the molecules involved in these and other IL-2 actions are
only partially known. We now provide a comprehensive compendium of the genes
expressed in T cells and of those regulatedby IL-2 based on a combination of DNA
microarrays and SAGE. The newly identified IL-2 target genes include many genes
previously linked to apoptosis in other cellular systems that may contribute to IL-2-
dependent survival functions. The mRNA expression of known regulators of
signaling pathways for their inductionin response to IL-2 was studied to identify
potential novel positive and/or negative feedback regulators of IL-2 signaling. We
show that IL-2 regulates only a limited number of these genes (see paper for
details). (Investigators: Panu Kovanen, Peter Munson, Warren Leonard).
14
CD4-MOE430AB MOE430A+B EG011 ***EDIT *** Mouse Th2 cells deficient for Gfi1 or GATA3 were stimulated with
PMA/ionomycin using Th1 cells as the control. CD4 T cells were purified from wild
type, Gfi1fl/fl or Gata3fl/fl mice. Cells were stimulated under Th2 conditions for 1
rounds. During the second round of stimulation under Th2 conditions, Cre-GFP was
introduced. GFP+ or GFPneg cells were sorted and further expanded for 2 rounds
under Th2 conditions. Cells were stimulated with PMA/ionomycin for 2 hr before
RNA isolation. (Investigators: Jeff Zhu, William Paul).
15
Mammary MOE430_2 EG013 EG014 One experiment (T.Robinson) investigated genes differentially regulated upon
estrogen/progesterone stimulation in RBPJ KO mammary epithelial cells. The other
experiment (D.Yamaji) were Stat5a/5b floxed/floxed mice (WT) and Stat5a/5b
floxed/floxed; MMTV-CreA mice (KO) were mated at 2 months old and mammary
tissue was collected after 6 days. (Investigators: Daisuke Yamaji, Lothar
16 Hennighausen, Weiping Chen).
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG001 40
A B C D E F G H I J K L M N O P
Simple Dur. Experiment
Principal Investigato Cell GSP ID Genes stim. Time Group ID Sample
1 Investigator rs type (10) GSP ID (9) WT/KO Stim. (11) (12) point Rep. (13) (1) ID (3) AffyPlat (14) Date (15) Affy .CEL file (16) Folder (17)
Lothar Bing-Mei fetal EG001- EG001- Stat5-null no- biological EG001 MOE430_2 6/8/2004 06-08- 06-08-
Hennighausen Zhu mouse 01 01.Erythroid. stimulatio 04_Hennighausen_Mouse4 04_Hennigh
liver Stat5KO.br1. n 30_2_KO1 ausen.Celfil
Ter119+ noStim es
erythroid
2
Lothar Bing-Mei fetal EG001- EG001- Stat5-null no- biological EG001 MOE430_2 6/8/2004 06-08- 06-08-
Hennighausen Zhu mouse 02 02.Erythroid. stimulatio 04_Hennighausen_Mouse4 04_Hennigh
liver Stat5KO.br2. n 30_2_KO2 ausen.Celfil
Ter119+ noStim es
erythroid
3
Lothar Bing-Mei fetal EG001- EG001- Stat5-null no- biological EG001 MOE430_2 6/8/2004 06-08- 06-08-
Hennighausen Zhu mouse 03 03.Erythroid. stimulatio 04_Hennighausen_Mouse4 04_Hennigh
liver Stat5KO.br3. n 30_2_KO3 ausen.Celfil
Ter119+ noStim es
erythroid
4
Lothar Bing-Mei fetal EG001- EG001- WT no- biological EG001 MOE430_2 6/8/2004 06-08- 06-08-
Hennighausen Zhu mouse 04 04.Erythroid. stimulatio 04_Hennighausen_Mouse4 04_Hennigh
liver WT.br1.noSt n 30_2_WT1 ausen.Celfil
Ter119+ im es
erythroid
5
Lothar Bing-Mei fetal EG001- EG001- WT no- biological EG001 MOE430_2 6/8/2004 06-08- 06-08-
Hennighausen Zhu mouse 05 05.Erythroid. stimulatio 04_Hennighausen_Mouse4 04_Hennigh
liver WT.br2.noSt n 30_2_WT2 ausen.Celfil
Ter119+ im es
erythroid
6
Lothar Bing-Mei fetal EG001- EG001- WT no- biological EG001 MOE430_2 6/8/2004 06-08- 06-08-
Hennighausen Zhu mouse 06 06.Erythroid. stimulatio 04_Hennighausen_Mouse4 04_Hennigh
liver WT.br3.noSt n 30_2_WT3 ausen.Celfil
Ter119+ im es
erythroid
7
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG001 41
Q
PCR
1 cycles
2
3
4
5
6
7
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG002 42
A B C D E F G H I J K L M N O
Simple Dur. Experime
Principal Cell GSP ID Genes stim. Time Rep. nt Group Sample ID AffyPlat
1 Investigator Investigators type (10) GSP ID (9) WT/KO Stim. (11) (12) point (13) ID (1) (3) (14) Date (15) Affy .CEL file (16)
Lothar Atsushi Hosui, mouse EG002- EG002- WT GH 3h EG002 69 MOE430_2 ####### 03-11-
Hennighausen Peter Klover, Ji liver 01 01.Liver.WT.69.G 08_Hennighausen_AH
Hoon Yu, H _Mouse430_2_69
Weiping Chen
2
Lothar Atsushi Hosui, mouse EG002- EG002- WT GH 3h EG002 70 MOE430_2 ####### 03-11-
Hennighausen Peter Klover, Ji liver 02 02.Liver.WT.70.G 08_Hennighausen_AH
Hoon Yu, H _Mouse430_2_70
Weiping Chen
3
Lothar Atsushi Hosui, mouse EG002- EG002- Stat5LKO GH 3h tech EG002 71a MOE430_2 ####### 03-11-
Hennighausen Peter Klover, Ji liver 03 03.Liver.Stat5LKO. 08_Hennighausen_AH
Hoon Yu, 71a.GH _Mouse430_2_71a
Weiping Chen
4
Lothar Atsushi Hosui, mouse EG002- EG002- WT GH 3h EG002 72 MOE430_2 ####### 03-11-
Hennighausen Peter Klover, Ji liver 05 05.Liver.WT.72.G 08_Hennighausen_AH
Hoon Yu, H _Mouse430_2_72
Weiping Chen
5
Lothar Atsushi Hosui, mouse EG002- EG002- Stat5LKO GH 3h EG002 73a MOE430_2 ####### 03-11-
Hennighausen Peter Klover, Ji liver 06 06.Liver.Stat5LKO. 08_Hennighausen_AH
Hoon Yu, 73a.GH _Mouse430_2_73a
Weiping Chen
6
Lothar Atsushi Hosui, mouse EG002- EG002- WT no- 3h EG002 74 MOE430_2 ####### 03-11-
Hennighausen Peter Klover, Ji liver 08 08.Liver.WT.75a.n stimulation 08_Hennighausen_AH
Hoon Yu, oStim _Mouse430_2_74
Weiping Chen
7
Lothar Atsushi Hosui, mouse EG002- EG002- Stat5LKO no- 3h EG002 77 MOE430_2 ####### 03-11-
Hennighausen Peter Klover, Ji liver 11 11.Liver.Stat5LKO. stimulation 08_Hennighausen_AH
Hoon Yu, 77.noStimulation _Mouse430_2_77
Weiping Chen
8
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG002 43
P Q
PCR
1 Folder (17) cycles
03-11-
08_Hennigh
augen_AH_
Mouse430_
2_STAT5_G
2 H
03-11-
08_Hennigh
augen_AH_
Mouse430_
2_STAT5_G
3 H
03-11-
08_Hennigh
augen_AH_
Mouse430_
2_STAT5_G
4 H
03-11-
08_Hennigh
augen_AH_
Mouse430_
2_STAT5_G
5 H
03-11-
08_Hennigh
augen_AH_
Mouse430_
2_STAT5_G
6 H
03-11-
08_Hennigh
augen_AH_
Mouse430_
2_STAT5_G
7 H
03-11-
08_Hennigh
augen_AH_
Mouse430_
2_STAT5_G
8 H
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG003.1 44
A B C D E F G H I J K L M N O
Dur.
Principal Simple GSP ID Genes Stim. stim. Time Experiment Sample AffyPlat
1 Investigator Investigators Cell type (10) GSP ID (9) WT/KO (11) (12) point Rep. (13) Group ID (1) ID (3) (14) Date (15) Affy .CEL file (16)
Lothar Peter Klover mouse EG003.1-01 EG003.1- Stat5MKO GH biological EG003.1 42 MOE430_2 2/9/2007 02-09-
Hennighausen muscle 01.Muscle.Stat 07_Hennighausen_PK_
5MKO.42.GH Mouse430_2_M42
2
Lothar Peter Klover mouse EG003.1-02 EG003.1- Stat5MKO GH biological EG003.1 43 MOE430_2 2/9/2007 02-09-
Hennighausen muscle 02.Muscle.Stat 07_Hennighausen_PK_
5MKO.43.GH Mouse430_2_M43
3
Lothar Peter Klover mouse EG003.1-03 EG003.1- WT GH biological EG003.1 44 MOE430_2 2/9/2007 02-09-
Hennighausen muscle 03.Muscle.WT. 07_Hennighausen_PK_
44.GH Mouse430_2_M44
4
Lothar Peter Klover mouse EG003.1-04 EG003.1- WT GH biological EG003.1 47 MOE430_2 2/9/2007 02-09-
Hennighausen muscle 04.Muscle.WT. 07_Hennighausen_PK_
47.GH Mouse430_2_M47
5
Lothar Peter Klover mouse EG003.1-05 EG003.1- Stat5MKO GH biological EG003.1 48 MOE430_2 2/9/2007 02-09-
Hennighausen muscle 05.Muscle.Stat 07_Hennighausen_PK_
5MKO.48.GH Mouse430_2_M48
6
Lothar Peter Klover mouse EG003.1-06 EG003.1- WT GH biological EG003.1 50 MOE430_2 2/9/2007 02-09-
Hennighausen muscle 06.Muscle.WT. 07_Hennighausen_PK_
50.GH Mouse430_2_M50
7
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG003.1 45
P Q
PCR
1 Folder (17) cycles
02-08-
07_Hennighau
sen_PK
2
02-08-
07_Hennighau
sen_PK
3
02-08-
07_Hennighau
sen_PK
4
02-08-
07_Hennighau
sen_PK
5
02-08-
07_Hennighau
sen_PK
6
02-08-
07_Hennighau
sen_PK
7
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG003.2 46
A B C D E F G H I J K L M N O P Q
Experim
Dur. ent
Principal Investigat Cell Simple GSP Genes stim. Time Rep. Group ID Sample AffyPlat PCR
1 Investigator ors type ID (10) GSP ID (9) WT/KO Stim. (11) (12) point (13) (1) ID (3) (14) Date (15) Affy .CEL file (16) Folder (17) cycles
Lothar Peter mouse EG003.2-01 EG003.2- WT no- biological EG003.2 4038WT MOE430_ 6/10/2008 06-10- 06-10-
Hennighausen Klover muscle 01.Muscle.WT. stimulation 2 08_Hennighausen_1P 2008_L.Hennigh
4038WT.noSti K_Mouse430_2_403 ausen-PK
2 m 8WT
Lothar Peter mouse EG003.2-02 EG003.2- WT no- biological EG003.2 4060WT MOE430_ 6/10/2008 06-10- 06-10-
Hennighausen Klover muscle 02.Muscle.WT. stimulation 2 08_Hennighausen_2P 2008_L.Hennigh
4060WT.noSti K_Mouse430_2_406 ausen-PK
3 m 0WT
Lothar Peter mouse EG003.2-03 EG003.2- WT no- biological EG003.2 4063WT MOE430_ 6/10/2008 06-10- 06-10-
Hennighausen Klover muscle 03.Muscle.WT. stimulation 2 08_Hennighausen_3P 2008_L.Hennigh
4063WT.noSti K_Mouse430_2_406 ausen-PK
4 m 3WT
Lothar Peter mouse EG003.2-04 EG003.2- Stat5MKO no- biological EG003.2 4035KO MOE430_ 6/10/2008 06-10- 06-10-
Hennighausen Klover muscle 04.Muscle.Stat stimulation 2 08_Hennighausen_4P 2008_L.Hennigh
5MKO.4035KO K_Mouse430_2_403 ausen-PK
5 .noStim 5KO
Lothar Peter mouse EG003.2-05 EG003.2- Stat5MKO no- biological EG003.2 4036KO MOE430_ 6/10/2008 06-10- 06-10-
Hennighausen Klover muscle 05.Muscle.Stat stimulation 2 08_Hennighausen_5P 2008_L.Hennigh
5MKO.4036KO K_Mouse430_2_403 ausen-PK
6 .noStim 6KO
Lothar Peter mouse EG003.2-06 EG003.2- Stat5MKO no- biological EG003.2 4042KO MOE430_ 6/10/2008 06-10- 06-10-
Hennighausen Klover muscle 06.Muscle.Stat stimulation 2 08_Hennighausen_6P 2008_L.Hennigh
5MKO.4042KO K_Mouse430_2_404 ausen-PK
7 .noStim 2KO
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG004 47
A B C D E F G H I J K L M N O
Dur. Experimen
Principal Investigat Simple GSP Genes Stim. stim. Time t Group ID Sample
1 Investigator ors Cell type ID (10) GSP ID (9) WT/KO (11) (12) point Rep. (13) (1) ID (3) AffyPlat (14) Date (15) Affy .CEL file (16)
Lothar Atsushi mouse EG004-01 EG004- WT STIM biological EG004 1AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 01.MEF.WT.1AH. 08_Hennighausen_1AH_Mo
2 STIM use430_2_STIM_C_1
Lothar Atsushi mouse EG004-02 EG004- STAT5-null STIM biological EG004 2AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 02.MEF.Stat5KO. 08_Hennighausen_2AH_Mo
3 2AH.STIM use430_2_STIM_KO_1
Lothar Atsushi mouse EG004-03 EG004- WT GH biological EG004 3AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 03.MEF.WT.3AH. 08_Hennighausen_3AH_Mo
4 GH use430_2_GH_C_1
Lothar Atsushi mouse EG004-04 EG004- STAT5-null GH biological EG004 4AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 04.MEF.Stat5KO. 08_Hennighausen_4AH_Mo
5 4AH.GH use430_2_GH_KO_1
Lothar Atsushi mouse EG004-05 EG004- WT IFNg biological EG004 5AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 05.MEF.WT.5AH.I 08_Hennighausen_5AH_Mo
6 FNg use430_2_IFNg_C_1
Lothar Atsushi mouse EG004-06 EG004- STAT5-null IFNg biological EG004 6AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 06.MEF.Stat5KO. 08_Hennighausen_6AH_Mo
7 6AH.IFNg use430_2_IFNg_KO_1
Lothar Atsushi mouse EG004-07 EG004- WT STIM biological EG004 7AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 07.MEF.WT.7AH. 08_Hennighausen_7AH_Mo
8 STIM use430_2_STIM_C_2
Lothar Atsushi mouse EG004-08 EG004- STAT5-null STIM biological EG004 8AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 08.MEF.Stat5KO. 08_Hennighausen_8AH_Mo
8AH.STIM use430_2_STIM_KO_2
9
Lothar Atsushi mouse EG004-09 EG004- WT GH biological EG004 9AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 09.MEF.WT.9AH. 08_Hennighausen_9AH_Mo
10 GH use430_2_GH_C_2
Lothar Atsushi mouse EG004-10 EG004- STAT5-null GH biological EG004 10AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 10.MEF.Stat5KO. 08_Hennighausen_10AH_M
11 10AH.GH ouse430_2_GH_KO_2
Lothar Atsushi mouse EG004-11 EG004- WT IFNg biological EG004 11AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 12.MEF.WT.11A 08_Hennighausen_11AH_M
12 H.IFNg ouse430_2_IFNg_C_2
Lothar Atsushi mouse EG004-12 EG004- STAT5-null IFNg biological EG004 12AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 12.MEF.Stat5KO. 08_Hennighausen_12AH_M
13 12AH.IFNg ouse430_2_IFNg_KO_2
Lothar Atsushi mouse EG004-13 EG004- WT STIM biological EG004 13AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 13.MEF.WT.13A 08_Hennighausen_13AH_M
14 H.STIM ouse430_2_STIM_C_3
Lothar Atsushi mouse EG004-14 EG004- STAT5-null STIM biological EG004 14AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 14.MEF.Stat5KO. 08_Hennighausen_14H_Mou
15 14AH.STIM se430_2_STIM_KO_3
Lothar Atsushi mouse EG004-15 EG004- WT GH biological EG004 15AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 15.MEF.WT.15A 08_Hennighausen_15AH_M
16 H.GH ouse430_2_GH_C_3
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG004 48
A B C D E F G H I J K L M N O
Lothar Atsushi mouse EG004-16 EG004- STAT5-null GH biological EG004 16AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 16.MEF.Stat5KO. 08_Hennighausen_16AH_M
17 16AH.GH ouse430_2_GH_KO_3
Lothar Atsushi mouse EG004-17 EG004- WT IFNg biological EG004 17AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 17.MEF.WT.17A 08_Hennighausen_17AH_M
18 H.IFNg ouse430_2_IFNg_C_3
Lothar Atsushi mouse EG004-18 EG004- STAT5-null IFNg biological EG004 18AH MOE430_2 07/22/08 07-22-
Hennighausen Hosui MEF 18.MEF.Stat5KO. 08_Hennighausen_18AH_M
19 K.18AH.IFNg ouse430_2_IFNg_KO_3
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG004 49
P Q
PCR
1 Folder (17) cycles
07-22-
2008_L.Hennigha
2 usen-AH
07-22-
2008_L.Hennigha
3 usen-AH
07-22-
2008_L.Hennigha
4 usen-AH
07-22-
2008_L.Hennigha
5 usen-AH
07-22-
2008_L.Hennigha
6 usen-AH
07-22-
2008_L.Hennigha
7 usen-AH
07-22-
2008_L.Hennigha
8 usen-AH
07-22-
2008_L.Hennigha
usen-AH
9
07-22-
2008_L.Hennigha
10 usen-AH
07-22-
2008_L.Hennigha
11 usen-AH
07-22-
2008_L.Hennigha
12 usen-AH
07-22-
2008_L.Hennigha
13 usen-AH
07-22-
2008_L.Hennigha
14 usen-AH
07-22-
2008_L.Hennigha
15 usen-AH
07-22-
2008_L.Hennigha
16 usen-AH
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG004 50
P Q
07-22-
2008_L.Hennigha
17 usen-AH
07-22-
2008_L.Hennigha
18 usen-AH
07-22-
2008_L.Hennigha
19 usen-AH
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG005.1 51
A B C D E F G H I J K L M N O
Sam
Dur. Time ple
Principal Investigator Simple GSP Genes stim. poin Experiment ID AffyPlat
1 Investigator s Cell type ID (10) GSP ID (9) WT/KO Stim. (11) (12) t Rep. (13) Group ID (1) (3) (14) Date (15) Affy .CEL file (16)
Lothar Akiko Fetal EG005.1-01 EG005.1-01.Liver- Stat5-null TPO, IL3, Flt3 technical EG005.1 MOE430_2 1/3/2008 01-03-
Hennighausen Kimura mouse KSL.Stat5KO.tr1.TP ligabnd, GM- 08_Hennighausen_AK_Mouse4
HSC liver- O+IL3+Flt3lig+GM- CSF, IL6 30_2_KO+
KSL CSF+IL6
2
Lothar Akiko Fetal EG005.1-02 EG005.1-02.Liver- Stat5-null no-stimulation technical EG005.1 MOE430_2 1/3/2008 01-03-
Hennighausen Kimura mouse KSL.Stat5KO.tr1.noS 08_Hennighausen_AK_Mouse4
HSC liver- tim 30_2_KO-
KSL
3
Lothar Akiko Fetal EG005.1-03 EG005.1-03.Liver- WT TPO, IL3, Flt3 technical EG005.1 MOE430_2 1/3/2008 01-03-
Hennighausen Kimura mouse KSL.WT.tr1.TPO+IL ligabnd, GM- 08_Hennighausen_AK_Mouse4
HSC liver- 3+Flt3lig+GM- CSF, IL6 30_2_WT+
KSL CSF+IL6
4
Lothar Akiko Fetal EG005.1-04 EG005.1-04.Liver- WT no-stimulation technical EG005.1 MOE430_2 1/3/2008 01-03-
Hennighausen Kimura mouse KSL.WT.tr1.noStim 08_Hennighausen_AK_Mouse4
HSC liver- 30_2_WT-
KSL
5
Lothar Akiko Fetal EG005.1-05 EG005.1-05.Liver- Stat5-null TPO, IL3, Flt3 technical EG005.1 MOE430_2 1/9/2008 01-09-
Hennighausen Kimura mouse KSL.Stat5KO.tr2.TP ligabnd, GM- 08_Hennighausen_AK_Mouse4
HSC liver- O+IL3+Flt3lig+GM- CSF, IL6 30_2_KO+
KSL CSF+IL6
6
Lothar Akiko Fetal EG005.1-06 EG005.1-06.Liver- Stat5-null no-stimulation technical EG005.1 MOE430_2 1/9/2008 01-09-
Hennighausen Kimura mouse KSL.Stat5KO.tr2.noS 08_Hennighausen_AK_Mouse4
HSC liver- tim 30_2_KO-
KSL
7
Lothar Akiko Fetal EG005.1-07 EG005.1-07.Liver- WT TPO, IL3, Flt3 technical EG005.1 MOE430_2 1/9/2008 01-09-
Hennighausen Kimura mouse KSL.WT.tr2.TPO+IL ligabnd, GM- 08_Hennighausen_AK_Mouse4
HSC liver- 3+Flt3lig+GM- CSF, IL6 30_2_WT+
KSL CSF+IL6
8
Lothar Akiko Fetal EG005.1-08 EG005.1-08.Liver- WT no-stimulation technical EG005.1 MOE430_2 1/9/2008 01-09-
Hennighausen Kimura mouse KSL.WT.tr2.noStim 08_Hennighausen_AK_Mouse4
HSC liver- 30_2_WT-
KSL
9
Lothar Akiko Fetal EG005.1-09 EG005.1-09.Liver- Stat5-null TPO, IL3, Flt3 biological EG005.1 MOE430_2 6/21/2008 06-21-
Hennighausen Kimura mouse KSL.Stat5KO.starved ligabnd, GM- 07_Hennighausen_Mouse430_2
HSC liver- _KO1.TPO+IL3+Flt3l CSF, IL6 _Starved_KO1
KSL ig+GM-CSF+IL6
10
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG005.1 52
A B C D E F G H I J K L M N O
Lothar Akiko Fetal EG005.1-10 EG005.1-10.Liver- WT no-stimulation biological EG005.1 MOE430_2 6/21/2008 06-21-
Hennighausen Kimura mouse KSL.WT.starved.TP 07_Hennighausen_Mouse430_2
HSC liver- O+IL3+Flt3lig+GM- _Starved_WT1
KSL CSF+IL6
11
Lothar Akiko Fetal EG005.1-11 EG005.1-11.Liver- Stat5-null TPO, IL3, Flt3 biological EG005.1 MOE430_2 6/21/2008 06-21-
Hennighausen Kimura mouse KSL.Stat5KO.stimula ligabnd, GM- 07_Hennighausen_Mouse430_2
HSC liver- ted.TPO+IL3+Flt3lig CSF, IL6 _Stimulated_KO2
KSL +GM-CSF+IL6
12
Lothar Akiko Fetal EG005.1-12 EG005.1-12.Liver- WT TPO, IL3, Flt3 biological EG005.1 MOE430_2 6/21/2008 06-21-
Hennighausen Kimura mouse KSL.WT.stimulated. ligabnd, GM- 07_Hennighausen_Mouse430_2
HSC liver- TPO+IL3+Flt3lig+GM- CSF, IL6 _Stimulated_WT2
KSL CSF+IL6
13
Lothar Akiko Fetal EG005.1-13 EG005.1-13.Liver- Stat5-null no-stimulation biological EG005.1 MOE430_2 8/23/2006 08-23-
Hennighausen Kimura mouse KSL.Stat5KO.CM- 06_Hennighausen_CM_Mou
HSC liver- br1.noStim se430_2_KO
KSL
14
Lothar Akiko Fetal EG005.1-14 EG005.1-14.Liver- WT no-stimulation biological EG005.1 MOE430_2 8/23/2006 08-23-
Hennighausen Kimura mouse KSL.WT.CM- 06_Hennighausen_CM_Mou
HSC liver- br2.noStim se430_2_WT
KSL
15
Lothar Akiko Fetal EG005.1-15 EG005.1-15.Liver- Stat5-null TPO, IL3, Flt3 biological EG005.1 MOE430_2 6/21/2008 02-11-
Hennighausen Kimura mouse KSL.Stat5KO.TPO+I ligabnd, GM- 08_Hennighausen_AK_Mouse4
HSC liver- L3+Flt3lig+GM- CSF, IL6 30_2_KO+
KSL CSF+IL6
16
Lothar Akiko Fetal EG005.1-16 EG005.1-16.Liver- Stat5-null no-stimulation biological EG005.1 MOE430_2 6/21/2008 02-11-
Hennighausen Kimura mouse KSL.Stat5KO.br2.no 08_Hennighausen_AK_Mouse4
HSC liver- Stim 30_2_KO-
KSL
17
Lothar Akiko Fetal EG005.1-17 EG005.1-17.Liver- WT TPO, IL3, Flt3 biological EG005.1 MOE430_2 6/21/2008 02-11-
Hennighausen Kimura mouse KSL.WT.tr3.TPO+IL ligabnd, GM- 08_Hennighausen_AK_Mouse4
HSC liver- 3+Flt3lig+GM- CSF, IL6 30_2_WT+
KSL CSF+IL6
18
Lothar Akiko Fetal EG005.1-18 EG005.1-18.Liver- WT no-stimulation biological EG005.1 MOE430_2 6/21/2008 02-11-
Hennighausen Kimura mouse KSL.WT.br3.noStim 08_Hennighausen_AK_Mouse4
HSC liver- 30_2_WT-
KSL
19
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG005.1 53
P Q
PCR
1 Folder (17) cycles
01-03- 2
08_Hennighause
n_AK_Mouse43
0_2_KSL
2
01-03- 2
08_Hennighause
n_AK_Mouse43
0_2_KSL
3
01-03- 2
08_Hennighause
n_AK_Mouse43
0_2_KSL
4
01-03- 2
08_Hennighause
n_AK_Mouse43
0_2_KSL
5
01-09- 2
08_Hennighause
n_AK_Mouse43
0_2_KSL
6
01-09- 2
08_Hennighause
n_AK_Mouse43
0_2_KSL
7
01-09- 2
08_Hennighause
n_AK_Mouse43
0_2_KSL
8
01-09- 2
08_Hennighause
n_AK_Mouse43
0_2_KSL
9
06-21- 2
07_Hennighause
n_CM_2cycle_1
10
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG005.1 54
P Q
06-21- 2
07_Hennighause
n_CM_2cycle_1
11
06-21-
07_Hennighause
n_CM_2cycle_1
12
06-21-
07_Hennighause
n_CM_2cycle_1
13
08-23-
2006_Hennigha
usen(CM)
14
08-23-
2006_Hennigha
usen(CM)
15
02-08-
2008_L.Hennigh
ausen-AK
16
02-08-
2008_L.Hennigh
ausen-AK
17
02-08-
2008_L.Hennigh
ausen-AK
18
02-08-
2008_L.Hennigh
ausen-AK
19
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG005.2 55
A B C D E F G H I J K L M N O
Dur. Experimen Sampl
Principal Cell Simple GSP Genes stim. Time t Group ID e ID AffyPlat
1 Investigator Investigators type ID (10) GSP ID (9) WT/KO Stim. (11) (12) point Rep. (13) (1) (3) (14) Date (15) Affy .CEL file (16)
Lothar Akiko Kimura, mouse EG005.2-01 EG005.2- Stat5HSCko no- biological EG005.2 MOE430_2 7/10/2007 07-10-
Hennighausen Cyril Martin bone 01.BM- stimulation 07_Hennighausen_Mouse
marrow- KSL.Stat5HSC 430_2_KSL_MX2
KSL ko.br2.noStim
2
Lothar Akiko Kimura, mouse EG005.2-02 EG005.2- Stat5HSCko no- biological EG005.2 MOE430_2 7/10/2007 07-10-
Hennighausen Cyril Martin bone 02.BM- stimulation 07_Hennighausen_Mouse
marrow- KSL.Stat5HSC 430_2_KSL_MX3
KSL ko.br3.noStim
3
Lothar Akiko Kimura, mouse EG005.2-03 EG005.2- Stat5HSCko no- biological EG005.2 MOE430_2 5/9/2007 05-09-
Hennighausen Cyril Martin bone 03.BM- stimulation 07_Hennighausen_Mouse
marrow- KSL.Stat5HSC 430_2_MX_KSL_KO
KSL ko.br1.noStim
4
Lothar Akiko Kimura, mouse EG005.2-04 EG005.2- WT no- biological EG005.2 MOE430_2 5/9/2007 05-09-
Hennighausen Cyril Martin bone 04.BM- stimulation 07_Hennighausen_Mouse
marrow- KSL.WT.br1.n 430_2_MX_KSL_CLT
5 KSL oStim
Lothar Akiko Kimura, mouse EG005.2-05 EG005.2- WT no- biological EG005.2 MOE430_2 7/10/2007 07-10-
Hennighausen Cyril Martin bone 05.BM- stimulation 07_Hennighausen_Mouse
marrow- KSL.WT.br2.n 430_2_KSL_CTL2
6 KSL oStim
Lothar Akiko Kimura, mouse EG005.2-06 EG005.2- WT no- biological EG005.2 MOE430_2 7/10/2007 07-10-
Hennighausen Cyril Martin bone 06.BM- stimulation 07_Hennighausen_Mouse
marrow- KSL.WT.br3.n 430_2_KSL_CTL3
7 KSL oStim
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG005.2 56
P Q
PCR
cycle
1 Folder (17) s
07-10- 2
07_Hennighau
sen_CM__2cy
cle
2
07-10- 2
07_Hennighau
sen_CM__2cy
cle
3
05-09- 2
07_Hennighau
sen_CM_2cycl
e
4
05-09- 2
07_Hennighau
sen_CM_2cycl
5 e
07-10- 2
07_Hennighau
sen_CM__2cy
6 cle
07-10- 2
07_Hennighau
sen_CM__2cy
7 cle
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG006 57
A B C D E F G H I J K L M N O P Q
Simple Dur. Experime Samp PCR
Principal Investigato GSP ID Genes stim. Time Rep. nt Group le ID AffyPlat cycle
1 Investigator rs Cell type (10) GSP ID (9) WT/KO Stim. (11) (12) point (13) ID (1) (3) (14) Date (15) Affy .CEL file (16) Folder (17) s
Lothar Akiko mouse EG006-01 EG006- WT GM-CSF biologi EG006 1AK MOS430 6/10/2008 2
Hennighausen Kimura GMP 01.GMP.WT.1AK.GM- cal _2 06-10-
CSF 06-10- 2008_L.Hen
08_Hennighausen_1AK_M nighausen-
2 ouse430_2_GMP_CTL+ AK-2_GMP
Lothar Akiko mouse EG006-02 EG006- WT no- biologi EG006 2AK MOS430 6/10/2008 2
Hennighausen Kimura GMP 02.GMP.WT.2AK.no stimulation cal _2 06-10-
Stim 06-10- 2008_L.Hen
08_Hennighausen_2AK_M nighausen-
3 ouse430_2_GMP_CTL- AK-2_GMP
Lothar Akiko mouse EG006-03 EG006- Stat5HSCko GM-CSF biologi EG006 3AK MOS430 6/10/2008 2
Hennighausen Kimura GMP 03.GMP.Stat5HSCko cal _2 06-10-
.3AK.GM-CSF 06-10- 2008_L.Hen
08_Hennighausen_3AK_M nighausen-
4 ouse430_2_GMP_KO+ AK-2_GMP
Lothar Akiko mouse EG006-04 EG006- Stat5HSCko no- biologi EG006 4AK MOS430 6/10/2008 2
Hennighausen Kimura GMP 04.GMP.Stat5HSCko stimulation cal _2 06-10-
.4AK.noStim 06-10- 2008_L.Hen
08_Hennighausen_4AK_M nighausen-
5 ouse430_2_GMP_KO- AK-2_GMP
Lothar Akiko mouse EG006-05 EG006- Stat5HSCko no- biologi EG006 11AK MOS430 8/18/2008 08-18- 2
Hennighausen Kimura GMP 05.GMP.Stat5HSCko stimulation cal _2 2008_Henni
.11AK.noStim ghausen_AK
08-05- _CMP_GMP
08_Hennighausen_11AK_ stim
6 Mouse430_2_702_KG-
Lothar Akiko mouse EG006-06 EG006- Stat5HSCko GM-CSF biologi EG006 12AK MOS430 8/18/2008 08-18- 2
Hennighausen Kimura GMP 06.GMP.Stat5HSCko cal _2 2008_Henni
.12AK.GM-CSF ghausen_AK
08-05- _CMP_GMP
08_Hennighausen_12AK_ stim
7 Mouse430_2_702_KG+
Lothar Akiko mouse EG006-07 EG006- WT no- biologi EG006 15AK MOS430 8/18/2008 08-18- 2
Hennighausen Kimura GMP 07.GMP.WT.15AK.n stimulation cal _2 2008_Henni
oStim ghausen_AK
08-05- _CMP_GMP
08_Hennighausen_15AK_ stim
8 Mouse430_2_702_CG-
Lothar Akiko mouse EG006-08 EG006- WT GM-CSF biologi EG006 16AK MOE430 8/18/2008 08-05- 08-18- 2
Hennighausen Kimura GMP 08.GMP.WT.16AK.G cal _2 08_Hennighausen_16AK_ 2008_Henni
M-CSF Mouse430_2_702_CG+ ghausen_AK
_CMP_GMP
stim
9
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG006 58
A B C D E F G H I J K L M N O P Q
Lothar Akiko mouse EG006-09 EG006- Stat5HSCko no- biologi EG006 3AK MOE430 8/18/2008 08-05- 08-18- 2
Hennighausen Kimura GMP 09.GMP.Stat5HSCko stimulation cal _2 08_Hennighausen_3AK_M 2008_Henni
.3AK.noStim ouse430_2_626_KG- ghausen_AK
_CMP_GMP
stim
10
Lothar Akiko mouse EG006-10 EG006- Stat5HSCko GM-CSF biologi EG006 4AK MOE430 8/18/2008 08-05- 08-18- 2
Hennighausen Kimura GMP 10.GMP.Stat5HSCko cal _2 08_Hennighausen_4AK_M 2008_Henni
.4AK.GM-CSF ouse430_2_626_KG+ ghausen_AK
_CMP_GMP
stim
11
Lothar Akiko mouse EG006-11 EG006- WT no- biologi EG006 7AK MOE430 8/18/2008 08-05- 08-18- 2
Hennighausen Kimura GMP 11.GMP.WT.7AK.no stimulation cal _2 08_Hennighausen_7AK_M 2008_Henni
Stim ouse430_2_626_CG- ghausen_AK
_CMP_GMP
stim
12
Lothar Akiko mouse EG006-12 EG006- WT GM-CSF biologi EG006 8AK MOE430 8/18/2008 08-05- 08-18- 2
Hennighausen Kimura GMP 12.GMP.WT.8AK.GM- cal _2 08_Hennighausen_8AK_M 2008_Henni
CSF ouse430_2_626_CG+ ghausen_AK
_CMP_GMP
stim
13
Lothar Akiko mouse EG006-13 EG006- WT GM-CSF biologi EG006 MOE430 3/25/2008 03-25- 03-25- 2
Hennighausen Kimura GMP 13.GMP.WT.br1.GM- cal _2 08_Hennighausen_AK_Mo 2008_Henn
CSF use430_2_GMPCTL+ ighausen_A
K_Mouse43
0_2_CMP_
GMP
14
Lothar Akiko mouse EG006-14 EG006- WT no- biologi EG006 MOE430 3/25/2008 03-25- 03-25- 2
Hennighausen Kimura GMP 14.GMP.WT.br1.noSt stimulation cal _2 08_Hennighausen_AK_Mo 2008_Henn
im use430_2_GMPCTL- ighausen_A
K_Mouse43
0_2_CMP_
GMP
15
Lothar Akiko mouse EG006-15 EG006- WT GM-CSF biologi EG006 MOE430 3/25/2008 03-25- 03-25- 2
Hennighausen Kimura GMP 15.GMP.WT.br2.GM- cal _2 08_Hennighausen_AK_Mo 2008_Henn
CSF use430_2_GMPKO+a ighausen_A
K_Mouse43
0_2_CMP_
GMP
16
Lothar Akiko mouse EG006-16 EG006- WT no- biologi EG006 MOE430 3/25/2008 03-25- 03-25- 2
Hennighausen Kimura GMP 16.GMP.WT.br2.noSt stimulation cal _2 08_Hennighausen_AK_Mo 2008_Henn
im use430_2_GMPKO- ighausen_A
K_Mouse43
0_2_CMP_
GMP
17
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG006 59
A B C D E F G H I J K L M N O P Q
Lothar Akiko mouse EG006-17 EG006- Stat5HSCko GM-CSF biologi EG006 MOE430 9/26/2008 09-26- 09-26- 2
Hennighausen Kimura GMP 17.GMP.Stat5HSCko cal _2 08_LHennighausen1_AK
08_Henni
.br1.GM-CSF _Mouse430_2_KOGMP
+
ghausen_
AK_CMP
18 _GMP
Lothar Akiko mouse EG006-18 EG006- Stat5HSCko no- biologi EG006 MOE430 9/26/2008 09-26- 09-26- 2
Hennighausen Kimura GMP 18.GMP.Stat5HSCko stimulation cal _2 08_LHennighausen1_AK
08_Henni
.br1.noStim _Mouse430_2_KOGMP-
C
ghausen_
AK_CMP
19 _GMP
Lothar Akiko mouse EG006-19 EG006- WT GM-CSF biologi EG006 MOE430 9/26/2008 09-26- 09-26- 2
Hennighausen Kimura GMP 19.GMP.WT.br2.GM- cal _2 08_LHennighausen1_AK
08_Henni
CSF _Mouse430_2_CTLGMP
+
ghausen_
AK_CMP
20 _GMP
Lothar Akiko mouse EG006-20 EG006- WT no- biologi EG006 MOE430 9/27/2008 09-26- 09-26- 2
Hennighausen Kimura GMP 20.GMP.WT.br3.noSt stimulation cal _3 08_LHennighausen1_AK
08_Henni
im _Mouse430_2_CTLGMP-
ghausen_
AK_CMP
21 _GMP
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG007 60
A B C D E F G H I J K L M N O P Q
Simple Dur. Experime Samp PCR
Principal Investigat GSP ID Genes stim. Time nt Group le ID AffyPlat cycl
1 Investigator ors Cell type (10) GSP ID (9) WT/KO Stim. (11) (12) point Rep. (13) ID (1) (3) (14) Date (15) Affy .CEL file (16) Folder (17) es
Lothar Akiko mouse EG007-01 EG007- WT GM-CSF biological EG007 br1 MOE430_ 3/25/2008 03-25- 03-25- 2
Hennighausen Kimura CMP 01.CMP.WT.br 2 08_Hennighausen_AK_Mous 2008_Hennigha
1.GM-CSF e430_2_CMPCTL+ usen_AK_Mous
e430_2_CMP_
2 GMP
Lothar Akiko mouse EG007-02 EG007- WT no- biological EG007 br1 MOE430_ 3/25/2008 03-25- 03-25- 2
Hennighausen Kimura CMP 02.CMP.WT.br stimulation 2 08_Hennighausen_AK_Mous 2008_Hennigha
1.noStim e430_2_CMPCTL- usen_AK_Mous
e430_2_CMP_
3 GMP
Lothar Akiko mouse EG007-03 EG007- Stat5HS GM-CSF biological EG007 br1 MOE430_ 3/25/2008 03-25- 03-25- 2
Hennighausen Kimura CMP 03.CMP.Stat5 Cko 2 08_Hennighausen_AK_Mous 2008_Hennigha
HSCko.br1.G e430_2_CMPKO+ usen_AK_Mous
M-CSF e430_2_CMP_
4 GMP
Lothar Akiko mouse EG007-04 EG007- Stat5HS no- biological EG007 br1 MOE430_ 3/25/2008 03-25- 03-25- 2
Hennighausen Kimura CMP 04.CMP.Stat5 Cko stimulation 2 08_Hennighausen_AK_Mous 2008_Hennigha
HSCko.br1.no e430_2_CMPKO- usen_AK_Mous
Stim e430_2_CMP_
5 GMP
Lothar Akiko mouse EG007-05 EG007- Stat5HS GM-CSF biological EG007 10AK MOE430_ 8/18/2008 08-05- 08-18- 2
Hennighausen Kimura CMP 05.CMP.Stat5 Cko 2 08_Hennighausen_10AK_Mo 2008_Hennighau
HSCko.10AK. use430_2_702_KC+ sen_AK_CMP_G
GM-CSF MPstim
6
Lothar Akiko mouse EG007-06 EG007- WT no- biological EG007 13AK MOE430_ 8/18/2008 08-05- 08-18- 2
Hennighausen Kimura CMP 06.CMP.WT.1 stimulation 2 08_Hennighausen_13AK_Mo 2008_Hennighau
3AK.noStim use430_2_702_CC- sen_AK_CMP_G
MPstim
7
Lothar Akiko mouse EG007-07 EG007- WT GM-CSF biological EG007 14AK MOE430_ 8/18/2008 08-05- 08-18- 2
Hennighausen Kimura CMP 07.CMP.WT.1 2 08_Hennighausen_14AK_Mo 2008_Hennighau
4AK.GM-CSF use430_2_702_CC+ sen_AK_CMP_G
MPstim
8
Lothar Akiko mouse EG007-08 EG007- Stat5HS no- biological EG007 9AK MOE430_ 8/18/2008 08-05- 08-18- 2
Hennighausen Kimura CMP 08.CMP.Stat5 Cko stimulation 2 08_Hennighausen_9AK_Mou 2008_Hennighau
HSCko.9AK.n se430_2_702_KC- sen_AK_CMP_G
oStim MPstim
9
Lothar Akiko mouse EG007-09 EG007- Stat5HS no- biological EG007 1AK MOE430_ 8/18/2008 08-05- 08-18- 2
Hennighausen Kimura CMP 09.CMP.Stat5 Cko stimulation 2 08_Hennighausen_1AK_M 2008_Hennighau
HSCko.1AK.G ouse430_2_626_KC- sen_AK_CMP_G
M-CSF MPstim
10
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG007 61
A B C D E F G H I J K L M N O P Q
Lothar Akiko mouse EG007-10 EG007- Stat5HS GM-CSF biological EG007 2AK MOE430_ 8/18/2008 08-05- 08-18- 2
Hennighausen Kimura CMP 10.CMP.Stat5 Cko 2 08_Hennighausen_2AK_Mou 2008_Hennighau
HSCko.2AK.G se430_2_626_KC+ sen_AK_CMP_G
M-CSF MPstim
11
Lothar Akiko mouse EG007-11 EG007- WT no- biological EG007 6AK MOE430_ 8/18/2008 08-05- 08-18- 2
Hennighausen Kimura CMP 11.CMP.WT.6 stimulation 2 08_Hennighausen_6AK_Mou 2008_Hennighau
AK.noStim se430_2_626_CC+ sen_AK_CMP_G
MPstim
12
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG008.1 62
A B C D E F G H I J K L M N
Simple Experimen
Principal Investigat GSP ID Genes Dur. stim. Time t Group ID Sample ID
1 Investigator ors Cell type (10) GSP ID (9) WT/KO Stim. (11) (12) point Rep. (13) (1) (3) AffyPlat (14) Date (15)
John O'Shea Lai Wei mouse EG008.1- EG008.1- WT B6 no-stimulation No No EG008.1 CD8 Naive MOE430_2 3/7/2007
CD8+ Naïve 01 01.CD8-Naïve-T- Con
T cell, B6.noStim
cultured
2
John O'Shea Lai Wei mouse EG008.1- EG008.1- WT B6 IL7 6 hs No EG008.1 CD8 Naïve MOE430_2 3/7/2007
CD8+ Naïve 02 02.CD8-Naïve-T- IL7
T cell, B6.IL7
cultured
3
John O'Shea Lai Wei mouse EG008.1- EG008.1- WT B6 no-stimulation No No EG008.1 MEM Con MOE430_2 4/18/2008
CD8+ 03 03.CD8-Mem-T- IL7
Memory T B6.noStim
cell, cultured
4
John O'Shea Lai Wei mouse EG008.1- EG008.1- WT B6 IL7 6 hs No EG008.1 MEM CD8 MOE430_2 4/18/2008
CD8+ 04 04.CD8-Mem-T- IL7
Memory T B6.IL7
cell, cultured
5
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG008.1 63
O P Q
Folder PCR
1 Affy .CEL file (16) (17) cycles
03-07- OShea_
07_OShea_Mouse430_ Wei
2_CD8 _Naive_Con
2
03-07- OShea_
07_OShea_Mouse430_ Wei
2_CD8 _Naive_IL7
3
04-18- OShea_
07_OShea_Mouse430_ Wei
2_MEM_CD8_Con
4
04-18- OShea_
07_OShea_Mouse430_ Wei
2_MEM_CD8_IL7
5
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG008.2 64
A B C D E F G H I J K L M N O
Simple Dur. Experime
Principal GSP ID Genes stim. Time Rep. nt Group Sample
1 Investigator Investigators Cell type (10) GSP ID (9) WT/KO Stim. (11) (12) point (13) ID (1) ID (3) AffyPlat (14) Date (15) Affy .CEL file (16)
John O'Shea Lai Wei, Hydae mouse EG008.2-01 EG008.2- Stat5-null LPS 4 hs No EG008.2 DC LPS MOE430_2 4/1/2008 04-01-
Ramos dentritic cell, 01.DC.Stat5KO. 08_OShea_LW_Mouse4
splenic, LPS 30_2_Stat5 KO DC LPS
culture
2
John O'Shea Lai Wei, Hydae mouse EG008.2-02 EG008.2- WT LPS 4 hours 4 hs No EG008.2 DC LPS MOE430_2 4/1/2008 04-01-
Ramos dentritic cell, 02.DC.WT.LPS 08_OShea_LW_Mouse4
splenic, 30_2_Stat5 WT DC LPS
culture
3
John O'Shea Lai Wei, Hydae mouse EG008.2-03 EG008.2- WT no-stimulation No EG008.2 DC MOE430_2 4/1/2008 04-01-
Ramos dentritic cell 03.DC.WT.noSti 08_OShea_LW_Mouse4
4 m 30_2_Stat5 WT DC
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG008.2 65
P Q
Folder PCR
1 (17) cycles
OShea_
Wei
2
OShea_
Wei
3
OShea_
Wei
4
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG008.3 66
A B C D E F G H I J K L M N O
Simple
Principal GSP ID Genes Dur. stim. Time Rep. Experiment Sample ID
1 Investigator Investigators Cell type (10) GSP ID (9) WT/KO Stim. (11) (12) point (13) Group ID (1) (3) AffyPlat (14) Date (15) Affy .CEL file (16)
John O'Shea Lai Wei, Arian mouse EG008.3- EG008.3- Stat5-null anti-CD3/CD28 24 hs No EG008.3 Th0 CD4 MOE430_2 7/3/2008 07-03-
Laurence CD4+ T 01 01.CD4+Tcell.St 08_OShea_Mouse430_
cell, at5KO.Th0- 2_Stat5 KO Th0 day1
cultured CD4.anti- CD4
CD3/CD28-
2 24hrs
John O'Shea Lai Wei, Arian mouse EG008.3- EG008.3- Stat5-null anti-CD3/CD28 48 hs No EG008.3 Th0 CD4 MOE430_2 7/3/2008 07-03-
Laurence CD4+ T 02 02.CD4+Tcell.St 08_OShea_Mouse430_
cell, at5KO.Th0- 2_Stat5 KO Th0 day3
cultured CD4.anti- CD4
CD3/CD28-
3 48hrs
John O'Shea Lai Wei, Arian mouse EG008.3- EG008.3- Stat5-null anti-CD3/CD28, 72 hs No EG008.3 Th0 CD4 MOE430_2 7/3/2008 07-03-
Laurence CD4+ T 03 03.CD4+Tcell.St IL2 08_OShea_Mouse430_
cell, at5KO.Th0- 2_Stat5 KO Th0 day5
cultured CD4.anti- CD4
CD3/CD28+IL2-
4 72hrs
John O'Shea Lai Wei, Arian mouse EG008.3- EG008.3- WT anti-CD3/CD28 24 hs No EG008.3 Th0 CD4 MOE430_2 7/3/2008 07-03-
Laurence CD4+ T 04 04.CD4+Tcell. 08_OShea_Mouse430_
cell, WT.Th0- 2_Stat5 WT Th0 day1
cultured CD4.anti- CD4
CD3/CD28-
5 24hrs
John O'Shea Lai Wei, Arian mouse EG008.3- EG008.3- WT anti-CD3/CD28 48 hs No EG008.3 Th0 CD4 MOE430_2 7/3/2008 07-03-
Laurence CD4+ T 05 05.CD4+Tcell. 08_OShea_Mouse430_
cell, WT.Th0- 2_Stat5 WT Th0 day3
cultured CD4.anti- CD4
CD3/CD28-
6 48hrs
John O'Shea Lai Wei, Arian mouse EG008.3- EG008.3- WT anti-CD3/CD28, 72 hs No EG008.3 Th0 CD4 MOE430_2 7/3/2008 07-03-
Laurence CD4+ T 06 06.CD4+Tcell. IL2 08_OShea_Mouse430_
cell, WT.Th0- 2_Stat5 WT Th0 day5
cultured CD4.anti- CD4
CD3/CD28-
7 72hrs+IL2
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG008.3 67
P Q
Folder PCR
1 (17) cycles
OShea_
Wei
2
OShea_
Wei
3
OShea_
Wei
4
OShea_
Wei
5
OShea_
Wei
6
OShea_
Wei
7
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG008.4 68
A B C D E F G H I J K L M N O
Dur. Time
Principal Investigato Simple GSP Genes stim. poin Rep. Experiment Sample ID
1 Investigator rs Cell type ID (10) GSP ID (9) WT/KO Stim. (11) (12) t (13) Group ID (1) (3) AffyPlat (14) Date (15) Affy .CEL file (16)
John O'Shea Lai Wei, mouse EG008.4-01 EG008.4- Stat3-null anti-CD3/CD28 72 hs No EG008.4 Th0 CD4 MOE430_2 12/5/2006 12-05-
Arian CD4+ T cell, 01.CD4+Tcell.St 06_OShea_Mouse430_
Laurence cultured at3KO.Th0- 2_Stat3 KO Th0 CD4
CD4.anti-
2 CD3/CD28
John O'Shea Lai Wei, mouse EG008.4-02 EG008.4- Stat3-null anti-CD3/CD28, 72 hs No EG008.4 Th17 CD4 MOE430_2 12/5/2006 12-05-
Arian CD4+ T cell, 02.CD4+Tcell.St IL6, Tgfb, anti- 06_OShea_Mouse430_
Laurence cultured at3KO.Th17- IFNg, anti-IL4 2_Stat3 KO Th17 CD4
CD4.anti-
CD3/CD28+IL6
+Tgfb+anti-
3 IFNg+anti-IL4
John O'Shea Lai Wei, mouse EG008.4-03 EG008.4- Stat3-null anti-CD3/CD28, 72 hs No EG008.4 iTreg CD4 MOE430_2 12/5/2006 12-05-
Arian CD4+ T cell, 03.CD4+Tcell.St Tgfb, IL2 06_OShea_Mouse430_
Laurence cultured at3KO.iTreg- 2_Stat3 KO iTreg CD4
CD4.anti-
CD3/CD28+Tgf
4 b+IL2
John O'Shea Lai Wei, mouse EG008.4-04 EG008.4- WT anti-CD3/CD28 72 hs No EG008.4 Th0 CD4 MOE430_2 12/5/2006 12-05-
Arian CD4+ T cell, 04.CD4+Tcell. 06_OShea_Mouse430_
Laurence cultured WT.Th17- 2_Stat3 WT Th0 CD4
CD4.anti-
5 CD3/CD28
John O'Shea Lai Wei, mouse EG008.4-05 EG008.4- WT anti-CD3/CD28, 72 hs No EG008.4 Th17 CD4 MOE430_2 12/5/2006 12-05-
Arian CD4+ T cell, 05.CD4+Tcell. IL-6, Tgfb, anti- 06_OShea_Mouse430_
Laurence cultured WT.Th17- IFNg, anti-IL4 2_Stat3 WT Th17 CD4
CD4.anti-
CD3/CD28+IL6
+Tgfb+anti-
6 IFNg+anti-IL4
John O'Shea Lai Wei, mouse EG008.4-06 EG008.4- WT anti-CD3/CD28, 72 hs No EG008.4 iTreg CD4 MOE430_2 12/5/2006 12-05-
Arian CD4+ T cell, 06.CD4+Tcell. Tgfb, IL2 06_OShea_Mouse430_
Laurence cultured WT.iTreg- 2_Stat3 WT iTreg CD4
CD4.anti-
CD3/CD28+Tgf
7 b+IL2
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG008.4 69
P Q
Folder PCR
1 (17) cycles
OShea_
Wei
2
OShea_
Wei
3
OShea_
Wei
4
OShea_
Wei
5
OShea_
Wei
6
OShea_
Wei
7
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A B C D E F G H I J K L M N O
Simple Experimen
Principal GSP ID Genes Dur. stim. Time Rep. t Group ID Sample ID
1 Investigator Investigators Cell type (10) GSP ID (9) WT/KO Stim. (11) (12) point (13) (1) (3) AffyPlat (14) Date (15) Affy .CEL file (16)
John O'Shea Lai Wei, Yuka mouse EG008.5- EG008.5- Stat4-null no- No EG008.5 Naive CD4 MOE430_2 7/3/2008 07-03-
Kanno, Wendy CD4+ Naïve 01 01.CD4+Naïve- stimulation 08_OShea_Mouse430_2_
Watford, Hiroaki T cell Tcell.Stat4KO. Stat4 KO Naive CD4
2 Takatori Naïve-
John O'Shea Lai Wei, Yuka mouse EG008.5- EG008.5- Stat4-null anti- 72 hs No EG008.5 Th0 CD4 MOE430_2 7/3/2008 07-03-
Kanno, Wendy CD4+ T cell, 02 02.CD4+Naïve- CD3/CD28 08_OShea_Mouse430_2_
Watford, Hiroaki cultured Tcell.Stat4KO.T Stat4 KO Th0 CD4
3 Takatori h0-CD4.anti-
John O'Shea Lai Wei, Yuka mouse EG008.5- EG008.5- Stat4-null anti- 72 hs No EG008.5 Th1 CD4 MOE430_2 7/3/2008 07-03-
Kanno, Wendy CD4+ T cell, 03 03.CD4+Naïve- CD3/CD28, 08_OShea_Mouse430_2_
Watford, Hiroaki cultured Tcell.Stat4KO.T IL12, anti-IL4 Stat4 KO Th1 CD4
4 Takatori h1-CD4.anti-
John O'Shea Lai Wei, Yuka mouse EG008.5- EG008.5- WT no- No EG008.5 Naïve CD4 MOE430_2 7/3/2008 07-03-
Kanno, Wendy CD4+ Naïve 04 04.CD4+Naïve- stimulation 08_OShea_Mouse430_2_
Watford, Hiroaki T cell Tcell.WT.Naïve- Stat4 WT Naive CD4
5 Takatori CD4.noStim
John O'Shea Lai Wei, Yuka mouse EG008.5- EG008.5- WT anti- 72 hs No EG008.5 Th0 CD4 MOE430_2 7/3/2008 07-03-
Kanno, Wendy CD4+ T cell, 05 05.CD4+Naïve- CD3/CD28 08_OShea_Mouse430_2_
Watford, Hiroaki cultured Tcell.WT.Th0- Stat4 WT Th0 CD4
6 Takatori CD4.anti-
John O'Shea Lai Wei, Yuka mouse EG008.5- EG008.5- WT anti- 72 hs No EG008.5 Th1 CD4 MOE430_2 7/3/2008 07-03-
Kanno, Wendy CD4+ T cell, 06 06.CD4+Naïve- CD3/CD28, 08_OShea_Mouse430_2_
Watford, Hiroaki cultured Tcell.WT.Th1- IL12, anti-IL4 Stat4 WT Th1 CD4
7 Takatori CD4.anti-
CD3/CD28+IL1
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG008.5 71
P Q
PCR
Folder cycle
1 (17) s
OShea_
Wei
2
OShea_
Wei
3
OShea_
Wei
4
OShea_
Wei
5
OShea_
Wei
6
OShea_
Wei
7
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A B C D E F G H I J K L M N O
Gene
s Dur. Experime
Principal Simple GSP WT/K stim. Time nt Group Sampl
1 Investigator Investigators Cell type ID (10) GSP ID (9) O Stim. (11) (12) point Rep. (13) ID (1) e ID (3) AffyPlat (14) Date (15) Affy .CEL file (16)
John O'Shea Linda Muul, Alan human EG009.1-01 EG009.1- no-stimulation 6 hr Day 5 biological EG009.1 1769 HG-U133A 11/3/2003 Sample_1769_Control_
Berger, Hong-Wei PBMCs 01.PBMC.1769. Achip
2 Sun noStim.A
John O'Shea Linda Muul, Alan human EG009.1-02 EG009.1- no-stimulation 6 hr Day5 biological EG009.1 1769 HG-U133B 11/6/2003 Sample_1769_Control_
Berger, Hong-Wei PBMCs 02.PBMC.1769. Bchip
3 Sun noStim.B
John O'Shea Linda Muul, Alan human EG009.1-03 EG009.1- no-stimulation 6 hr Day 5 biological EG009.1 1775 HG-U133A 10/30/2003 Sample_1775_Control_
Berger, Hong-Wei PBMCs 03.PBMC.1775. Achip
4 Sun noStim.A
John O'Shea Linda Muul, Alan human EG009.1-04 EG009.1- no-stimulation 6 hr Day 5 biological EG009.1 1775 HG-U133B 11/5/2003 Sample_1775_Control_
Berger, Hong-Wei PBMCs 04.PBMC.1775. Bchip
5 Sun noStim.B
John O'Shea Linda Muul, Alan human EG009.1-05 EG009.1- no-stimulation 6 hr Day 5 biological EG009.1 546 HG-U133A 4/18/2003 Sample_546_Control_A
Berger, Hong-Wei PBMCs 05.PBMC.546.n chip
6 Sun oStim.A
John O'Shea Linda Muul, Alan human EG009.1-06 EG009.1- no-stimulation 6 hr Day 5 biological EG009.1 546 HG-U133B 4/29/2003 Sample_546_Control_B
Berger, Hong-Wei PBMCs 06.PBMC.546.n chip
7 Sun oStim.B
John O'Shea Linda Muul, Alan human EG009.1-07 EG009.1- no-stimulation 6 hr Day 5 biological EG009.1 541 HG-U133A 4/22/2003 Sample_541_Control_A
Berger, Hong-Wei PBMCs 07.PBMC.541.n chip
8 Sun oStim.A
John O'Shea Linda Muul, Alan human EG009.1-08 EG009.1- no-stimulation 6 hr Day 5 biological EG009.1 541 HG-U133B 5/15/2003 Sample_541_Control_B
Berger, Hong-Wei PBMCs 08.PBMC.541.n chip
9 Sun oStim.B
John O'Shea Linda Muul, Alan human EG009.1-09 EG009.1- IFN-alpha 6 hr Day 5 biological EG009.1 1769 HG-U133A 11/3/2003 Sample_1769_IFNalpha
Berger, Hong-Wei PBMCs 09.PBMC.1769.I _Achip
10 Sun FN-alpha.A
John O'Shea Linda Muul, Alan human EG009.1-10 EG009.1- IFN-alpha 6 hr Day 5 biological EG009.1 1769 HG-U133B 11/6/2003 Sample_1769_IFNalpha
Berger, Hong-Wei PBMCs 10.PBMC.1769.I _Bchip
11 Sun FN-alpha.B
John O'Shea Linda Muul, Alan human EG009.1-11 EG009.1- IFN-alpha 6 hr Day 5 biological EG009.1 1775 HG-U133A 10/30/2003 Sample_1775_IFNalpha
Berger, Hong-Wei PBMCs 11.PBMC.1775.I _Achip
12 Sun FN-alpha.A
John O'Shea Linda Muul, Alan human EG009.1-12 EG009.1- IFN-alpha 6 hr Day 5 biological EG009.1 1775 HG-U133B 11/5/2003 Sample_1775_IFNalpha
Berger, Hong-Wei PBMCs 12.PBMC.1775.I _Bchip
13 Sun FN-alpha.B
John O'Shea Linda Muul, Alan human EG009.1-13 EG009.1- IFN-alpha 6 hr Day 5 biological EG009.1 546 HG-U133A 4/18/2003 Sample_546_IFNalpha_
Berger, Hong-Wei PBMCs 13.PBMC.546.IF Achip
14 Sun N-alpha.A
John O'Shea Linda Muul, Alan human EG009.1-14 EG009.1- IFN-alpha 6 hr Day 5 biological EG009.1 546 HG-U133B 4/29/2003 Sample_546_IFNalpha_
Berger, Hong-Wei PBMCs 14.PBMC.546.IF Bchip
15 Sun N-alpha.B
John O'Shea Linda Muul, Alan human EG009.1-15 EG009.1- IFN-alpha 6 hr Day 5 biological EG009.1 541 HG-U133A 4/22/2003 Sample_541_IFNalpha_
Berger, Hong-Wei PBMCs 15.PBMC.541.IF Achip
16 Sun N-alpha.A
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.1 73
A B C D E F G H I J K L M N O
John O'Shea Linda Muul, Alan human EG009.1-16 EG009.1- IFN-alpha 6 hr Day 5 biological EG009.1 541 HG-U133B 5/15/2003 Sample_541_IFNalpha_
Berger, Hong-Wei PBMCs 16.PBMC.541.I Bchip
Sun FN-alpha.B
17
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.1 74
P Q
PCR
1 Folder (17) cycles
OShea-
IFNalpha_GS
2 P
OShea-
IFNalpha_GS
3 P
OShea-
IFNalpha_GS
4 P
OShea-
IFNalpha_GS
5 P
OShea-
IFNalpha_GS
6 P
OShea-
IFNalpha_GS
7 P
OShea-
IFNalpha_GS
8 P
OShea-
IFNalpha_GS
9 P
OShea-
IFNalpha_GS
10 P
OShea-
IFNalpha_GS
11 P
OShea-
IFNalpha_GS
12 P
OShea-
IFNalpha_GS
13 P
OShea-
IFNalpha_GS
14 P
OShea-
IFNalpha_GS
15 P
OShea-
IFNalpha_GS
16 P
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.1 75
P Q
OShea-
IFNalpha_GS
P
17
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.2 76
A B C D E F G H I J K L M N O
Simple Experime
Principal GSP ID Genes Dur. Time nt Group Sampl
1 Investigator Investigators Cell type (10) GSP ID (9) WT/KO Stim. (11) stim. (12) point Rep. (13) ID (1) e ID (3) AffyPlat (14) Date (15) Affy .CEL file (16)
John O'Shea Linda Muul, human EG009.2- EG009.2- no- 6 hr Day 5 biological EG009.2 1769 HG-U133A 11/3/2003 Sample_1769_Contr
Alan Berger, PBMCs 01 01.PBMC.1769. stimulation ol_Achip
Hong-Wei Sun noStim.A
2
John O'Shea Linda Muul, human EG009.2- EG009.2- no- 6 hr Day5 biological EG009.2 1769 HG-U133B 11/6/2003 Sample_1769_Contr
Alan Berger, PBMCs 02 02.PBMC.1769. stimulation ol_Bchip
Hong-Wei Sun noStim.B
3
John O'Shea Linda Muul, human EG009.2- EG009.2- no- 6 hr Day 5 biological EG009.2 1775 HG-U133A 10/30/2003 Sample_1775_Contr
Alan Berger, PBMCs 03 03.PBMC.1775. stimulation ol_Achip
Hong-Wei Sun noStim.A
4
John O'Shea Linda Muul, human EG009.2- EG009.2- no- 6 hr Day 5 biological EG009.2 1775 HG-U133B 11/5/2003 Sample_1775_Contr
Alan Berger, PBMCs 04 04.PBMC.1775. stimulation ol_Bchip
Hong-Wei Sun noStim.B
5
John O'Shea Linda Muul, human EG009.2- EG009.2- no- 6 hr Day 5 biological EG009.2 635 HG-U133A 7/16/2003 Sample_635_Control
Alan Berger, PBMCs 05 05.PBMC.635.n stimulation _Achip
Hong-Wei Sun oStim.A
6
John O'Shea Linda Muul, human EG009.2- EG009.2- no- 6 hr Day 5 biological EG009.2 635 HG-U133B 7/21/2003 Sample_635_Control
Alan Berger, PBMCs 06 06.PBMC.635.n stimulation _Bchip
Hong-Wei Sun oStim.B
7
John O'Shea Linda Muul, human EG009.2- EG009.2- no- 6 hr Day 5 biological EG009.2 541 HG-U133A 4/22/2003 Sample_541_Control
Alan Berger, PBMCs 07 07.PBMC.541.n stimulation _Achip
Hong-Wei Sun oStim.A
8
John O'Shea Linda Muul, human EG009.2- EG009.2- no- 6 hr Day 5 biological EG009.2 541 HG-U133B 5/15/2003 Sample_541_Control
Alan Berger, PBMCs 08 08.PBMC.541.n stimulation _Bchip
Hong-Wei Sun oStim.B
9
John O'Shea Linda Muul, human EG009.2- EG009.2- no- 6 hr Day 5 biological EG009.2 337 HG-U133A 3/29/2004 Sample_377_Control
Alan Berger, PBMCs 09 09.PBMC.337.n stimulation _Achip
Hong-Wei Sun oStim.A
10
John O'Shea Linda Muul, human EG009.2- EG009.2- no- 6 hr Day 5 biological EG009.2 337 HG-U133B 4/12/2004 Sample_377_Control
Alan Berger, PBMCs 10 10.PBMC.337.n stimulation _Bchip
Hong-Wei Sun oStim.B
11
John O'Shea Linda Muul, human EG009.2- EG009.2- IL2 6 hr Day 5 biological EG009.2 1769 HG-U133A 11/3/2003 Sample_1769_IL2_A
Alan Berger, PBMCs 11 11.PBMC.1769.I chip
Hong-Wei Sun L2.A
12
John O'Shea Linda Muul, human EG009.2- EG009.2- IL2 6 hr Day 5 biological EG009.2 1769 HG-U133B 11/6/2003 Sample_1769_IL2_B
Alan Berger, PBMCs 12 12PBMC.1769.I chip
Hong-Wei Sun L2.B
13
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.2 77
A B C D E F G H I J K L M N O
John O'Shea Linda Muul, human EG009.2- EG009.2- IL2 6 hr Day 5 biological EG009.2 1775 HG-U133A 10/30/2003 Sample_1775_IL2_A
Alan Berger, PBMCs 13 13.PBMC.1775.I chip
Hong-Wei Sun L2.A
14
John O'Shea Linda Muul, human EG009.2- EG009.2- IL2 6 hr Day 5 biological EG009.2 1775 HG-U133B 1152003 Sample_1775_IL2_B
Alan Berger, PBMCs 14 14.PBMC.1775.I chip
Hong-Wei Sun L2.B
15
John O'Shea Linda Muul, human EG009.2- EG009.2- IL2 6 hr Day 5 biological EG009.2 635 HG-U133A 7/16/2003 Sample_635_IL2_Ac
Alan Berger, PBMCs 15 15.PBMC.635.IL hip
Hong-Wei Sun 2.A
16
John O'Shea Linda Muul, human EG009.2- EG009.2- IL2 6 hr Day 5 biological EG009.2 635 HG-U133B 7/21/2003 Sample_635_IL2_Bc
Alan Berger, PBMCs 16 16.PBMC.635.IL hip
Hong-Wei Sun 2.B
17
John O'Shea Linda Muul, human EG009.2- EG009.2- IL2 6 hr Day 5 biological EG009.2 541 HG-U133A 7/17/2003 Sample_541_IL2_Ac
Alan Berger, PBMCs 17 17.PBMC.541.IL hip
Hong-Wei Sun 2.A
18
John O'Shea Linda Muul, human EG009.2- EG009.2- IL2 6 hr Day 5 biological EG009.2 541 HG-U133B 7/23/2003 Sample_541_IL2_Bc
Alan Berger, PBMCs 18 18.PBMC.541.IL hip
Hong-Wei Sun 2.B
19
John O'Shea Linda Muul, human EG009.2- EG009.2- IL2 6 hr Day 5 biological EG009.2 377 HG-U133A 3/29/2004 Sample_377_IL2_Ac
Alan Berger, PBMCs 19 19.PBMC.337.IL hip
Hong-Wei Sun 2.A
20
John O'Shea Linda Muul, human EG009.2- EG009.2- IL2 6 hr Day 5 biological EG009.2 377 HG-U133B 4/12/2004 Sample_377_IL2_Bc
Alan Berger, PBMCs 20 20.PBMC.337.IL hip
Hong-Wei Sun 2.B
21
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.2 78
P Q
PCR
cycle
1 Folder (17) s
OShea-IL2_GSP
2
OShea-IL2_GSP
3
OShea-IL2_GSP
4
OShea-IL2_GSP
5
OShea-IL2_GSP
6
OShea-IL2_GSP
7
OShea-IL2_GSP
8
OShea-IL2_GSP
9
OShea-IL2_GSP
10
OShea-IL2_GSP
11
OShea-IL2_GSP
12
OShea-IL2_GSP
13
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.2 79
P Q
OShea-IL2_GSP
14
OShea-IL2_GSP
15
OShea-IL2_GSP
16
OShea-IL2_GSP
17
OShea-IL2_GSP
18
OShea-IL2_GSP
19
OShea-IL2_GSP
20
OShea-IL2_GSP
21
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.3 80
A B C D E F G H I J K L M N
Principal Simple GSP ID Genes Dur. stim. Time Experiment Sample AffyPlat
1 Investigator Investigators Cell type (10) GSP ID (9) WT/KO Stim. (11) (12) point Rep. (13) Group ID (1) ID (3) (14) Date (15)
John O'Shea Linda Muul, Alan human EG009.3-01 EG009.3- no- 6 hr Day 5 biological EG009.3 1769 HG-U133A 11/3/2003
Berger, Hong-Wei PBMCs 01.PBMC.1769. stimulation
2 Sun noStim.A
John O'Shea Linda Muul, Alan human EG009.3-02 EG009.3- no- 6 hr Day5 biological EG009.3 1769 HG-U133B 11/6/2003
Berger, Hong-Wei PBMCs 02.PBMC.1769. stimulation
3 Sun noStim.B
John O'Shea Linda Muul, Alan human EG009.3-03 EG009.3- no- 6 hr Day 5 biological EG009.3 1775 HG-U133A 10/30/2003
Berger, Hong-Wei PBMCs 03.PBMC.1775. stimulation
4 Sun noStim.A
John O'Shea Linda Muul, Alan human EG009.3-04 EG009.3- no- 6 hr Day 5 biological EG009.3 1775 HG-U133B 11/5/2003
Berger, Hong-Wei PBMCs 04.PBMC.1775. stimulation
5 Sun noStim.B
John O'Shea Linda Muul, Alan human EG009.3-05 EG009.3- no- 6 hr Day 5 biological EG009.3 635 HG-U133A 7/16/2003
Berger, Hong-Wei PBMCs 05.PBMC.635.n stimulation
6 Sun oStim.A
John O'Shea Linda Muul, Alan human EG009.3-06 EG009.3- no- 6 hr Day 5 biological EG009.3 635 HG-U133B 7/21/2003
Berger, Hong-Wei PBMCs 06.PBMC.635.n stimulation
7 Sun oStim.B
John O'Shea Linda Muul, Alan human EG009.3-07 EG009.3- no- 6 hr Day 5 biological EG009.3 541 HG-U133A 4/22/2003
Berger, Hong-Wei PBMCs 07.PBMC.541.n stimulation
8 Sun oStim.A
John O'Shea Linda Muul, Alan human EG009.3-08 EG009.3- no- 6 hr Day 5 biological EG009.3 541 HG-U133B 5/15/2003
Berger, Hong-Wei PBMCs 08.PBMC.541.n stimulation
9 Sun oStim.B
John O'Shea Linda Muul, Alan human EG009.3-09 EG009.3- no- 6 hr Day 5 biological EG009.3 337 HG-U133A 3/29/2004
Berger, Hong-Wei PBMCs 09.PBMC.337.n stimulation
10 Sun oStim.A
John O'Shea Linda Muul, Alan human EG009.3-10 EG009.3- no- 6 hr Day 5 biological EG009.3 337 HG-U133B 4/12/2004
Berger, Hong-Wei PBMCs 10.PBMC.337.n stimulation
11 Sun oStim.B
John O'Shea Linda Muul, Alan human EG009.3-11 EG009.3- IL2+IL12 6 hr Day 5 biological EG009.3 1769 HG-U133A 11/3/2003
Berger, Hong-Wei PBMCs 11.PBMC.1769.I
12 Sun L2+IL12.A
John O'Shea Linda Muul, Alan human EG009.3-12 EG009.3- IL2+IL12 6 hr Day 5 biological EG009.3 1769 HG-U133B 11/6/2003
Berger, Hong-Wei PBMCs 12.PBMC.1769.I
13 Sun L2+IL12.B
John O'Shea Linda Muul, Alan human EG009.3-13 EG009.3- IL2+IL12 6 hr Day 5 biological EG009.3 1775 HG-U133A 10/30/2003
Berger, Hong-Wei PBMCs 13.PBMC.1775.I
14 Sun L2+IL12.A
John O'Shea Linda Muul, Alan human EG009.3-14 EG009.3- IL2+IL12 6 hr Day 5 biological EG009.3 1775 HG-U133B 11/5/2003
Berger, Hong-Wei PBMCs 14.PBMC.1775.I
15 Sun L2+IL12.B
John O'Shea Linda Muul, Alan human EG009.3-15 EG009.3- IL2+IL12 6 hr Day 5 biological EG009.3 337 HG-U133A 3/29/2004
Berger, Hong-Wei PBMCs 15.PBMC.635.IL
16 Sun 2+IL12.A
John O'Shea Linda Muul, Alan human EG009.3-16 EG009.3- IL2+IL12 6 hr Day 5 biological EG009.3 337 HG-U133B 4/12/2004
Berger, Hong-Wei PBMCs 16.PBMC.635.IL
17 Sun 2+IL12.B
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.3 81
A B C D E F G H I J K L M N
John O'Shea Linda Muul, Alan human EG009.3-17 EG009.3- IL2+IL12 6 hr Day 5 biological EG009.3 541 HG-U133A 7/17/2003
Berger, Hong-Wei PBMCs 17.PBMC.541.IL
18 Sun 2+IL12.A
John O'Shea Linda Muul, Alan human EG009.3-18 EG009.3- IL2+IL12 6 hr Day 5 biological EG009.3 541 HG-U133B 7/23/2003
Berger, Hong-Wei PBMCs 18.PBMC.541.IL
19 Sun 2+IL12.B
John O'Shea Linda Muul, Alan human EG009.3-19 EG009.3- IL2+IL12 6 hr Day 5 biological EG009.3 635 HG-U133A 7/16/2003
Berger, Hong-Wei PBMCs 19.PBMC.337.IL
20 Sun 2+IL12.A
John O'Shea Linda Muul, Alan human EG009.3-20 EG009.3- IL2+IL12 6 hr Day 5 biological EG009.3 635 HG-U133B 7/21/2003
Berger, Hong-Wei PBMCs 20.PBMC.337.IL
21 Sun 2+IL12.B
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.3 82
O P Q
PCR
1 Affy .CEL file (16) Folder (17) cycles
Sample_1769_Control_Achip OShea-
IL2_plus_IL12_GSP
2
Sample_1769_Control_Bchip OShea-
IL2_plus_IL12_GSP
3
Sample_1775_Control_Achip OShea-
IL2_plus_IL12_GSP
4
Sample_1775_Control_Bchip OShea-
IL2_plus_IL12_GSP
5
Sample_635_Control_Achip OShea-
IL2_plus_IL12_GSP
6
Sample_635_Control_Bchip OShea-
IL2_plus_IL12_GSP
7
Sample_541_Control_Achip OShea-
IL2_plus_IL12_GSP
8
Sample_541_Control_Bchip OShea-
IL2_plus_IL12_GSP
9
Sample_377_Control_Achip OShea-
IL2_plus_IL12_GSP
10
Sample_377_Control_Bchip OShea-
IL2_plus_IL12_GSP
11
Sample_1769_IL2plusIL12_Achi OShea-
p IL2_plus_IL12_GSP
12
Sample_1769_IL2plusIL12_Bchi OShea-
p IL2_plus_IL12_GSP
13
Sample_1775_IL2plusIL12_Achi OShea-
p IL2_plus_IL12_GSP
14
Sample_1775_IL2plusIL12_Bchi OShea-
p IL2_plus_IL12_GSP
15
Sample_377_IL2plusIL12_Achip OShea-
IL2_plus_IL12_GSP
16
Sample_377_IL2plusIL12_Bchip OShea-
IL2_plus_IL12_GSP
17
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.3 83
O P Q
Sample_541_IL2plusIL12_Achip OShea-
IL2_plus_IL12_GSP
18
Sample_541_IL2plusIL12_Bchip OShea-
IL2_plus_IL12_GSP
19
Sample_635_IL2plusIL12_Achip OShea-
IL2_plus_IL12_GSP
20
Sample_635_IL2plusIL12_Bchip OShea-
IL2_plus_IL12_GSP
21
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.4 84
A B C D E F G H I J K L M N
Dur. Experimen
Principal Simple Genes stim. Time t Group ID Sample
1 Investigator Investigators Cell type GSP ID (10) GSP ID (9) WT/KO Stim. (11) (12) point Rep. (13) (1) ID (3) AffyPlat (14) Date (15)
John O'Shea Linda Muul, Alan human EG009.4-01 EG009.4- no- 6 hr Day 5 biological EG009.4 2115 HG-U133A 12/9/2002
Berger, Hong-Wei PBMCs 01.PBMC.2115. stimulation
2 Sun noStim.A
John O'Shea Linda Muul, Alan human EG009.4-02 EG009.4- no- 6 hr Day 5 biological EG009.4 2115 HG-U133B 12/17/2002
Berger, Hong-Wei PBMCs 02.PBMC.2115. stimulation
3 Sun noStim.B
John O'Shea Linda Muul, Alan human EG009.4-03 EG009.4- no- 6 hr Day 5 biological EG009.4 1769 HG-U133A 11/3/2003
Berger, Hong-Wei PBMCs 03.PBMC.1769. stimulation
4 Sun noStim.A
John O'Shea Linda Muul, Alan human EG009.4-04 EG009.4- no- 6 hr Day5 biological EG009.4 1769 HG-U133B 11/6/2003
Berger, Hong-Wei PBMCs 04.PBMC.1769. stimulation
5 Sun noStim.B
John O'Shea Linda Muul, Alan human EG009.4-05 EG009.4- no- 6 hr Day 5 biological EG009.4 1775 HG-U133A 10/30/2003
Berger, Hong-Wei PBMCs 05.PBMC.1775. stimulation
6 Sun noStim.A
John O'Shea Linda Muul, Alan human EG009.4-06 EG009.4- no- 6 hr Day 5 biological EG009.4 1775 HG-U133B 11/5/2003
Berger, Hong-Wei PBMCs 06.PBMC.1775. stimulation
7 Sun noStim.B
John O'Shea Linda Muul, Alan human EG009.4-07 EG009.4- no- 6 hr Day 5 biological EG009.4 635 HG-U133A 7/16/2003
Berger, Hong-Wei PBMCs 07.PBMC.635.n stimulation
8 Sun oStim.A
John O'Shea Linda Muul, Alan human EG009.4-08 EG009.4- no- 6 hr Day 5 biological EG009.4 635 HG-U133B 7/21/2003
Berger, Hong-Wei PBMCs 08.PBMC.635.n stimulation
9 Sun oStim.B
John O'Shea Linda Muul, Alan human EG009.4-09 EG009.4- no- 6 hr Day 5 biological EG009.4 546 HG-U133A 4/18/2003
Berger, Hong-Wei PBMCs 09.PBMC.546.n stimulation
10 Sun oStim.A
John O'Shea Linda Muul, Alan human EG009.4-10 EG009.4- no- 6 hr Day 5 biological EG009.4 546 HG-U133B 4/29/2003
Berger, Hong-Wei PBMCs 10.PBMC.546.n stimulation
11 Sun oStim.B
John O'Shea Linda Muul, Alan human EG009.4-11 EG009.4- no- 6 hr Day 5 biological EG009.4 541 HG-U133A 4/22/2003
Berger, Hong-Wei PBMCs 11.PBMC.541.n stimulation
12 Sun oStim.A
John O'Shea Linda Muul, Alan human EG009.4-12 EG009.4- no- 6 hr Day 5 biological EG009.4 541 HG-U133B 5/15/2003
Berger, Hong-Wei PBMCs 12.PBMC.541.n stimulation
13 Sun oStim.B
John O'Shea Linda Muul, Alan human EG009.4-13 EG009.4- IL12+IL18 6 hr Day 5 biological EG009.4 2115 HG-U133A 12/9/2002
Berger, Hong-Wei PBMCs 13.PBMC.2115.I
14 Sun L12+IL18.A
John O'Shea Linda Muul, Alan human EG009.4-14 EG009.4- IL12+IL18 6 hr Day 5 biological EG009.4 2115 HG-U133B 12/17/2002
Berger, Hong-Wei PBMCs 14.PBMC.2115.I
15 Sun L12+IL18.B
John O'Shea Linda Muul, Alan human EG009.4-15 EG009.4- IL12+IL18 6 hr Day 5 biological EG009.4 1769 HG-U133A 11/3/2003
Berger, Hong-Wei PBMCs 15.PBMC.1769.I
16 Sun L12+IL18.A
John O'Shea Linda Muul, Alan human EG009.4-16 EG009.4- IL12+IL18 6 hr Day 5 biological EG009.4 1769 HG-U133B 11/6/2003
Berger, Hong-Wei PBMCs 16.PBMC.1769.I
17 Sun L12+IL18.B
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.4 85
A B C D E F G H I J K L M N
John O'Shea Linda Muul, Alan human EG009.4-17 EG009.4- IL12+IL18 6 hr Day 5 biological EG009.4 1775 HG-U133A 11/30/2003
Berger, Hong-Wei PBMCs 17.PBMC.1775.I
18 Sun L12+IL18.A
John O'Shea Linda Muul, Alan human EG009.4-18 EG009.4- IL12+IL18 6 hr Day 5 biological EG009.4 1775 HG-U133B 11/5/2003
Berger, Hong-Wei PBMCs 18.PBMC.1775.I
19 Sun L12+IL18.B
John O'Shea Linda Muul, Alan human EG009.4-19 EG009.4- IL12+IL18 6 hr Day 5 biological EG009.4 635 HG-U133A 7/17/2003
Berger, Hong-Wei PBMCs 19.PBMC.635.IL
20 Sun 12+IL18
John O'Shea Linda Muul, Alan human EG009.4-20 EG009.4- IL12+IL18 6 hr Day 5 biological EG009.4 635 HG-U133B 7/23/2003
Berger, Hong-Wei PBMCs 20.PBMC.635.IL
21 Sun 12+IL18.A
John O'Shea Linda Muul, Alan human EG009.4-21 EG009.4- IL12+IL18 6 hr Day 5 biological EG009.4 546 HG-U133A 4/18/2003
Berger, Hong-Wei PBMCs 21.PBMC.546.IL
22 Sun 12+IL18.B
John O'Shea Linda Muul, Alan human EG009.4-22 EG009.4- IL12+IL18 6 hr Day 5 biological EG009.4 546 HG-U133B 4/29/2003
Berger, Hong-Wei PBMCs 22.PBMC.546.IL
23 Sun 12+IL18.B
John O'Shea Linda Muul, Alan human EG009.4-23 EG009.4- IL12+IL18 6 hr Day 5 biological EG009.4 541 HG-U133A 4/22/2003
Berger, Hong-Wei PBMCs 23.PBMC.541.IL
24 Sun 12+IL18.A
John O'Shea Linda Muul, Alan human EG009.4-24 EG009.4- IL12+IL18 6 hr Day 5 biological EG009.4 541 HG-U133B 5/15/2003
Berger, Hong-Wei PBMCs 24.PBMC.541.IL
25 Sun 12+IL18.B
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.4 86
O P Q
PCR
1 Affy .CEL file (16) Folder (17) cycles
Sample_2115_Control_Achip OShea-
IL12_plus_IL18_GS
2 P
Sample_2115_Control_Bchip OShea-
IL12_plus_IL18_GS
3 P
Sample_1769_Control_Achip OShea-
IL12_plus_IL18_GS
4 P
Sample_1769_Control_Bchip OShea-
IL12_plus_IL18_GS
5 P
Sample_1775_Control_Achip OShea-
IL12_plus_IL18_GS
6 P
Sample_1775_Control_Bchip OShea-
IL12_plus_IL18_GS
7 P
Sample_635_Control_Achip OShea-
IL12_plus_IL18_GS
8 P
Sample_635_Control_Bchip OShea-
IL12_plus_IL18_GS
9 P
Sample_546_Control_Achip OShea-
IL12_plus_IL18_GS
10 P
Sample_546_Control_Bchip OShea-
IL12_plus_IL18_GS
11 P
Sample_541_Control_Achip OShea-
IL12_plus_IL18_GS
12 P
Sample_541_Control_Bchip OShea-
IL12_plus_IL18_GS
13 P
Sample_2115_IL12plusIL18_Ac OShea-
hip IL12_plus_IL18_GS
14 P
Sample_2115_IL12plusIL18_Bc OShea-
hip IL12_plus_IL18_GS
15 P
Sample_1769_IL12plusIL18_Ac OShea-
hip IL12_plus_IL18_GS
16 P
Sample_1769_IL12plusIL18_Bc OShea-
hip IL12_plus_IL18_GS
17 P
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.4 87
O P Q
Sample_1775_IL12plusIL18_Ac OShea-
hip IL12_plus_IL18_GS
18 P
Sample_1775_IL12plusIL18_Bc OShea-
hip IL12_plus_IL18_GS
19 P
Sample_635_IL12plusIL18_Achi OShea-
p IL12_plus_IL18_GS
20 P
Sample_635_IL12plusIL18_Bchi OShea-
p IL12_plus_IL18_GS
21 P
Sample_546_IL12plusIL18_Achi OShea-
p IL12_plus_IL18_GS
22 P
Sample_546_IL12plusIL18_Bchi OShea-
p IL12_plus_IL18_GS
23 P
Sample_541_IL12plusIL18_Achi OShea-
p IL12_plus_IL18_GS
24 P
Sample_541_IL12plusIL18_Bchi OShea-
p IL12_plus_IL18_GS
25 P
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.5 88
A B C D E F G H I J K L M N O
Gene
s Dur. Experimen Samp
Principal Simple GSP WT/K stim. Time t Group ID le ID AffyPlat
1 Investigator Investigators Cell type ID (10) GSP ID (9) O Stim. (11) (12) point Rep. (13) (1) (3) (14) Date (15) Affy .CEL file (16)
John O'Shea Linda Muul, Alan human EG009.5-01 EG009.5- no- 6 hr Day 5 biological EG009.5 2115 HG- 12/9/2002 Sample_2115_Control_Achip
Berger, Hong-Wei PBMCs 01.PBMC.2115. stimulation U133A
2 Sun noStim.A
John O'Shea Linda Muul, Alan human EG009.5-02 EG009.5- no- 6 hr Day 5 biological EG009.5 2115 HG- 12/17/2002 Sample_2115_Control_Bchip
Berger, Hong-Wei PBMCs 02.PBMC.2115. stimulation U133B
3 Sun noStim.B
John O'Shea Linda Muul, Alan human EG009.5-03 EG009.5- no- 6 hr Day 5 biological EG009.5 1769 HG- 11/3/2003 Sample_1769_Control_Achip
Berger, Hong-Wei PBMCs 03.PBMC.1769. stimulation U133A
4 Sun noStim.B
John O'Shea Linda Muul, Alan human EG009.5-04 EG009.5- no- 6 hr Day5 biological EG009.5 1769 HG- 11/6/2003 Sample_1769_Control_Bchip
Berger, Hong-Wei PBMCs 04.PBMC.1769. stimulation U133B
5 Sun noStim.B
John O'Shea Linda Muul, Alan human EG009.5-05 EG009.5- no- 6 hr Day 5 biological EG009.5 1775 HG- 10/30/2003 Sample_1775_Control_Achip
Berger, Hong-Wei PBMCs 05.PBMC.1775. stimulation U133A
6 Sun noStim.A
John O'Shea Linda Muul, Alan human EG009.5-06 EG009.5- no- 6 hr Day 5 biological EG009.5 1775 HG- 11/5/2003 Sample_1775_Control_Bchip
Berger, Hong-Wei PBMCs 06.PBMC.1775. stimulation U133B
7 Sun noStim.B
John O'Shea Linda Muul, Alan human EG009.5-07 EG009.5- no- 6 hr Day 5 biological EG009.5 635 HG- 7/16/2003 Sample_635_Control_Achip
Berger, Hong-Wei PBMCs 07.PBMC.635.n stimulation U133A
8 Sun oStim.A
John O'Shea Linda Muul, Alan human EG009.5-08 EG009.5- no- 6 hr Day 5 biological EG009.5 635 HG- 7/21/2003 Sample_635_Control_Bchip
Berger, Hong-Wei PBMCs 08.PBMC.635.n stimulation U133B
9 Sun oStim.B
John O'Shea Linda Muul, Alan human EG009.5-09 EG009.5- no- 6 hr Day 5 biological EG009.5 541 HG- 4/22/2003 Sample_541_Control_Achip
Berger, Hong-Wei PBMCs 09.PBMC.541.n stimulation U133A
10 Sun oStim.A
John O'Shea Linda Muul, Alan human EG009.5-10 EG009.5- no- 6 hr Day 5 biological EG009.5 541 HG- 5/15/2003 Sample_541_Control_Bchip
Berger, Hong-Wei PBMCs 10.PBMC.541.n stimulation U133B
11 Sun oStim.B
John O'Shea Linda Muul, Alan human EG009.5-11 EG009.5- no- 6 hr Day 5 biological EG009.5 337 HG- 3/29/2004 Sample_377_Control_Achip
Berger, Hong-Wei PBMCs 11.PBMC.337.n stimulation U133A
12 Sun oStim.A
John O'Shea Linda Muul, Alan human EG009.5-12 EG009.5- no- 6 hr Day 5 biological EG009.5 337 HG- 4/12/2004 Sample_377_Control_Bchip
Berger, Hong-Wei PBMCs 12.PBMC.337.n stimulation U133B
13 Sun oStim.B
John O'Shea Linda Muul, Alan human EG009.5-13 EG009.5- no- 6 hr Day 5 biological EG009.5 254 HG- 3/29/2004 Sample_254_Control_Achip
Berger, Hong-Wei PBMCs 13.PBMC.254.n stimulation U133A
14 Sun oStim.A
John O'Shea Linda Muul, Alan human EG009.5-14 EG009.5- no- 6 hr Day 5 biological EG009.5 254 HG- 4/12/2004 Sample_254_Control_Bchip
Berger, Hong-Wei PBMCs 14.PBMC.254.n stimulation U133B
15 Sun oStim.B
John O'Shea Linda Muul, Alan human EG009.5-15 EG009.5- IL18 6 hr Day 5 biological EG009.5 2115 HG- 12/9/2002 Sample_2115_IL18_Achip
Berger, Hong-Wei PBMCs 15.PBMC.2115.I U133A
16 Sun L18.A
John O'Shea Linda Muul, Alan human EG009.5-16 EG009.5- IL18 6 hr Day 5 biological EG009.5 2115 HG- 12/17/2002 Sample_2115_IL18_Bchip
Berger, Hong-Wei PBMCs 16.PBMC.2115.I U133B
17 Sun L18.B
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.5 89
A B C D E F G H I J K L M N O
John O'Shea Linda Muul, Alan human EG009.5-17 EG009.5- IL18 6 hr Day 5 biological EG009.5 1769 HG- 11/3/2003 Sample_1769_IL18_Achip
Berger, Hong-Wei PBMCs 17.PBMC.1769.I U133A
18 Sun L18.A
John O'Shea Linda Muul, Alan human EG009.5-18 EG009.5- IL18 6 hr Day 5 biological EG009.5 1769 HG- 11/6/2003 Sample_1769_IL18_Bchip
Berger, Hong-Wei PBMCs 18.PBMC.1769.I U133B
19 Sun L18.B
John O'Shea Linda Muul, Alan human EG009.5-19 EG009.5- IL18 6 hr Day 5 biological EG009.5 1775 HG- 10/30/2003 Sample_1775_IL18_Achip
Berger, Hong-Wei PBMCs 19.PBMC.1775.I U133A
20 Sun L18.A
John O'Shea Linda Muul, Alan human EG009.5-20 EG009.5- IL18 6 hr Day 5 biological EG009.5 1775 HG- 11/5/2003 Sample_1775_IL18_Bchip
Berger, Hong-Wei PBMCs 20.PBMC.1775.I U133B
21 Sun L18.B
John O'Shea Linda Muul, Alan human EG009.5-21 EG009.5- IL18 6 hr Day 5 biological EG009.5 635 HG- 3/29/2004 Sample_635_IL18_Achip
Berger, Hong-Wei PBMCs 21.PBMC.635.IL U133A
22 Sun 18.A
John O'Shea Linda Muul, Alan human EG009.5-22 EG009.5- IL18 6 hr Day 5 biological EG009.5 635 HG- 4/12/2004 Sample_635_IL18_Bchip
Berger, Hong-Wei PBMCs 22.PBMC.635.IL U133B
23 Sun 18.b
John O'Shea Linda Muul, Alan human EG009.5-23 EG009.5- IL18 6 hr Day 5 biological EG009.5 541 HG- 3/29/2004 Sample_541_IL18_Achip
Berger, Hong-Wei PBMCs 23.PBMC.541.IL U133A
24 Sun 18
John O'Shea Linda Muul, Alan human EG009.5-24 EG009.5- IL18 6 hr Day 5 biological EG009.5 541 HG- 4/22/2004 Sample_541_IL18_Bchip
Berger, Hong-Wei PBMCs 24.PBMC.541.IL U133B
25 Sun 18.A
John O'Shea Linda Muul, Alan human EG009.5-25 EG009.5- IL18 6 hr Day 5 biological EG009.5 377 HG- 3/29/2004 Sample_377_IL18_Achip
Berger, Hong-Wei PBMCs 25.PBMC.337.IL U133A
26 Sun 18.B
John O'Shea Linda Muul, Alan human EG009.5-26 EG009.5- IL18 6 hr Day 5 biological EG009.5 377 HG- 4/12/2004 Sample_377_IL18_Bchip
Berger, Hong-Wei PBMCs 26.PBMC.337.IL U133B
27 Sun 18.A
John O'Shea Linda Muul, Alan human EG009.5-27 EG009.5- IL18 6 hr Day 5 biological EG009.5 254 HG- 3/29/2004 Sample_254_IL18_Achip
Berger, Hong-Wei PBMCs 27.PBMC.254.IL U133A
28 Sun 18.A
John O'Shea Linda Muul, Alan human EG009.5-28 EG009.5- IL18 6 hr Day 5 biological EG009.5 254 HG- 4/12/2004 Sample_254_IL18_Bchip
Berger, Hong-Wei PBMCs 28.PBMC.254.IL U133B
29 Sun 18.B
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.5 90
P Q
PCR
1 Folder (17) cycles
OShea-
IL18_GSP
2
OShea-
IL18_GSP
3
OShea-
IL18_GSP
4
OShea-
IL18_GSP
5
OShea-
IL18_GSP
6
OShea-
IL18_GSP
7
OShea-
IL18_GSP
8
OShea-
IL18_GSP
9
OShea-
IL18_GSP
10
OShea-
IL18_GSP
11
OShea-
IL18_GSP
12
OShea-
IL18_GSP
13
OShea-
IL18_GSP
14
OShea-
IL18_GSP
15
OShea-
IL18_GSP
16
OShea-
IL18_GSP
17
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.5 91
P Q
OShea-
IL18_GSP
18
OShea-
IL18_GSP
19
OShea-
IL18_GSP
20
OShea-
IL18_GSP
21
OShea-
IL18_GSP
22
OShea-
IL18_GSP
23
OShea-
IL18_GSP
24
OShea-
IL18_GSP
25
OShea-
IL18_GSP
26
OShea-
IL18_GSP
27
OShea-
IL18_GSP
28
OShea-
IL18_GSP
29
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.6 92
A B C D E F G H I J K L M N O
Experim
Dur. ent
Principal Simple Genes stim. Time Group ID Sampl AffyPlat
1 Investigator Investigators Cell type GSP ID (10) GSP ID (9) WT/KO Stim. (11) (12) point Rep. (13) (1) e ID (3) (14) Date (15) Affy .CEL file (16)
John O'Shea Linda Muul, Alan human EG009.6-01 EG009.6- no- 6 hr Day 5 biological EG009.6 2115 HG-U133A 12/9/2002 Sample_2115_Control_Ach
Berger, Hong-Wei PBMCs 01.PBMC.211 stimulation ip
2 Sun 5.noStim.A
John O'Shea Linda Muul, Alan human EG009.6-02 EG009.6- no- 6 hr Day 5 biological EG009.6 2115 HG-U133B 12/17/2002 Sample_2115_Control_Bch
Berger, Hong-Wei PBMCs 02.PBMC.211 stimulation ip
3 Sun 5.noStim.B
John O'Shea Linda Muul, Alan human EG009.6-03 EG009.6- no- 6 hr Day 5 biological EG009.6 1769 HG-U133A 11/3/2003 Sample_1769_Control_Ach
Berger, Hong-Wei PBMCs 03.PBMC.176 stimulation ip
4 Sun 9.noStim.A
John O'Shea Linda Muul, Alan human EG009.6-04 EG009.6- no- 6 hr Day5 biological EG009.6 1769 HG-U133B 11/6/2003 Sample_1769_Control_Bch
Berger, Hong-Wei PBMCs 04.PBMC.176 stimulation ip
5 Sun 9.noStim.B
John O'Shea Linda Muul, Alan human EG009.6-05 EG009.6- no- 6 hr Day 5 biological EG009.6 1775 HG-U133A 10/30/2003 Sample_1775_Control_Ach
Berger, Hong-Wei PBMCs 05.PBMC.177 stimulation ip
6 Sun 5.noStim.A
John O'Shea Linda Muul, Alan human EG009.6-06 EG009.6- no- 6 hr Day 5 biological EG009.6 1775 HG-U133B 11/5/2003 Sample_1775_Control_Bch
Berger, Hong-Wei PBMCs 06.PBMC.177 stimulation ip
7 Sun 5.noStim.B
John O'Shea Linda Muul, Alan human EG009.6-07 EG009.6- no- 6 hr Day 5 biological EG009.6 1193 HG-U133A 3/29/2004 Sample_1193_Control_Ach
Berger, Hong-Wei PBMCs 07.PBMC.119 stimulation ip
8 Sun 3.noStim.A
John O'Shea Linda Muul, Alan human EG009.6-08 EG009.6- no- 6 hr Day 5 biological EG009.6 1193 HG-U133B 4/12/2004 Sample_1193_Control_Bch
Berger, Hong-Wei PBMCs 08.PBMC.119 stimulation ip
9 Sun 3.noStim.B
John O'Shea Linda Muul, Alan human EG009.6-09 EG009.6- no- 6 hr Day 5 biological EG009.6 635 HG-U133A 7/16/2003 Sample_635_Control_Achi
Berger, Hong-Wei PBMCs 09.PBMC.635. stimulation p
10 Sun noStim.A
John O'Shea Linda Muul, Alan human EG009.6-10 EG009.6- no- 6 hr Day 5 biological EG009.6 635 HG-U133B 7/21/2003 Sample_635_Control_Bchi
Berger, Hong-Wei PBMCs 10.PBMC.635. stimulation p
11 Sun noStim.B
John O'Shea Linda Muul, Alan human EG009.6-11 EG009.6- no- 6 hr Day 5 biological EG009.6 546 HG-U133A 4/18/2003 Sample_546_Control_Achi
Berger, Hong-Wei PBMCs 11.PBMC546. stimulation p
12 Sun noStim.A
John O'Shea Linda Muul, Alan human EG009.6-12 EG009.6- no- 6 hr Day 5 biological EG009.6 546 HG-U133B 4/29/2003 Sample_546_Control_Bchi
Berger, Hong-Wei PBMCs 12.PBMC.546. stimulation p
13 Sun noStim.B
John O'Shea Linda Muul, Alan human EG009.6-13 EG009.6- no- 6 hr Day 5 biological EG009.6 541 HG-U133A 4/22/2003 Sample_541_Control_Achi
Berger, Hong-Wei PBMCs 13.PBMC.541. stimulation p
14 Sun noStim.A
John O'Shea Linda Muul, Alan human EG009.6-14 EG009.6- no- 6 hr Day 5 biological EG009.6 541 HG-U133B 5/15/2003 Sample_541_Control_Bchi
Berger, Hong-Wei PBMCs 14.PBMC.541. stimulation p
15 Sun noStim.B
John O'Shea Linda Muul, Alan human EG009.6-15 EG009.6- IL12 6 hr Day 5 biological EG009.6 2115 HG-U133A 4/18/2003 Sample_2115_IL12_Achip
Berger, Hong-Wei PBMCs 15.PBMC.211
16 Sun 5.IL12.A
John O'Shea Linda Muul, Alan human EG009.6-16 EG009.6- IL12 6 hr Day 5 biological EG009.6 2115 HG-U133B 4/29/2003 Sample_2115_IL12_Bchip
Berger, Hong-Wei PBMCs 16.PBMC.211
17 Sun 5.IL12.B
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.6 93
A B C D E F G H I J K L M N O
John O'Shea Linda Muul, Alan human EG009.6-17 EG009.6- IL12 6 hr Day 5 biological EG009.6 1775 HG-U133A 4/18/2003 Sample_1775_IL12_Achip
Berger, Hong-Wei PBMCs 17.PBMC.176
18 Sun 9.IL12.A
John O'Shea Linda Muul, Alan human EG009.6-18 EG009.6- IL12 6 hr Day 5 biological EG009.6 1775 HG-U133B 4/29/2003 Sample_1775_IL12_Bchip
Berger, Hong-Wei PBMCs 18.PBMC.176
19 Sun 9.IL12.B
John O'Shea Linda Muul, Alan human EG009.6-19 EG009.6- IL12 6 hr Day 5 biological EG009.6 1769 HG-U133A 4/18/2003 Sample_1769_IL12_Achip
Berger, Hong-Wei PBMCs 19.PBMC.177
20 Sun 5.IL12.A
John O'Shea Linda Muul, Alan human EG009.6-20 EG009.6- IL12 6 hr Day 5 biological EG009.6 1769 HG-U133B 4/29/2003 Sample_1769_IL12_Bchip
Berger, Hong-Wei PBMCs 20.PBMC.177
21 Sun 5.IL12.B
John O'Shea Linda Muul, Alan human EG009.6-21 EG009.6- IL12 6 hr Day 5 biological EG009.6 1193 HG-U133A 4/18/2003 Sample_1193_IL12_Achip
Berger, Hong-Wei PBMCs 21.PBMC.119
22 Sun 3.IL12.A
John O'Shea Linda Muul, Alan human EG009.6-22 EG009.6- IL12 6 hr Day 5 biological EG009.6 1193 HG-U133B 4/29/2003 Sample_1193_IL12_Bchip
Berger, Hong-Wei PBMCs 22.PBMC.119
23 Sun 3.IL12.B
John O'Shea Linda Muul, Alan human EG009.6-23 EG009.6- IL12 6 hr Day 5 biological EG009.6 635 HG-U133A 4/18/2003 Sample_635_IL12_Achip
Berger, Hong-Wei PBMCs 23.PBMC.635.
24 Sun IL12.A
John O'Shea Linda Muul, Alan human EG009.6-24 EG009.6- IL12 6 hr Day 5 biological EG009.6 635 HG-U133B 4/29/2003 Sample_635_IL12_Bchip
Berger, Hong-Wei PBMCs 24.PBMC.635.
25 Sun IL12.B
John O'Shea Linda Muul, Alan human EG009.6-25 EG009.6- IL12 6 hr Day 5 biological EG009.6 546 HG-U133A 4/18/2003 Sample_546_IL12_Achip
Berger, Hong-Wei PBMCs 25.PBMC546.I
26 Sun L12.A
John O'Shea Linda Muul, Alan human EG009.6-26 EG009.6- IL12 6 hr Day 5 biological EG009.6 546 HG-U133B 4/29/2003 Sample_546_IL12_Bchip
Berger, Hong-Wei PBMCs 26.PBMC.546.
27 Sun IL12.B
John O'Shea Linda Muul, Alan human EG009.6-27 EG009.6- IL12 6 hr Day 5 biological EG009.6 541 HG-U133A 4/22/2003 Sample_541_IL12_Achip
Berger, Hong-Wei PBMCs 27.PBMC.541.
28 Sun IL12.A
John O'Shea Linda Muul, Alan human EG009.6-28 EG009.6- IL12 6 hr Day5 biological EG009.6 541 HG-U133B 5/15/2003 Sample_541_IL12_Bchip
Berger, Hong-Wei PBMCs 28.PBMC.541.
29 Sun IL12.B
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.6 94
P Q
PCR
1 Folder (17) cycles
OShea-
IL12GEOsubmis
2 sion
OShea-
IL12GEOsubmis
3 sion
OShea-
IL12GEOsubmis
4 sion
OShea-
IL12GEOsubmis
5 sion
OShea-
IL12GEOsubmis
6 sion
OShea-
IL12GEOsubmis
7 sion
OShea-
IL12GEOsubmis
8 sion
OShea-
IL12GEOsubmis
9 sion
OShea-
IL12GEOsubmis
10 sion
OShea-
IL12GEOsubmis
11 sion
OShea-
IL12GEOsubmis
12 sion
OShea-
IL12GEOsubmis
13 sion
OShea-
IL12GEOsubmis
14 sion
OShea-
IL12GEOsubmis
15 sion
OShea-
IL12GEOsubmis
16 sion
OShea-
IL12GEOsubmis
17 sion
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG009.6 95
P Q
OShea-
IL12GEOsubmis
18 sion
OShea-
IL12GEOsubmis
19 sion
OShea-
IL12GEOsubmis
20 sion
OShea-
IL12GEOsubmis
21 sion
OShea-
IL12GEOsubmis
22 sion
OShea-
IL12GEOsubmis
23 sion
OShea-
IL12GEOsubmis
24 sion
OShea-
IL12GEOsubmis
25 sion
OShea-
IL12GEOsubmis
26 sion
OShea-
IL12GEOsubmis
27 sion
OShea-
IL12GEOsubmis
28 sion
OShea-
IL12GEOsubmis
29 sion
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG010 96
A B C D E F G H I J K L M N O
Simple Genes
Principal GSP ID WT/K Dur. stim. Time Experiment Sample
1 Investigator Investigators Cell type (10) GSP ID (9) O Stim. (11) (12) point Rep. (13) Group ID (1) ID (3) AffyPlat (14) Date (15) Affy .CEL file (16)
Warren Leonard Panu Human EG010-01 EG010- no-stimulation No EG010 J12minus HG_U95Av2 5/1/2001 PJM30801wl1J12-
Kovanen, PBMS 01.PBMC.J12 U95Av2
Peter Munson minus.noStim
2
Warren Leonard Panu Human EG010-02 EG010- IL2 No EG010 J12plus HG_U95Av2 5/1/2001 PJM30801wl2J12+U95A
Kovanen, PBMS 02.PBMC.J12 v2
Peter Munson plus.IL2
3
Warren Leonard Panu Human EG010-03 EG010- IL2 No EG010 J14minus HG_U95Av2 5/1/2001 PJM30801wl3J14-
Kovanen, PBMS 03.PBMC.J14 U95Av2
Peter Munson minus.IL2
4
Warren Leonard Panu Human EG010-04 EG010- no-stimulation No EG010 J14plus HG_U95Av2 5/1/2001 PJM30801wl4J14+U95A
Kovanen, PBMS 04.PBMC.J14 v2
Peter Munson plus.noStim
5
Warren Leonard Panu Human EG010-05 EG010- no-stimulation No EG010 J15minus HG_U95Av2 5/1/2001 PJM30801wl5J15-
Kovanen, PBMS 05.PBMC.J15 U95Av2
Peter Munson minus.noStim
6
Warren Leonard Panu Human EG010-06 EG010- IL2 No EG010 J15plus HG_U95Av2 5/1/2001 PJM30801wl6J15+U95A
Kovanen, PBMS 06.PBMC.J15 v2
Peter Munson plus.IL2
7
Warren Leonard Panu Human EG010-07 EG010- IL2 No EG010 A3plus HG_U95Av2 5/1/2001 PJM41801panuA3+HG_
Kovanen, PBMS 07.PBMC.A3pl 95A12
Peter Munson us.IL2
8
Warren Leonard Panu Human EG010-08 EG010- no-stimulation No EG010 A3minus HG_U95Av2 5/1/2001 PJM41801panuA3-
Kovanen, PBMS 08.PBMC.A3m HG_95A1
Peter Munson inus.noStim
9
Warren Leonard Panu Human EG010-09 EG010- IL2 No EG010 A4plus HG_U95Av2 5/1/2001 PJM41801panuA4+HG_
Kovanen, PBMS 09.PBMC.A4pl 95A14
Peter Munson us.IL2
10
Warren Leonard Panu Human EG010-10 EG010- no-stimulation No EG010 A4minus HG_U95Av2 5/1/2001 PJM41801panuA4-
Kovanen, PBMS 10.PBMC.A4m HG_95A13
Peter Munson inus.noStim
11
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG010 97
P Q
PCR
Folder cycle
1 (17) s
LeonardDa
ta
2
LeonardDa
ta
3
LeonardDa
ta
4
LeonardDa
ta
5
LeonardDa
ta
6
LeonardDa
ta
7
LeonardDa
ta
8
LeonardDa
ta
9
LeonardDa
ta
10
LeonardDa
ta
11
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG011 98
A B C D E F G H I J K L M N O
Simple Dur. Experime
Principal Investigat GSP ID Genes stim. Rep. nt Group Sample AffyPlat
1 Investigator ors Cell type (10) GSP ID (9) WT/KO Stim. (11) (12) Time point (13) ID (1) ID (3) (14) Date (15) Affy .CEL file (16)
William Paul Jeff Zhu mouse CD4+ EG011-01 EG011-01.CD4+T- WT anti- 4 days of priming No EG011 Th1 MOE430A 9/13/2005 JeffZhu-Th1A.cel
T cell, cultured cells.WT.Th1.anti- CD3/CD28, plus
CD3/CD28+IL2+IL1 IL2, PMA/ionomycin
2+anti-IL4.A IL12+anti- stimulation for
2 IL4 2hr
William Paul Jeff Zhu mouse CD4+ EG011-02 EG011-02.CD4+T- WT anti- 4 days of priming No EG011 Th1 MOE430B 9/13/2005 JeffZhu-Th1B.cel
T cell, cultured cells.WT.Th1.anti- CD3/CD28, plus
CD3/CD28+IL2+IL1 IL2, PMA/ionomycin
2+anti-IL4.B IL12+anti- stimulation for
3 IL4 2hr
William Paul Jeff Zhu mouse CD4+ EG011-03 EG011-03.CD4+T- Gfi1WT anti- Cre-GFP No EG011 control MOE430A 9/13/2005 JeffZhu-
T cell, cultured cells.Gfi1WT.control- CD3/CD28, infection during Th2 controlTh2A
Th2.anti- IL2, IL4+anti- second round of
CD3/CD28+IL2+IL4 IL-12, anti- Th2 priming (1
+anti-IL12+anti- IFNg week/round),
IFNg.A sorted GFPneg
cells were further
expanded for 2
rounds and then
PMA/ionomycing
stimulation for 2
hr
4
William Paul Jeff Zhu mouse CD4+ EG011-04 EG011-04.CD4+T- Gfi1WT anti- Cre-GFP No EG011 control MOE430B 9/13/2005 JeffZhu-
T cell, cultured cells.Gfi1WT.control- CD3/CD28, infection during Th2 controlTh2B
Th2.anti- IL2, IL4+anti- second round of
CD3/CD28+IL2+IL4 IL12, anti- Th2 priming (1
+anti-IL12+anti- IFNg week/round),
IFNg.B sorted GFPneg
cells were further
expanded for 2
rounds and then
PMA/ionomycing
stimulation for 2
hr
5
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG011 99
A B C D E F G H I J K L M N O
William Paul Jeff Zhu mouse CD4+ EG011-05 EG011-05.CD4+T- Gfi1KO anti- Cre-GFP No EG011 Gfi1KOT MOE430A 9/13/2005 JeffZhu-
T cell, cultured cells.Gfi1KO.Gfi1K CD3/CD28, infection during h2 Gfi1KOTh2A
OT-h2.anti- IL2, IL4+anti- second round of
CD3/CD28+IL2+IL4 IL12, anti- Th2 priming (1
+anti-IL12+anti- IFNg week/round),
IFNg.A sorted GFP+
cells were further
expanded for 2
rounds and then
PMA/ionomycing
stimulation for 2
hr
6
William Paul Jeff Zhu mouse CD4+ EG011-06 EG011-06.CD4+T- Gfi1KO anti- Cre-GFP No EG011 Gfi1KOT MOE430B 9/13/2005 JeffZhu-
T cell, cultured cells.Gfi1KO.Gfi1K CD3/CD28, infection during h2 Gfi1KOTh2B
OT-h2.anti- IL2, IL4+anti- second round of
CD3/CD28+IL2+IL4 IL12, anti- Th2 priming (1
+anti-IL12+anti- IFNg week/round),
IFNg.B sorted GFP+
cells were further
expanded for 2
rounds and then
PMA/ionomycing
stimulation for 2
hr
7
William Paul Jeff Zhu mouse CD4+ EG011-07 EG011-07.CD4+T- Gata3W anti- Cre-GFP No EG011 WT Th2 MOE430A 8/18/2005 JeffZhu-WTTh2A
T cell, cultured cells.Gata3WT.WT- T CD3/CD28, infection during
Th2.anti- IL2, IL4+anti- second round of
CD3/CD28+IL2+IL4 IL12, anti- Th2 priming (1
+anti-IL12+anti- IFNg week/round),
IFNg.A sorted GFP+
cells were further
expanded for 2
rounds and then
PMA/ionomycing
stimulation for 2
hr
8
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG011 100
A B C D E F G H I J K L M N O
William Paul Jeff Zhu mouse CD4+ EG011-08 EG011-08.CD4+T- Gata3W anti- Cre-GFP No EG011 WT Th2 MOE430B 8/18/2005 JeffZhu-WTTh2B
T cell, cultured cells.Gata3WT.WT- T CD3/CD28, infection during
Th2.anti- IL2, IL- second round of
CD3/CD28+IL2+IL4 4+anti-IL12, Th2 priming (1
+anti-IL12+anti- anti-IFNg week/round),
IFNg.B sorted GFP+
cells were further
expanded for 2
rounds and then
PMA/ionomycing
stimulation for 2
hr
9
William Paul Jeff Zhu mouse CD4+ EG011-09 EG011-09.CD4+T- Gata3KO anti- Cre-GFP No EG011 Gata3KO MOE430A 8/18/2005 JeffZhu-
T cell, cultured cells.Gata3KO- CD3/CD28, infection during Th2 GATA3KOTh2A
Gata3KOTh2.anti- IL2, IL4+anti- second round of
CD3/CD28+IL2+IL4 IL12, anti- Th2 priming (1
+anti-IL12+anti- IFNg week/round),
IFNg.A sorted GFP+
cells were further
expanded for 2
rounds and then
PMA/ionomycing
stimulation for 2
hr
10
William Paul Jeff Zhu mouse CD4+ EG011-10 EG011-10.CD4+T- Gata3KO anti- Cre-GFP No EG011 Gata3KO MOE430B 8/18/2005 JeffZhu-
T cell, cultured cells.Gata3KO- CD3/CD28, infection during Th2 GATA3KOTh2B
Gata3KOTh2.anti- IL2, IL4+anti- second round of
CD3/CD28+IL2+IL4 IL12, anti- Th2 priming (1
+anti-IL12+anti- IFNg week/round),
IFNg.B sorted GFP+
cells were further
expanded for 2
rounds and then
PMA/ionomycing
stimulation for 2
hr
11
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG011 101
P Q
PCR
1 Folder (17) cycles
2005-JeffZhu-
Affy-data
2
2005-JeffZhu-
Affy-data
3
2005-JeffZhu-
Affy-data
4
2005-JeffZhu-
Affy-data
5
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG011 102
P Q
2005-JeffZhu-
Affy-data
6
2005-JeffZhu-
Affy-data
7
2005-JeffZhu-
Affy-data
8
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/2011 5:16 AM EG011 103
P Q
2005-JeffZhu-
Affy-data
9
2005-JeffZhu-
Affy-data
10
2005-JeffZhu-
Affy-data
11
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG012 104
A B C D E F G H I J K L M N O
Experi
Simple Dur. ment Samp
Principal GSP ID Genes Stim. stim. Time Rep. Group le ID AffyPlat
1 Investigator Investigators Cell type (10) GSP ID (9) WT/KO (11) (12) point (13) ID (1) (3) (14) Date (15) Affy .CEL file (16)
Lothar Lothar Mouse EG012- EG012- WT TPO 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-
Hennighausen Hennighausen, hematopoietic 01 01.HSC.WT.FL1HSC l 08_Hennighausen1FLHSC+_MR_Mous
Michael Rieger stem cells .TPO e430_2_FL1HSC+
2
Lothar Lothar Mouse EG012- EG012- WT no- 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-08_Hennighausen1FLHSC-
Hennighausen Hennighausen, hematopoietic 02 02.HSC.WT.FL1HSC- stimulatio l _MR_Mouse430_2_FL1HSC-
Michael Rieger stem cells noStim n
3
Lothar Lothar Mouse EG012- EG012- WT TPO 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-
Hennighausen Hennighausen, hematopoietic 03 03.HSC.WT.FL1KSL- l 08_Hennighausen1FLKSL+_MR_Mous
Michael Rieger stem cells TPO e430_2_FL1KSL+
4
Lothar Lothar Mouse EG012- EG012- WT no- 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-08_Hennighausen1FLKSL-
Hennighausen Hennighausen, hematopoietic 04 04.HSC.WT.FL1KSL- stimulatio l _MR_Mouse430_2_FL1KSL-
Michael Rieger stem cells noStim n
5
Lothar Lothar Mouse EG012- EG012- Stat5- TPO 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-
Hennighausen Hennighausen, hematopoietic 05 05.HSC.Stat5KO.MX null l 08_Hennighausen1MXHSC+_MR_Mou
Michael Rieger stem cells 1HSC.TPO se430_2_MX1HSC+
6
Lothar Lothar Mouse EG012- EG012- Stat5- no- 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-08_Hennighausen1MXHSC-
Hennighausen Hennighausen, hematopoietic 06 06.HSC.Stat5KOT.M null stimulatio l _MR_Mouse430_2_MX1HSC-
Michael Rieger stem cells X1HSC-noStim n
7
Lothar Lothar Mouse EG012- EG012- Stat5- TPO 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-
Hennighausen Hennighausen, hematopoietic 07 07.HSC.Stat5KO.MX null l 08_Hennighausen1MXKSL+_MR_M
Michael Rieger stem cells 1KSL-TPO ouse430_2_MX1KSL+
8
Lothar Lothar Mouse EG012- EG012- Stat5- no- 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-08_Hennighausen1MXKSL-
Hennighausen Hennighausen, hematopoietic 08 08.HSC.Stat5KO.MX null stimulatio l _MR_Mouse430_2_MX1KSL-
Michael Rieger stem cells 1KSL-noStim n
9
Lothar Lothar Mouse EG012- EG012- WT TPO 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-
Hennighausen Hennighausen, hematopoietic 09 09.HSC.WT.FL2HSC l 08_Hennighausen2FLHSC+_MR_M
Michael Rieger stem cells .TPO ouse430_2_FL2HSC+
10
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG012 105
A B C D E F G H I J K L M N O
Lothar Lothar Mouse EG012- EG012- WT no- 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-08_Hennighausen2FLHSC-
Hennighausen Hennighausen, hematopoietic 10 10.HSC.WT.FL2HSC- stimulatio l _MR_Mouse430_2_FL2HSC-
Michael Rieger stem cells noStim n
11
Lothar Lothar Mouse EG012- EG012- WT TPO 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-
Hennighausen Hennighausen, hematopoietic 11 11.HSC.WT.FL2KSL- l 08_Hennighausen2FLKSL+_MR_Mo
Michael Rieger stem cells TPO use430_2_FL2KSL+
12
Lothar Lothar Mouse EG012- EG012- WT no- 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-08_Hennighausen2FLKSL-
Hennighausen Hennighausen, hematopoietic 12 12.HSC.WT.FL2KSL- stimulatio l _MR_Mouse430_2_FL2KSL-
Michael Rieger stem cells noStim n
13
Lothar Lothar Mouse EG012- EG012- Stat5- TPO 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-
Hennighausen Hennighausen, hematopoietic 13 13.HSC.Stat5KO.MX null l 08_Hennighausen2MXHSC+_MR_M
Michael Rieger stem cells 2HSC.TPO ouse430_2_MX2HSC+
14
Lothar Lothar Mouse EG012- EG012- Stat5- no- 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-08_Hennighausen2MXHSC-
Hennighausen Hennighausen, hematopoietic 14 14.HSC.Stat5KO.MX null stimulatio l _MR_Mouse430_2_MX2HSC-
Michael Rieger stem cells 2HSC-noStim n
15
Lothar Lothar Mouse EG012- EG012- Stat5- TPO 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-
Hennighausen Hennighausen, hematopoietic 15 15.HSC.Stat5KO.MX null l 08_Hennighausen2MXKSL+_MR_M
Michael Rieger stem cells 2KSL-TPO ouse430_2_MX2KSL+
16
Lothar Lothar Mouse EG012- EG012- Stat5- no- 2h 2h biologica EG012 MOE430_2 12/30/2008 12-30-08_Hennighausen2MXKSL-
Hennighausen Hennighausen, hematopoietic 16 16.HSC.Stat5KO.MX null stimulatio l _MR_Mouse430_2_MX2KSL-
Michael Rieger stem cells 2KSL-noStim n
17
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG012 106
P Q
PCR
cycle
1 Folder (17) s
08-12-
30_L.Hennighaus
en_MR_Mouse43
2 0_2_HSC_KSL
08-12-
30_L.Hennighaus
en_MR_Mouse43
3 0_2_HSC_KSL
08-12-
30_L.Hennighaus
en_MR_Mouse43
4 0_2_HSC_KSL
08-12-
30_L.Hennighaus
en_MR_Mouse43
5 0_2_HSC_KSL
08-12-
30_L.Hennighaus
en_MR_Mouse43
6 0_2_HSC_KSL
08-12-
30_L.Hennighaus
en_MR_Mouse43
7 0_2_HSC_KSL
08-12-
30_L.Hennighaus
en_MR_Mouse43
8 0_2_HSC_KSL
08-12-
30_L.Hennighaus
en_MR_Mouse43
9 0_2_HSC_KSL
08-12-
30_L.Hennighaus
en_MR_Mouse43
10 0_2_HSC_KSL
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG012 107
P Q
08-12-
30_L.Hennighaus
en_MR_Mouse43
11 0_2_HSC_KSL
08-12-
30_L.Hennighaus
en_MR_Mouse43
12 0_2_HSC_KSL
08-12-
30_L.Hennighaus
en_MR_Mouse43
13 0_2_HSC_KSL
08-12-
30_L.Hennighaus
en_MR_Mouse43
14 0_2_HSC_KSL
08-12-
30_L.Hennighaus
en_MR_Mouse43
15 0_2_HSC_KSL
08-12-
30_L.Hennighaus
en_MR_Mouse43
16 0_2_HSC_KSL
08-12-
30_L.Hennighaus
en_MR_Mouse43
17 0_2_HSC_KSL
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG013 108
A B C D E F G H I J K L M N O
Simple Dur. Experiment
Principal Investigato Cell GSP ID Genes stim. Time Group ID Sample Affy .CEL file
1 Investigator rs type (10) GSP ID (9) WT/KO Stim. (11) (12) point Rep. (13) (1) ID (3) AffyPlat (14) Date (15) (16)
Lothar Traudl mouse EG013- EG013- WT untreated 48hrs biological EG013 407-l MOE430_2 1/28/2009
Hennighausen Robinson, mamma 01 01.Mammary.WT.407l.untr
Weiping ry tissue eated
2 Chen 01-28-09_14
Lothar Traudl mouse EG013- EG013- RBPJCreA untreated 48hrs biological EG013 407-r MOE430_2 1/28/2009
Hennighausen Robinson, mamma 02 02.Mammary.RBPJCreA.4
Weiping ry tissue 07r.untreated
3 Chen 01-28-09_15
Lothar Traudl mouse EG013- EG013- WT untreated 48hrs biological EG013 408-l MOE430_2 1/28/2009
Hennighausen Robinson, mamma 03 03.Mammary.WT.408l.untr
Weiping ry tissue eated
4 Chen 01-28-09_16
Lothar Traudl mouse EG013- EG013- RBPJCreA untreated 48hrs biological EG013 408-r MOE430_2 1/28/2009
Hennighausen Robinson, mamma 04 04.Mammary.RBPJCreA.4
Weiping ry tissue 08r.untreated
5 Chen 01-28-09_17
Lothar Traudl mouse EG013- 48hrs biological EG013 410-l MOE430_2 1/28/2009
Hennighausen Robinson, mamma 05 EG013-
Weiping ry tissue 05.Mammary.WT.410l.trea
6 Chen ted WT treated 01-28-09_18
Lothar Traudl mouse EG013- 48hrs biological EG013 410-r MOE430_2 1/28/2009
Hennighausen Robinson, mamma 06 EG013-
Weiping ry tissue 06.Mammary.RBPJCreA.4
7 Chen 10r.treated RBPJCreA treated 01-28-09_19
Lothar Traudl mouse EG013- 48hrs biological EG013 411-l MOE430_2 1/28/2009
Hennighausen Robinson, mamma 07 EG013-
Weiping ry tissue 07.Mammary.WT.411l.trea
8 Chen ted WT treated 01-28-09_20
Lothar Traudl mouse EG013- 48hrs biological EG013 411-r MOE430_2 1/28/2009
Hennighausen Robinson, mamma 08 EG013-
Weiping ry tissue 08.Mammary.RBPJCreA.4
9 Chen 11r.treated RBPJCreA treated 01-28-09_21
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG013 109
P Q
PCR
1 Folder (17) cycles
?? ??
2
?? ??
3
?? ??
4
?? ??
5
?? ??
6
?? ??
7
?? ??
8
?? ??
9
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG014 110
A B C D E F G H I J K L M N
Simple Dur. Experiment
Principal Investigato Cell GSP ID stim. Time Group ID Sample
1 Investigator rs type (10) GSP ID (9) Genes WT/KO Stim. (11) (12) point Rep. (13) (1) ID (3) AffyPlat (14) Date (15)
Lothar Daisuke mouse EG014-01 EG014- Stat5a/5b pregnant day 6 biological EG014 D6_KO_1 MOE430_2 1/28/2009
Hennighausen Yamaji, mamma 01.Mammary.Stat5ab- floxed/floxed; D6 040_10
Weiping ry tissue ff-MMTV- MMTV-CreA
Chen CreA.bio1.pregnantD6
2
Lothar Daisuke mouse EG014-02 EG014- Stat5a/5b pregnant day 6 biological EG014 D6_KO_1 MOE430_2 1/28/2009
Hennighausen Yamaji, mamma 02.Mammary.Stat5ab- floxed/floxed; D6 043_12
Weiping ry tissue ff-MMTV- MMTV-CreA
Chen CreA.bio2.pregnantD6
3
Lothar Daisuke mouse EG014-03 EG014- Stat5a/5b pregnant day 6 biological EG014 D6_WT_1 MOE430_2 1/28/2009
Hennighausen Yamaji, mamma 03.Mammary.Stat5ab- floxed/floxed D6 047_9
Weiping ry tissue ff.bio1.pregnantD6
4 Chen
Lothar Daisuke mouse EG014-04 EG014- Stat5a/5b pregnant day 6 biological EG014 D6_WT_1 MOE430_2 1/28/2009
Hennighausen Yamaji, mamma 04.Mammary.Stat5ab- floxed/floxed D6 048_11
Weiping ry tissue ff.bio2.pregnantD6
5 Chen
bb676ae0-9012-47d9-a432-e1d5444febca.xls 12/1/20115:16 AM EG014 111
O P Q
PCR
1 Affy .CEL file (16) Folder (17) cycles
01-28-09_Hennighausen10_MR_Mouse430_2_10 ?? ??
2
01-28-09_Hennighausen12_MR_Mouse430_2_12 ?? ??
3
01-28-09_Hennighausen9_MR_Mouse430_2_9 ?? ??
4
01-28-09_Hennighausen11_MR_Mouse430_2_11 ?? ??
5