title: ZR-75-30_day3_expression

description:
ZR-75-30_day3
jhu_251485070425_S01_GE2_107_Sep09_1_2_ZR-75-30 Mock Day3 RNA-Cy3_ZR-75-30 AZA Day3 RNA_Cy5

hyb_protocol: 825 ng of labeled RNA was fragmented, denatured and hybridized to the array at 60ºC for 17 hours in a hybridization oven with rotation. After hybridization, arrays were washed and dried according to the Agilent microarray processing protocol.

scan_protocol: Arrays were scanned by Agilent G2505C Scanner controlled by Agilent Scan Control 7.0 Software. Data were extracted with Agilent Feature Extraction Software.

data_processing: Raw median foreground signals were taken for both channels. LOESS normalization for within-array normalization, and A-quantile normalization for between-arrays normalization were performed using R and Bioconductor. 2-channel arrays were analyzed as single-channel.  The second color is not analyzed in this analysis.

source_name: ZR-75-30 breast cancer cell line, day 3

label_protocol: 400 ng total RNA was amplified and labeled using the Low RNA Input Fluorescent Linear Amplification Kit (Cat# 5190-0447, Agilent Technologies) with oligo dT primers (Cat# RA300A-2, System Bioscience) and cyanine-labeled CTPs (Perkin Elmer) according to manufacturer’s manual. Labeled cRNA was purified using RNeasy Mini Kit (Qiagen). RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to manufacturer’s protocol.

extract_protocol: Total RNA was isolated using TriZol (Invitrogen) followed by RNeasy Mini Kit (Qiagen) according to manufacturers’ manuals. RNA quality was assessed by Nanodrop-1000 spectrometer for OD260/280 and OD260/230 ratio and Bioanalyzer (Agilent Technologies).

tag: disease

value: Breast cancer

tag: er


title: SUM159PT_day3_expression

status: Public on Jul 12 2013

type: RNA

city: Baltimore

first: Francescopaolo

last: Di Cello

state: MD

address: 1650 Orleans Street

country: USA

institute: The Johns Hopkin University School of Medicine

description:
SUM159PT_day3
jhu_251485070422_S01_GE2_107_Sep09_1_2_SUM159 Mock Day3 RNA-Cy3_SUM159 AZA Day3 RNA_Cy5

molecule: total RNA

organism: Homo sapiens

source_name: SUM159PT breast cancer cell line, day 3

growth_protocol: Cells were grown for three days changing media every day

tag: gender

value: Female


title: ZR-75-1_day3_expression

description:
ZR-75-1_day3
jhu_251485067907_S01_GE2_107_Sep09_1_2_ZR-75-1 Mock Day3-Cy3_ZR-75-1 AZA Day3-Cy5

source_name: ZR-75-1 breast cancer cell line, day 3


title: I_MCF10DCIS:RMF (1:1 ratio, 48hrs, replicate 2)

city: Chapel Hill

first: Melissa

last: Troester

state: NC

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

hyb_protocol: Agilent protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent scanner and image intensity data were analyzed with Agilent software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Human Reference B

label_protocol: Agilent protocol

extract_protocol: Qiagen Rneasy Mini

tag: reference

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

label_protocol: Described in Hu et al. 2005, BioTechniques, 38:121-124 (PMID 15679094).

growth_protocol: growth in DMEM:F12 complete media with supplements

treatment_protocol: coculture with reduction mammary fibroblasts

tag: cell line

tag: sample type

value: indirect coculture

tag: treatment


title: SUM149PT_day3_expression

description:
SUM149PT_day3
jhu_251485070421_S01_GE2_107_Sep09_1_2_SUM149 Mock Day3 RNA-Cy3_SUM149 AZA Day3 RNA_Cy5

source_name: SUM149PT breast cancer cell line, day 3


title: Clone 3 (31627B) Dox Replicate 2

city: Worcester

first: Benjamin

middle: R

last: Carone

state: Massachusetts

address: 364 Plantation St

department: BMP

institute: UMass Medical School

description:
Gene expression data from iPS cell lines treated with Doxycycline
JJ29

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Primeview Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 with 7g upgrade.

data_processing: The data were analyzed with Affymetrix Gene Expression Console.  RMA normalization was applied to all samples.

label: Biotin

source_name: iPS cell line Clone 3 (31627B) Dox Replicate 2

label_protocol: Gene Chip 3' IVT Express Kit was used to label RNA from 1 ug total RNA

growth_protocol: DS iPSC parent line (DS1-iPS4) was provided by George Q. Daley (Children’s Hospital Boston, USA) and maintained on irradiated mouse embryonic fibroblasts (iMEFs) (R & D Systems, PSC001) in hiPSC medium containing DNEM/F12 supplemented with 20% knockout Serum Replacement (Invitrogen), 1mM glutamine (Invitrogen), 100 µM non-essential amino acids (Invitrogen), 100 µM β-mercaptoethanol (Sigma) and 10 ng/ml FGF-β (Invitrogen, PHG0024).  Cultures were passaged every 5-7 days with 1 mg/ml of collagenase type IV (Invitrogen).

extract_protocol: High Pure RNA extraction kit (Roche) was used to extract RNA  and was performed according to the manufacturer's instructions.

treatment_protocol: + or - doxycycline (ug/ml) for 22days

value: induced Pluripotent Stem cells

tag: cell line type

value: subclone 3 (31627B)

value: Doxycycline


title: T47D_day3_expression

description:
T47D_day3
jhu_251485064913_S01_GE2_107_Sep09_1_2_T47D Mock Day3 RNA-Cy5_T47D AZA Day3 RNA-Cy3

source_name: T47D breast cancer cell line, day 3


title: Clone 3 (31627B) Dox Replicate 1

description:
Gene expression data from iPS cell lines treated with Doxycycline
JJ28

source_name: iPS cell line Clone 3 (31627B) Dox Replicate 1


title: Clone 2 (3258-9) Dox Replicate 2

description:
Gene expression data from iPS cell lines treated with Doxycycline
JJ23

source_name: iPS cell line Clone 2 (3258-9) Dox Replicate 2


title: Clone 3 (31627B) no Dox Replicate 1

description:
Gene expression data from iPS cell lines
JJ25

source_name: iPS cell line Clone 3 (31627B) no Dox Replicate 1

value: control


title: MDA-MB-453_day3_expression

description:
MDA-MB-453_day3
jhu_251485067911_S01_GE2_107_Sep09_1_2_MDA468 Mock Day3-Cy3_MDA468 AZA Day3-Cy5

source_name: MDA-MB-453 breast cancer cell line, day 3


title: I_MCF10AT1:RMF (1:1 ratio, 48hrs, replicate 2)

value: coculture with reduction mammary fibroblasts


title: Clone 3 (31627B) Dox Replicate 3

description:
Gene expression data from iPS cell lines treated with Doxycycline
JJ30

source_name: iPS cell line Clone 3 (31627B) Dox Replicate 3


title: Clone 3 (31627B) no Dox Replicate 2

description:
Gene expression data from iPS cell lines
JJ26

source_name: iPS cell line Clone 3 (31627B) no Dox Replicate 2


title: SK-BR-3_day3_expression

description:
SK-BR-3_day3
jhu_251485071078_S01_GE2_107_Sep09_1_2_SKBR3  Mock Day3 RNA-Cy3_SKBR3  AZA Day3 RNA-Cy5

source_name: SK-BR-3 breast cancer cell line, day 3


title: Clone 3 (31627B) no Dox Replicate 3

description:
Gene expression data from iPS cell lines
JJ27

source_name: iPS cell line Clone 3 (31627B) no Dox Replicate 3


title: I_MCF10DCIS:RMF (1:1 ratio, 48hrs, replicate 1)


title: Clone 2 (3258-9) Dox Replicate 3

description:
Gene expression data from iPS cell lines treated with Doxycycline
JJ24

source_name: iPS cell line Clone 2 (3258-9) Dox Replicate 3


title: Clone 2 (3258-9) Dox Replicate 1

description:
Gene expression data from iPS cell lines treated with Doxycycline
JJ22

source_name: iPS cell line Clone 2 (3258-9) Dox Replicate 1


title: MDA-MB-468_day3_expression

description:
MDA-MB-468_day3
jhu_251485067910_S01_GE2_107_Sep09_1_2_MDA453 Mock Day3-Cy3_MDA453 AZA Day3-Cy5

source_name: MDA-MB-468 breast cancer cell line, day 3


title: I_MCF10A:RMF (1:1 ratio, 48hrs, replicate 2)


title: I_MCF10AT1:RMF (1:1 ratio, 48hrs, replicate 1)


title: MDA-MB-436_day3_expression

description:
MDA-MB-436_day3
jhu_251485071079_S01_GE2_107_Sep09_1_2_MDA436  Mock Day3 RNA-Cy3_MDA436  AZA Day3 RNA-Cy5

source_name: MDA-MB-436 breast cancer cell line, day 3


title: C_RMF:MCF10AT1(1:2,48h)_rep1

value: direct coculture


title: C_RMF:MCF10AT1(2:1,48h)_rep1


title: I_MCF10A:RMF (1:1 ratio, 48hrs, replicate1)


title: C_RMF:MCF10AT1(1:4,48h)_rep1


title: MDA-MB-415_day3_expression

description:
MDA-MB-415_day3
jhu_251485071077_S01_GE2_107_Sep09_1_2_MDA415  Mock Day3 RNA-Cy3_MDA415  AZA Day3 RNA-Cy5

source_name: MDA-MB-415 breast cancer cell line, day 3


title: MDA-MB-361_day3_expression

description:
MDA-MB-361_day3
jhu_251485067908_S01_GE2_107_Sep09_1_2_MDA361Mock Day3-Cy3_MDA361AZA Day3-Cy5

source_name: MDA-MB-361 breast cancer cell line, day 3


title: MDA-MB-175-VII_day3_expression

description:
MDA-MB-175-VII_day3
jhu_251485071080_S01_GE2_107_Sep09_1_2_MDA175  Mock Day3 RNA-Cy3_MDA175  AZA Day3 RNA-Cy5

source_name: MDA-MB-175-VII breast cancer cell line, day 3


title: C_RMF:MCF10AT1(1:1,48h)_rep1

source_name: Human Reference B


city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

description:
Saccharomyces bayanus var uvarum
ACY959 Sb Ime1 mutant 90 minute alpha factor

hyb_protocol: reference URL : http://genomics.princeton.edu/caudylab/Yeast_RNA_Prep_and_Labeling_070925.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 14:06:21 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 6.1.0.4
Datafile type : GenePix Results 3
Image Origin : 0, 0

organism: Saccharomyces bayanus

source_name: Universal reference

extract_protocol:
Extracted molecule : RNA
Extraction method : acid phenol extraction

treatment_protocol: Growth Condition : mixed

tag: species

value: S. bayanus

tag: strain name

value: mixed

treatment_protocol:
Time : 90 minutes
Compound Based Treatment : 50 ng/ml alpha factor
Growth Condition : 25C YPD

tag: genotype

tag: sex/mating type

value: MATa


title: C_RMF:MCF10AT1(1:0,48h)

value: monoculutre


title: Clone 2 (3258-9) no Dox Replicate 2

description:
Gene expression data from iPS cell lines
JJ20

source_name: iPS cell line Clone 2 (3258-9) no Dox Replicate 2


description:
Saccharomyces bayanus var uvarum
ACY959 Ime1 mutant 0 minute alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 14:50:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

label_protocol: reference URL : http://genomics.princeton.edu/caudylab/Yeast_RNA_Prep_and_Labeling_070925.pdf

treatment_protocol:
Time : 0 minutes
Compound Based Treatment : 50 ng/ml alpha factor
Growth Condition : 25C YPD


title: Clone 1 (3131D) Dox Replicate 2

description:
Gene expression data from iPS cell lines treated with Doxycycline
JJ17

source_name: iPS cell line Clone 1 (3131D) Dox Replicate 2

value: subclone 1 (3131D)


title: Clone 2 (3258-9) no Dox Replicate 3

description:
Gene expression data from iPS cell lines
JJ21

source_name: iPS cell line Clone 2 (3258-9) no Dox Replicate 3


title: MCF7_day3_expression

description:
MCF7_day3
jhu_251485070373_S01_GE2_107_Sep09_1_2_MCF7  Mock Day3 RNA-Cy3_MCF7  AZA Day3 RNA_Cy5

source_name: MCF7 breast cancer cell line, day 3


title: Clone 2 (3258-9) no Dox Replicate 1

description:
Gene expression data from iPS cell lines
JJ19

source_name: iPS cell line Clone 2 (3258-9) no Dox Replicate 1


title: Clone 1 (3131D) Dox Replicate 1

description:
Gene expression data from iPS cell lines treated with Doxycycline
JJ16

source_name: iPS cell line Clone 1 (3131D) Dox Replicate 1


title: MDA-MB-231_day3_expression

description:
MDA-MB-231_day3
jhu_251485067909_S01_GE2_107_Sep09_1_2_MDA231 Mock Day3-Cy3_MDA231 AZA Day3-Cy5

source_name: MDA-MB-231 breast cancer cell line, day 3


title: Clone 1 (3131D) no Dox Replicate 3

description:
Gene expression data from iPS cell lines
JJ15

source_name: iPS cell line Clone 1 (3131D) no Dox Replicate 3


description:
Saccharomyces bayanus var uvarum
ACY959 Sb Ime1 mutant 60 minute alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 14:15:42 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

treatment_protocol:
Time : 60 minutes
Compound Based Treatment : 50 ng/ml alpha factor
Growth Condition : 25C YPD


title: C_RMF:MCF10AT1(0:1,48h)_rep1


title: C_RMF:MCF10A(1:4,48h)_rep1


description:
Saccharomyces bayanus var uvarum
ACY959 Sb Ime1 mutant 30 minute alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 15:00:10 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

treatment_protocol:
Time : 30 minutes
Compound Based Treatment : 50 ng/ml alpha factor
Growth Condition : 25C YPD


title: Clone 1 (3131D) Dox Replicate 3

description:
Gene expression data from iPS cell lines treated with Doxycycline
JJ18

source_name: iPS cell line Clone 1 (3131D) Dox Replicate 3


title: C_RMF:MCF10AT1(0:1,48h)


title: C_RMF:MCF10A(1:2,48h)_rep1


title: C_RMF:MCF10A(2:1,48h)_rep1


title: HCC38_day3_expression

description:
HCC38_day3
jhu_251485070374_S01_GE2_107_Sep09_1_2_HCC38 Mock Day3 RNA-Cy3_HCC38 AZA Day3 RNA_Cy5

source_name: HCC38 breast cancer cell line, day 3


title: ACY958 90 minute alpha factor

description:
Saccharomyces bayanus var uvarum
ACY958 90 minute alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 15:18:38 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: ACY958 wild type 90 minute alpha factor

value: prototroph


title: ACY958 60 minute alpha factor

description:
Saccharomyces bayanus var uvarum
ACY958 60 minute alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 15:09:09 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: ACY958 wild type 60 minute alpha factor


title: HCC1954_day3_expression

description:
HCC1954_day3
jhu_251485071037_S01_GE2_107_Sep09_1_2_HCC1954 Mock Day3 RNA-Cy3_HCC1954 AZA Day3 RNA-Cy5

source_name: HCC1954 breast cancer cell line, day 3


title: HCC1937_day3_expression

description:
HCC1937_day3
jhu_251485068036_S01_GE2_107_Sep09_1_2_HCC1937 Mock Day3-Cy3_HCC1937 AZA Day3-Cy5

source_name: HCC1937 breast cancer cell line, day 3


title: C_RMF:MCF10A(1:1,48h)_rep1


title: Clone 1 (3131D) no Dox Replicate 2

description:
Gene expression data from iPS cell lines
JJ14

source_name: iPS cell line Clone 1 (3131D) no Dox Replicate 2


title: HCC1500_day3_expression

description:
HCC1500_day3
jhu_251485070424_S01_GE2_107_Sep09_1_2_HCC1500 Mock Day3 RNA-Cy3_HCC1500 AZA Day3 RNA_Cy5

source_name: HCC1500 breast cancer cell line, day 3


title: Clone 1 (3131D) no Dox Replicate 1

description:
Gene expression data from iPS cell lines
JJ13

source_name: iPS cell line Clone 1 (3131D) no Dox Replicate 1


title: HCC1569_day3_expression

description:
HCC1569_day3
jhu_251485070370_S01_GE2_107_Sep09_1_2_HCC1569 Mock Day3 RNA-Cy3_HCC1569 AZA Day3 RNA_Cy5

source_name: HCC1569 breast cancer cell line, day 3


title: C_RMF:MCF10A(1:0,48h)_rep2

source_name: Human Reference B


title: ACY958 30 minute alpha factor

description:
Saccharomyces bayanus var uvarum
ACY958 30 minute alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 14:34:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Universal reference

source_name: ACY958 wild type 30 minute alpha factor


title: Gtf2i Mutant line, biological rep 2

city: Barcelona

first: Victoria

last: Campuzano

address: Dr Aiguader, 88

department: CEXS

country: Spain

institute: Universitat Pompeu Fabra

hyb_protocol: Only those samples with an RNA Integrity Number (RIN) >7 were used for hybridization. Samples of 500ng/ul were used to perform a Affymetric mouse 430_2 expression array

scan_protocol: The images were processed with Microarray Analysis Suite 5.0 (Affymetrix).

data_processing: Raw expression values obtained directly from .CEL files were preprocessed using the RMA method (Irizarry et al., 2003), a three-step process which integrates background correction, normalization and summarization of probe values

label: biotin

organism: Mus musculus

source_name: gene-targeted derived R1 cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cell lines were cultured in standard conditions, Knockout DMEM medium (10829), supplemented with 20% Knockout Serum Replacement for ES cells (10828) both things from GIBCO (Invitrogen). Penicillin/streptomycin, LIF, no essentials aminoacids and -mercaptoethanol were also added to the medium. Cells were always cultures in a monolayer of feeder cells. Cells were maintained at 37ºC in a humidified 5% CO2 chamber.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: tissue

value: Embrionic stem cell line

tag: genotype/variation


title: HCC1419_day3_expression

description:
HCC1419_day3
jhu_251485071041_S01_GE2_107_Sep09_1_2_HCC1419  Mock Day3 RNA-Cy3_HCC1419  AZA Day3 RNA-Cy5

source_name: HCC1419 breast cancer cell line, day 3

value: Breast cancer


description:
Saccharomyces bayanus var uvarum
ACY957 Sb Ime1 mutant 60 minutes alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 13:19:29 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


description:
Saccharomyces bayanus var uvarum
ACY957 Sb Ime1 mutant 90 minutes alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 13:28:36 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: HCC1187_day3_expression

description:
HCC1187_day3
jhu_251485071040_S01_GE2_107_Sep09_1_2_HCC1187  Mock Day3 RNA-Cy3_HCC1187  AZA Day3 RNA-Cy5

source_name: HCC1187 breast cancer cell line, day 3

value: Female


title: EFM192A_day3_expression

description:
EFM192A_day3
jhu_251485071039_S01_GE2_107_Sep09_1_2_EFM192A  Mock Day3 RNA-Cy3_EFM192A  AZA Day3 RNA-Cy5

source_name: EFM192A breast cancer cell line, day 3


description:
Saccharomyces bayanus var uvarum
ACY957 Sb Ime1 mutant 30 minutes alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 13:10:28 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: Parental Dox Replicate 3

description:
Gene expression data from iPS cell lines treated with Doxycycline
JJ12

source_name: Parental iPS cell line Dox Replicate 3

value: parental


title: Gtf2i Mutant line, biological rep 1


description:
Saccharomyces bayanus var uvarum
ACY957 Sb Ime1 mutant 0 minutes alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 13:02:11 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: EFM19_day3_expression

description:
EFM19_day3
jhu_251485070372_S01_GE2_107_Sep09_1_2_EFM19  Mock Day3 RNA-Cy3_EFM19  AZA Day3 RNA_Cy5

source_name: EFM19 breast cancer cell line, day 3


title: Parental no Dox Replicate 3

description:
Gene expression data from iPS cell lines
JJ09

source_name: Parental iPS cell lineno Dox Replicate 3


title: Parental no Dox Replicate 2

description:
Gene expression data from iPS cell lines
JJ08

source_name: Parental iPS cell lineno Dox Replicate 2


title: Parental Dox Replicate 1

description:
Gene expression data from iPS cell lines treated with Doxycycline
JJ10

source_name: Parental iPS cell line Dox Replicate 1


title: C_RMF:MCF10A(0:1,48h)_rep1

value: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs


title: ACY958 0 minute alpha factor

description:
Saccharomyces bayanus var uvarum
ACY958 0 minute alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 14:25:07 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: ACY958 wild type 0 minute alpha factor


title: Parental Dox Replicate 2

description:
Gene expression data from iPS cell lines treated with Doxycycline
JJ11

source_name: Parental iPS cell line Dox Replicate 2

value: induced Pluripotent Stem cells


title: ACY382 90 minutes alpha factor

description:
Saccharomyces bayanus var uvarum
ACY382 90 minutes alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 12:52:46 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: ACY382 90 minutes alpha factor


title: Parental no Dox Replicate 1

description:
Gene expression data from iPS cell lines
JJ07

source_name: Parental iPS cell line no Dox Replicate 1


title: GTF2iTrap line, biological rep 2

hyb_protocol: Only those samples with an RNA Integrity Number (RIN) >7 were used for hybridization. Samples of 500ng/l were used to perform a Affymetric mouse 430_2 expression array

source_name: gentrap derived AB2.2 ES cell

tag: cell type

value: HPRT -/-:GTF2I +/-


title: Wild-type, biological rep2

source_name: Wild-type ES cells

value: wild-type


title: Wild-type, biological rep1


title: ACY382 60 minutes alpha factor

description:
Saccharomyces bayanus var uvarum
ACY382 60 minutes alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 13:37:40 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: Universal reference

source_name: ACY382 60 minutes alpha factor


title: CAMA1_day3_expression

description:
CAMA1_day3
jhu_251485071076_S01_GE2_107_Sep09_1_2_CAMA1  Mock Day3 RNA-Cy3_CAMA1  AZA Day3 RNA-Cy5

scan_protocol: Arrays were scanned by Agilent G2505C Scanner controlled by Agilent Scan Control 7.0 Software. Data were extracted with Agilent Feature Extraction Software.

source_name: CAMA1 breast cancer cell line, day 3


title: BT-474_day3_expression

description:
BT-474_day3
jhu_251485071038_S01_GE2_107_Sep09_1_2_BT474 Mock Day3 RNA-Cy3_BT474 AZA Day3 RNA-Cy5

source_name: BT-474 breast cancer cell line, day 3


title: BT-20_day3_expression

description:
BT-20_day3
jhu_251485070371_S01_GE2_107_Sep09_1_2_BT20 Mock Day3 RNA-Cy3_BT20 AZA Day3 RNA_Cy5

source_name: BT-20 breast cancer cell line, day 3


title: HPRTKO, biological rep2

source_name: HPRT KO ES cells

value: HPRT -/-


title: ACY382 30 minutes alpha factor

description:
Saccharomyces bayanus var uvarum
ACY382 30 minutes alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 13:47:09 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: ACY382 30 minutes alpha factor


title: HPRTKO, biological rep1


title: ACY382 0 minute alpha factor

description:
Saccharomyces bayanus var uvarum
ACY382 0 minute alpha factor

scan_protocol: Pixel Size : 5 Scan Date : 2009-07-07 Scan Time : 13:56:39 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

source_name: ACY382 0 minute alpha factor


title: Male iPS Replicate 3

description:
Gene expression data from iPS cell lines
JJ03

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 with 7g upgrade.

source_name: Male iPS cell line Replicate 3

value: normal, disomic male

value: control


title: cGvHDnoIS6

status: Public on Jul 11 2013

city: Stanford

first: Li

last: Li

state: CA

address: 300 pastuer dr.,

department: Pediatric

institute: Stanford University

description:
Sample name: 202d6
Agilent Feature Extraction file (original name):
US84703594_251485063798_S01_GE2_105_Dec08_1_4(202 d6).txt

hyb_protocol: We followed Agilent’s hybridization protocol. Equal amounts of the exposed and negative control sample (825 ng) were competitively hybridized onto Agilent Whole 4×44K Human oligonucleotide arrays in a hybridization oven at 65°C for 17 hours. Slides were washed according to the manufacturer’s instructions with washing buffers and finally dipped in Stabilization and Drying Solution (Agilent Technologies, Palo Alto, CA) to protect them from environmental ozone.

scan_protocol: We followed Agilent’s scan protocol. The arrays were scanned on an Agilent scanner (G2565BA, Agilent Technologies, Palo Alto, CA), and further processed using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software was used for background subtraction GeneSpring was used for normalization

source_name: cGvHD sample (control)

label_protocol: Cy5-CTP (exposed samples) and Cy3-CTP (negative control samples) were fluorescently labeled during the step of cDNA was transcribed into complimentary RNA (cRNA). We used Agilent LIRAK PLUS, two color Low Input RNA Linear Amplification Kit method according manufacturer’s instructions

extract_protocol: The blood was drawn in the presence of sodium heparin. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA).

value: peripheral blood

tag: set

value: control set

source_name: human reference total RNA pool

value: 10 human cell lines


title: cGvHDnoIS4

description:
Sample name: 196c1
Agilent Feature Extraction file (original name):
US84703594_251485037180_S01_GE2_107_Sep09_1_2(196 c1).txt


title: GTF2iTrap line, biological rep 1


title: Male iPS Replicate 1

description:
Gene expression data from iPS cell lines
JJ01

source_name: Male iPS cell line Replicate 1


title: cGvHDnoIS2

description:
Sample name: 138d2
Agilent Feature Extraction file (original name):
US84703594_251485067314_S01_GE2_107_Sep09_1_2(138 d2).txt


title: Male iPS Replicate 2

description:
Gene expression data from iPS cell lines
JJ02

source_name: Male iPS cell line Replicate 2


title: cGvHDnoIS5

description:
Sample name: 196h1
Agilent Feature Extraction file (original name):
US84703594_251485037180_S01_GE2_107_Sep09_1_3(196 h1).txt


title: cGvHDnoIS7

description:
Sample name: 216g6
Agilent Feature Extraction file (original name):
US84703594_251485067314_S01_GE2_107_Sep09_1_3(216 g6).txt


title: cGvHDnoIS3

description:
Sample name: 192a6
Agilent Feature Extraction file (original name):
US84703594_251485037180_S01_GE2_107_Sep09_1_1(192 a6).txt


title: cGvHD31

description:
Sample name: C83b6
Agilent Feature Extraction file (original name):
US45102891_251485027463_S01_GE2-v5_95_Feb07_1_1.txt

hyb_protocol: We followed Agilent’s hybridization protocol. Equal amounts of the sample and reference (825 ng) were competitively hybridized onto Agilent Whole 4×44K Human oligonucleotide arrays in a hybridization oven at 65°C for 17 hours. Slides were washed according to the manufacturer’s instructions with washing buffers and finally dipped in Stabilization and Drying Solution (Agilent Technologies, Palo Alto, CA) to protect them from environmental ozone.

source_name: cGvHD sample

label_protocol: Cy5-CTP (samples) and Cy3-CTP (reference) were fluorescently labeled during the step of cDNA was transcribed into complimentary RNA (cRNA). We used Agilent LIRAK PLUS, two color Low Input RNA Linear Amplification Kit method according manufacturer’s instructions

tag: disease state

value: cGvHD

value: test set


title: cGvHD35

description:
Sample name: C81h1h2
Agilent Feature Extraction file (original name):
US45102891_251485033406_S01_GE2-v5_95_Feb07_1_1.txt


title: cGvHD34

description:
Sample name: C82c1
Agilent Feature Extraction file (original name):
US45102891_251485027461_S01_GE2-v5_95_Feb07_1_3.txt


title: cGvHD32

description:
Sample name: C88a1
Agilent Feature Extraction file (original name):
US45102891_251485033100_S01_GE2-v5_95_Feb07_1_3.txt


title: cGvHD29

description:
Sample name: C83g6
Agilent Feature Extraction file (original name):
US45102891_251485033096_S01_GE2-v5_95_Feb07_1_1.txt


title: cGvHDnoIS1

description:
Sample name: 103eg
Agilent Feature Extraction file (original name):
US84703594_251485067314_S01_GE2_107_Sep09_1_1(103 eg).txt


title: cGvHD28

description:
Sample name: C82i6i7
Agilent Feature Extraction file (original name):
US45102891_251485033406_S01_GE2-v5_95_Feb07_1_3.txt


title: cGvHD30

description:
Sample name: C86f6
Agilent Feature Extraction file (original name):
US45102891_251485033098_S01_GE2-v5_95_Feb07_1_4.txt


title: cGvHD26

description:
Sample name: C84f6
Agilent Feature Extraction file (original name):
US45102891_251485027833_S01_GE2-v5_95_Feb07_1_1.txt


title: non-cGvHD25

description:
Sample name: C88i1
Agilent Feature Extraction file (original name):
US45102891_251485027834_S01_GE2-v5_95_Feb07_1_2.txt

source_name: non cGvHD sample

value: non-cGvHD


title: non-cGvHD27

description:
Sample name: C81d6
Agilent Feature Extraction file (original name):
US45102891_251485027482_S01_GE2-v5_95_Feb07_1_3.txt


title: non-cGvHD24

description:
Sample name: C79c6
Agilent Feature Extraction file (original name):
US45102891_251485033404_S01_GE2-v5_95_Feb07_1_4.txt


title: cGvHD25

description:
Sample name: C69h1
Agilent Feature Extraction file (original name):
US45102891_251485027834_S01_GE2-v5_95_Feb07_1_1.txt


title: non-cGvHD23

description:
Sample name: C82a1
Agilent Feature Extraction file (original name):
US45102891_251485027461_S01_GE2-v5_95_Feb07_1_2.txt


title: non-cGvHD22

description:
Sample name: C89b6
Agilent Feature Extraction file (original name):
US45102891_251485033407_S01_GE2-v5_95_Feb07_1_3.txt


title: non-cGvHD28

description:
Sample name: C83e6
Agilent Feature Extraction file (original name):
US45102891_251485027463_S01_GE2-v5_95_Feb07_1_2.txt


title: cGvHD24

description:
Sample name: C80e6e7
Agilent Feature Extraction file (original name):
US45102891_251485033405_S01_GE2-v5_95_Feb07_1_4.txt


title: non-cGvHD21

description:
Sample name: C88e1
Agilent Feature Extraction file (original name):
US45102891_251485033407_S01_GE2-v5_95_Feb07_1_2.txt


title: non-cGvHD26

description:
Sample name: C79b6
Agilent Feature Extraction file (original name):
US45102891_251485033404_S01_GE2-v5_95_Feb07_1_2.txt


title: cGvHD27

description:
Sample name: C79e2
Agilent Feature Extraction file (original name):
US45102891_251485033405_S01_GE2-v5_95_Feb07_1_1.txt


title: cGvHD22

description:
Sample name: C87g6
Agilent Feature Extraction file (original name):
US45102891_251485033099_S01_GE2-v5_95_Feb07_1_4.txt

value: training set


title: cGvHD23

description:
Sample name: C79c1
Agilent Feature Extraction file (original name):
US45102891_251485033404_S01_GE2-v5_95_Feb07_1_3.txt


title: cGvHD21

description:
Sample name: C87e1
Agilent Feature Extraction file (original name):
US45102891_251485033099_S01_GE2-v5_95_Feb07_1_3.txt


title: non-cGvHD20

description:
Sample name: C88d1
Agilent Feature Extraction file (original name):
US45102891_251485033100_S01_GE2-v5_95_Feb07_1_4.txt


title: cGvHD18

description:
Sample name: C85c1
Agilent Feature Extraction file (original name):
US45102891_251485027833_S01_GE2-v5_95_Feb07_1_4.txt


title: cGvHD16

description:
Sample name: C86j6
Agilent Feature Extraction file (original name):
US45102891_251485033099_S01_GE2-v5_95_Feb07_1_2.txt


title: cGvHD14

description:
Sample name: C83g2
Agilent Feature Extraction file (original name):
US45102891_251485027463_S01_GE2-v5_95_Feb07_1_4.txt


title: cGvHD9

description:
Sample name: C80i2
Agilent Feature Extraction file (original name):
US45102891_251485027481_S01_GE2-v5_95_Feb07_1_4.txt


title: cGvHD17

description:
Sample name: C84g6
Agilent Feature Extraction file (original name):
US45102891_251485027833_S01_GE2-v5_95_Feb07_1_2.txt


title: cGvHD5

description:
Sample name: C81j6j7
Agilent Feature Extraction file (original name):
US45102891_251485033406_S01_GE2-v5_95_Feb07_1_2.txt


title: cGvHD6

description:
Sample name: C83a1
Agilent Feature Extraction file (original name):
US45102891_251485027462_S01_GE2-v5_95_Feb07_1_3.txt


title: cGvHD8

description:
Sample name: C80c1
Agilent Feature Extraction file (original name):
US45102891_251485027481_S01_GE2-v5_95_Feb07_1_1.txt


title: cGvHD12

description:
Sample name: C79i7
Agilent Feature Extraction file (original name):
US45102891_251485033405_S01_GE2-v5_95_Feb07_1_2.txt


title: cGvHD11

description:
Sample name: C83f1
Agilent Feature Extraction file (original name):
US45102891_251485027463_S01_GE2-v5_95_Feb07_1_3.txt


title: cGvHD4

description:
Sample name: C80h6
Agilent Feature Extraction file (original name):
US45102891_251485027481_S01_GE2-v5_95_Feb07_1_3.txt


title: cGvHD7

description:
Sample name: C83a6
Agilent Feature Extraction file (original name):
US45102891_251485027462_S01_GE2-v5_95_Feb07_1_4.txt


title: cGvHD13

description:
Sample name: C81j1
Agilent Feature Extraction file (original name):
US45102891_251485027461_S01_GE2-v5_95_Feb07_1_1.txt


title: non-cGvHD12

description:
Sample name: C82j2
Agilent Feature Extraction file (original name):
US45102891_251485027462_S01_GE2-v5_95_Feb07_1_1.txt


title: non-cGvHD9

description:
Sample name: C87h1
Agilent Feature Extraction file (original name):
US45102891_251485033100_S01_GE2-v5_95_Feb07_1_1.txt


title: non-cGvHD13

description:
Sample name: C82j6
Agilent Feature Extraction file (original name):
US45102891_251485027462_S01_GE2-v5_95_Feb07_1_2.txt


title: non-cGvHD17

description:
Sample name: C81e6
Agilent Feature Extraction file (original name):
US45102891_251485027482_S01_GE2-v5_95_Feb07_1_4.txt


title: non-cGvHD19

description:
Sample name: C83h1
Agilent Feature Extraction file (original name):
US45102891_251485033096_S01_GE2-v5_95_Feb07_1_2.txt


title: cGvHD2

description:
Sample name: C77j1j2
Agilent Feature Extraction file (original name):
US45102891_251485033404_S01_GE2-v5_95_Feb07_1_1.txt


title: cGvHD1

description:
Sample name: C77h6
Agilent Feature Extraction file (original name):
US45102891_251485027834_S01_GE2-v5_95_Feb07_1_4.txt


title: non-cGvHD14

description:
Sample name: C78c1
Agilent Feature Extraction file (original name):
US45102891_251485033407_S01_GE2-v5_95_Feb07_1_4.txt


title: cGvHD10

description:
Sample name: C81d1
Agilent Feature Extraction file (original name):
US45102891_251485027482_S01_GE2-v5_95_Feb07_1_2.txt


title: non-cGvHD11

description:
Sample name: C83d6d7
Agilent Feature Extraction file (original name):
US45102891_251485033406_S01_GE2-v5_95_Feb07_1_4.txt


title: cGvHD3

description:
Sample name: C79j6
Agilent Feature Extraction file (original name):
US45102891_251485033405_S01_GE2-v5_95_Feb07_1_3.txt


title: non-cGvHD15

description:
Sample name: C80c6
Agilent Feature Extraction file (original name):
US45102891_251485027481_S01_GE2-v5_95_Feb07_1_2.txt


title: non-cGvHD16

description:
Sample name: C81c7
Agilent Feature Extraction file (original name):
US45102891_251485027482_S01_GE2-v5_95_Feb07_1_1.txt


title: non-cGvHD18

description:
Sample name: C82i1
Agilent Feature Extraction file (original name):
US45102891_251485027461_S01_GE2-v5_95_Feb07_1_4.txt


title: non-cGvHD10

description:
Sample name: C86e6
Agilent Feature Extraction file (original name):
US45102891_251485033098_S01_GE2-v5_95_Feb07_1_2.txt


title: cGvHD15

description:
Sample name: C86d6
Agilent Feature Extraction file (original name):
US45102891_251485033098_S01_GE2-v5_95_Feb07_1_1.txt


title: non-cGvHD2

description:
Sample name: C84d1
Agilent Feature Extraction file (original name):
US45102891_251485033096_S01_GE2-v5_95_Feb07_1_4.txt


title: non-cGvHD4

description:
Sample name: C85h6
Agilent Feature Extraction file (original name):
US45102891_251485033097_S01_GE2-v5_95_Feb07_1_1.txt


title: cGvHD33

description:
Sample name: C85b6
Agilent Feature Extraction file (original name):
US45102891_251485027833_S01_GE2-v5_95_Feb07_1_3.txt


title: non-cGvHD7

description:
Sample name: C86g6
Agilent Feature Extraction file (original name):
US45102891_251485033099_S01_GE2-v5_95_Feb07_1_1.txt


title: non-cGvHD6

description:
Sample name: C86f1
Agilent Feature Extraction file (original name):
US45102891_251485033098_S01_GE2-v5_95_Feb07_1_3.txt


title: non-cGvHD3

description:
Sample name: C85d2
Agilent Feature Extraction file (original name):
US45102891_251485027832_S01_GE2-v5_95_Feb07_1_4.txt


title: non-cGvHD1

description:
Sample name: C84b6
Agilent Feature Extraction file (original name):
US45102891_251485033096_S01_GE2-v5_95_Feb07_1_3.txt


title: non-cGvHD8

description:
Sample name: C86h1h2
Agilent Feature Extraction file (original name):
US45102891_251485033407_S01_GE2-v5_95_Feb07_1_1.txt


title: non-cGvHD5

description:
Sample name: C86c1
Agilent Feature Extraction file (original name):
US45102891_251485033097_S01_GE2-v5_95_Feb07_1_4.txt


title: WS iPSC iWS229 TERT (clone 21) rep2

city: Bethesda

first: Hoi Hung

last: Cheung

address: 49 Convent Dr, Rm.2C08 Bldg.49

institute: NICHD

description: Gene expression data from genetically modified WS iPSC culture

hyb_protocol: cDNA was hybridization at 45C overnight. Wash and staining was performed by GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: Arrays were scanned by GeneChip Scanner 3000 7G controlled AGCC Scan Control (Affymetrix)

data_processing: Microarray data were analyzed by Partek Genomics Suite 6.6 with quantile normalization and RMA background correction. A batch effect due to scan date was removed before One-way ANOVA analysis for differentially expressed genes between normal and WS fibroblasts.

source_name: WS iPSC, hTERT expressed

label_protocol: cDNA was labeled by biotin using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Fibroblast culture was maintained in alpha MEM medium containing 15% FBS. iPSC/hESC culture was maintained on Matrigel with mTeSR1 medium.

extract_protocol: Total RNA was extracted by Trizol and purified by Direct-zol RNA MiniPrep (Zymo Research). RNA integrity was assessed by BioAnalyzer.

value: Male

tag: age

value: WRN mutant

value: Werner Syndrome iPSC, hTERT expressed


title: Normal male ESC rep2

description: Gene expression data from normal human embryonic stem cells

source_name: Normal hESC

value: embryonic

value: WT

value: Normal hESC


title: WS iPSC iWS797 TERT rep2


title: WS iPSC iWS229 p53i rep2

source_name: WS iPSC, p53 knockdown

value: Werner Syndrome iPSC, p53 knockdown


title: WS iPSC iWS229 p53i rep1


title: WS iPSC iWS797 TERT rep1


title: Normal iPSC from AN2 rep2

description: Gene expression data from normal iPSC culture

source_name: Normal iPSC

value: Normal iPSC


title: WS iPSC iWS229 TERT (clone 21) rep1


title: WS iPSC iWS229 TERT (clone 13) rep2


title: Normal male ESC rep1


title: Normal iPSC from BC rep2


title: Normal female ESC rep2

value: Female


title: Normal iPSC from BC rep1


title: WS iPSC iWS229 TERT (clone 13) rep1


title: Normal iPSC from AN3 rep1


title: Normal iPSC from AN3 rep2


title: Normal iPSC from AN1 rep2


title: Normal iPSC from AN1 rep1


title: Normal female ESC rep1


title: Normal iPSC from AN2 rep1


title: CD8 Tnaive 2

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description:
replicate 2
5452241001_B

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization

source_name: Mouse spleen

label_protocol: Biotinylated cRNA were prepared with the TargetAmp Nano-g Biotin-aRNA Labeling Kit

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: After extensive washing, cells were lysed in Trizol reagent

tag: strain

value: 6-8 weeks

value: spleen

value: CD8 Tnaive


title: CD8 Tnaive 1

description:
replicate 1
5452241001_A


title: CD8 Tnaive 5

description:
replicate 5
5452647001_B


title: BM-DC 2

description:
replicate 2
4299599060_D

source_name: Mouse bone marrow

value: day 7

value: bone marrow


title: MF 2

description:
replicate 2
5392293021_C


title: ESdM 22 3

description:
replicate 3
5993312075_E

source_name: ES cells

value: >day 51 of culture

value: cultured ES cells

value: ES cells


title: CD8 Tnaive 4

description:
replicate 4
5452647001_A


title: cGvHD19

description:
Sample name: C86a1
Agilent Feature Extraction file (original name):
US45102891_251485033097_S01_GE2-v5_95_Feb07_1_2.txt

value: peripheral blood

value: cGvHD

value: training set

value: 10 human cell lines


title: MF 3

description:
replicate 3
5417796005_D


title: Astrocyte 2

description:
replicate 2
5511125072_D

source_name: Mouse brain

value: day 3

value: brain

value: Astrocyte


title: CD8 Tnaive 3

description:
replicate 3
5452241003_F


title: Neuron 2

description:
replicate 2
5511125072_C

value: Neuron


title: BM-DC 3

description:
replicate 3
4299599060_F


title: cGvHD20

description:
Sample name: C86b1
Agilent Feature Extraction file (original name):
US45102891_251485033097_S01_GE2-v5_95_Feb07_1_3.txt


title: MF 4

description:
replicate 4
5417796005_F


title: ESdM 20 3

description:
replicate 3
5993312075_C


title: Neuron 1

description:
replicate 1
5511125072_B


title: Neuron 3

description:
replicate 3
5511125072_F


title: ESdM 20 1

description:
replicate 3
5993312070_C


title: Microglia 1

description:
replicate 1
5993312070_A

value: Microglia


title: ESdM 20 2

description:
replicate 3
5993312070_E


title: ESdM 22 2

description:
replicate 3
5993312075_B


title: Astrocyte 1

description:
replicate 1
5511125072_A


title: Astrocyte 3

description:
replicate 3
5511125072_E


title: ESdM 22 1

description:
replicate 3
5993312070_D


title: Microglia 3

description:
replicate 3
5993312075_F


title: Microglia 2

description:
replicate 2
5993312075_A


title: MF 1

description:
replicate 1
5392293019_E


title: BM-DC 1

description:
replicate 1
4299599060_B


title: BA OBCs, post doxycyclin withdrawal, rep3

city: San Francisco

first: Emmanuelle

last: Passegué

state: California

address: 35 Medical Center Way, RMB-1017 Pod B, box 0667

department: Medicine

institute: University of California San Francisco

hyb_protocol: Biotinylated cRNA were prepared according to the GeneChip Expression Analysis Technical Manual 702232 Rev. 3

scan_protocol: GeneChips were scanned using the Affymetric GCS 3000 Scanner

data_processing: Data was processed using AGCC 3.2.2. Data were GC-RMA normalized and statistically significant differentially expressed genes were determined using Significance Analysis of Microarrays (SAM) (Tusher et al., 2001).

source_name: BA osteoblastic lineage cells 5-6 weeks post doxycylin withdrawal

label_protocol: Sense-strand cDNA targets were generated using the Nugen WT-Ovation Exon Module, and then fragmented and biotinylated using the Nugen Encore Biotin Module according to manufacturers’ instructions.

growth_protocol: Control and BA mice were withdrawn from doxycycline at 5 week of age to induce MPN development in BA mice. Five to 6 weeks later, bones were harvested for OBC isolation and RNA extraction

extract_protocol: Total RNA was isolated from 500-2300 purified OBCs using the Arcterus PicoPure RNA kit and a modified protocol for Trizol samples according to manufacturers’ instruction. RNA was then amplified using the Nugen Pico WTA kit and amplified products were cleaned using the Qiagen QiaQuick PCR purification kit following Nugen’s protocols.

treatment_protocol: Crushed bones were washed with HBSS until the bone chips were white and endosteal stromal cells were released by digestion for 1 hour at 37°C at 110 rpm with 3 mg/ml type I collagenase (Worthington) dissolved in HBSS. The released endosteal cells were washed with HBSS + 2% FBS, and residual bone material was removed by filtering through a 45 μm filter. Cells were stained with unconjugated rat anti-lineage (B220, CD3, CD4, CD5, CD8, Ter119, Mac-1, Gr-1) antibodies followed by goat anti-rat-Cy5PE or Qdot605 secondary antibodies and directly conjugated CD31-FITC, Sca-1-PB, CD45- Cy7APC and CD51-bio/streptavidin-APC antibodies. Cells were sorted on a FACS ARIAII upon PI exclusion of dead cells. OBCs were single-sorted and directly collected in Trizol.

value: Osteoblastic lineage cell

tag: phenotype

tag: time point

value: 5-6 weeks post doxycylcin withdrawal


title: Ctrl OBCs, post doxycyclin withdrawal, rep5

source_name: Control osteoblastic lineage cells 5-6 weeks post doxycylin withdrawal

value: Control


title: BCL6 WT BACH2 ER 3

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

description: BCR-ABL1 transformed BCL6 WT cells were transduced with an inducible BACH2 overexpression vector

hyb_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

data_processing: RMA

source_name: Total RNA from Ph+ ALL

label_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site.

value: 4 weeks

value: BCR-ABL1 transformed pre-B cells

value: BCR-ABL1-driven ALL

value: Wild-type


title: BA OBCs, post doxycyclin withdrawal, rep2


title: BCL6 KO BACH2 ER 2

description: BCR-ABL1 transformed BCL6 KO cells were transduced with an inducible BACH2 overexpression vector

scan_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

value: BCL6 KO


title: Ctrl OBCs, post doxycyclin withdrawal, rep1


title: Ctrl OBCs, post doxycyclin withdrawal, rep4


title: BA OBCs, post doxycyclin withdrawal, rep5


title: Ctrl OBCs, post doxycyclin withdrawal, rep2


title: BA OBCs, post doxycyclin withdrawal, rep4


title: Ctrl OBCs, post doxycyclin withdrawal, rep3


title: uchain in Ph+ ALL (uchain-s1)

source_name: Total RNA from Ph+ ALL (C57Bl6 Ighm KO)

value: Ighm KO

tag: transduction

value: uchain


title: BA OBCs, post doxycyclin withdrawal, rep1


title: BCL6 KO BACH2 ER 3


title: BCL6 WT BACH2 ER 2


title: uchain in Ph+ ALL (uchain-s2)


title: uchain in Ph+ ALL (uchain-s3)


title: BCL6 WT BACH2 ER 1


title: uchain in Ph+ ALL (CD8-s1)

value: CD8 (empty vector control)


title: BCL6 KO BACH2 ER 1


title: uchain in Ph+ ALL (CD8-s3)


title: MYC in Ph+ ALL (CRE3)

source_name: Total RNA from Ph+ ALL (C57Bl6)

value: Conditional Myc Knockout

value: CRE


title: MYC in Ph+ ALL (CRE1)


title: PAX5 in Ph+ ALL (PAX5-3)


title: uchain in Ph+ ALL (CD8-s2)


title: PAX5 in Ph+ ALL (PAX5-2)


title: MYC in Ph+ ALL (CRE2)


title: MYC in Ph+ ALL (MIG1)

value: pMIG


title: PAX5 in Ph+ ALL (EGZ2)

value: EGZ


title: PAX5 in Ph+ ALL (PAX5-1)


title: BACH2-/- ALL + Imatinib (Sample2)

source_name: Total RNA from Ph+ ALL (C57Bl6 and Bach2 -/- background)

value: Bach2 knockout

value: Imatinib (2uM for 16h)


title: BACH2-/- ALL + Imatinib (Sample1)


title: splenocytes-sorted-TCRb+_WT

city: New Haven

first: NINGWEN

last: TAI

state: CT

address: 300 Cedar Street

department: Internal Medicine

institute: Yale University

description:
SAMPLE 4
replicate 1

data_processing: The data were normalized using quantile normalisation with IlluminaGUI in R

source_name: splenocytes

label_protocol: Biotinylated cRNA were prepared with Illumina TotalPrep RNA Amplification Kit.

growth_protocol: Splenocytes of 6-7 week-old WT and TLR9-deficient NOD mice.

extract_protocol: Total RNAs were extracted from cells with Qiagen RNeasy mini kit.

treatment_protocol: FACS sorted TCRb+ cells.

value: NOD

value: wild type

value: 6-7 weeks

value: spleen

value: splenocytes-sorted-TCRb+


title: BACH2+/+ ALL + Imatinib (Sample3)

value: 4 weeks

value: BCR-ABL1 transformed pre-B cells

value: BCR-ABL1-driven ALL


title: splenocytes-sorted-TCRb+_TLR9-deficient

description:
SAMPLE 8
replicate 1


title: PAX5 in Ph+ ALL (EGZ1)

value: Wild-type


title: PAX5 in Ph+ ALL (EGZ3)


title: BACH2-/- ALL (Sample3)


title: BACH2+/+ ALL + Imatinib (Sample2)


title: BACH2-/- ALL (Sample1)


title: BACH2+/+ ALL + Imatinib (Sample1)


title: MYC in Ph+ ALL (MIG3)


title: Sox11(-/-) cortex at E17.5

city: Biddeford

first: Lei

last: Lei

state: ME

address: 11 Hills Beach Road

department: Biology

institute: University of New England

description: gene expression data from E17.5 cortex of a Sox11(-/-) mouse embryo

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 degree Celsius on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with the Affymetrix Expression Console using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: E17.5 cortex from a Sox11(-/-) embryo

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix).

growth_protocol: A timed pregnant female Sox11(+/-) mouse, mated with a Sox11(+/-) male mouse, was used to collect embryos at E17.5.

treatment_protocol: The brain was dissected out from each embryo under a microscope and the cerebral cortex from each brain was isolated and transferred into an Eppendorf tube containing 1 ml of Trizol. The tissue was frozen in liquid nitrogen. The tail clip from each embryo was used for genotyping by PCR.

value: Sox -/-

value: embryonic cortex

tag: genetic background


title: BACH2-/- ALL + Imatinib (Sample3)

tag: treatment


title: BACH2+/+ ALL (Sample3)


title: BACH2-/- ALL (Sample2)


title: Sox11(+/+) cortex at E17.5

description: gene expression data from E17.5 cortex of a wild type mouse embryo

source_name: E17.5 cortex from a wild type embryo


title: BACH2+/+ ALL (Sample1)


title: ML_ALV-J infected_32W_rep3

city: Guangzhou

first: yuhao

last: li

state: Guangdong

address: 483 Wushan Road, Tianhe District,

department: College of Veterinary Medicine

country: China

institute: South China Agricultural University

description: Gene expression of ALV-J infected myeloid leucosis of chicken liver

hyb_protocol: Cyanine-3-CTP, linearly amplified 1.65ug per cRNA sample was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent and prepared for One-Color based hybridization using the Gene Expression Hybridization Kit, Agilent Technologies. On completion of the fragmentation reaction, 55ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and cRNA samples were hybridized at 65˚C for 17 hours on separate Agilent Chicken V2 4x44K Gene Expression Microarrays. The microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control A.8.4.1 Software (Agilent Technologies) on the Agilent DNA Microarray Scanner (Agilent p/n G2565BA) and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies) (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The software tools Feature Extraction 10.7.3.1, GeneSpring GX 12.5 (both Agilent Technologies) and Spotfire Decision Site 9.1.2 (TIBCO) was used for quality control, statistical analysis, Gene Ontology annotation and visualization. The Gene Expression Data Analysis tool of the PANTHER database, release 8.0 was applied for enrichment analysis.

organism: Gallus gallus

source_name: ML liver, ALV-J infected, 32 week age, replicate 1

label_protocol: 1 ug total RNA per sample was reverse transcribed into cDNA and then converted into labeled RNA by in-vitro transcription incorporating Cyanine-3-CTP, this was done using the Low Input Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from frozen tumor tissues using TRIzol® Reagent (Invitrogen life technologies) following manufacturer's instructions. The protocol includes Homogenization, Phase Separation, RNA Precipitation, RNA Wash and Redissolving the RNA. The RNA was clean-up with RNasey Mini Kit (Qiagen p/n 74104) and Baseline-ZERO DNase (EPICENTRE, Cat. Nos. DB0711K), following manufacturer's protocol. The final volume of the eluate was 40ul. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

treatment_protocol: Tissue samples were aseptically collected from chickens with ML and non-ALV-J-infected birds at age 32 weeks. Tissue was submerged in RNALater (SIGMA), stored at -80˚C, until processed.

value: liver

tag: gender

value: female

value: avian leukosis virus subgroup J (ALV-J) integration in myeloid leukosis (ML)


title: 8.9 mg/kg BW Csa 11d 101253-58

city: Bilthoven

first: Anne

middle: Susan

last: Kienhuis

address: A. van Leeuwenhoeklaan 9

country: Netherlands

institute: RIVM

description: quality control: approved

hyb_protocol: According to the Affymetrix Hybridization, Wash and Stain Kit (#901530)

scan_protocol: According to Affymetrix protocols

data_processing: CEL files generated using Affymetrix GeneChip Command Console (v3.0) software were normalized using RMA and the MBNI custon CDF (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF/). Quality control consisted of the various RMA QC parameters as well as visual inspection of residual plots created in RMA express. Two samples did not meet these quality criteria.

source_name: CsA mid 11d

label_protocol: According to the protocol provided with the Affymetrix 3'IVT Express Labeling Kit (#901229)

extract_protocol: Upon sacrifice, liver was immediately dissected. Central half of the left lateral lobe was collected in RNA later and kept for a maximum of one week at 4 oC and frozen at -80 oC until use for RNA isolation. RNA was isolated using the RNeasy Mini Kit.

treatment_protocol: Mice treated for 1, 4, 11 days with vehicle (olive oil) or 3, 8.9, or 26.7 mg/kg BW CsA

value: male

value: 10 weeks

tag: weight

value: 8.9 mg/kg BW Csa

tag: time


title: olive oil 1d 101253-59

description: quality control: approved

source_name: CsA v 1d

value: olive oil


title: BACH2+/+ ALL (Sample2)


title: 3 mg/kg BW Csa 1d 101253-57

description: quality control: approved

source_name: CsA low 1d

value: 3 mg/kg BW Csa


title: 8.9 mg/kg BW Csa 4d 101253-56

description: quality control: approved

source_name: CsA mid 4d


title: 26.7 mg/kg BW Csa 11d 101253-53

description: quality control: approved

source_name: CsA high 11d

value: 26.7 mg/kg BW Csa


title: olive oil 4d 101253-55

description: quality control: approved

source_name: CsA v 4d


title: ML_ALV-J infected_32W_rep4


title: 8.9 mg/kg BW Csa 1d 101253-60

description: quality control: approved

source_name: CsA mid 1d


title: ML_ALV-J infected_32W_rep1


title: 3 mg/kg BW Csa 4d 101253-54

description: quality control: approved

source_name: CsA low 4d


title: olive oil 11d 101253-49

description: quality control: approved

source_name: CsA v 11d


title: olive oil 1d 101253-51

description: quality control: approved


title: 3 mg/kg BW Csa 1d 101253-46

description: quality control: approved


title: 8.9 mg/kg BW Csa mid 101253-52

description: quality control: approved

source_name: 11d mid

value: mid


title: ML_ALV-J infected_32W_rep2


title: 8.9 mg/kg BW Csa 1d 101253-48

description: quality control: approved


title: olive oil 4d 101253-44

description: quality control: approved


title: Nom-tum_control_32w_rep1

description: Gene expression of non-ALV-J infected nonneoplastic tissue of chicken liver

source_name: Nonneoplastic liver, non-ALV-J infected, 32 week age, replicate 1

value: control


title: 8.9 mg/kg BW Csa 11d 101253-50

description: quality control: approved


title: Spherules at day 8 biological replicate 3

city: London

first: Akul

last: Singhania

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Gene expression data from spherule form 8 days post-inocculation with arthroconidia of C. immitis

hyb_protocol: Cy3 labeled cDNA was hybridized to custom Nimblegen arrays according to the Nimblegen protocol.

scan_protocol: GeneChips were scanned using a  GenePix 4000B Axon Instruments scanner

data_processing: Once the microarray data passed quality control analysis, differentially expressed probes were identified between mycelium, day 2 spherule and day 8 spherule conditions using a one-way ANOVA and the Tukey post hoc test implemented in GeneSpring GX version 11.5 (Agilent Technologies Inc.)

organism: Coccidioides immitis RS

source_name: C. immitis RS strain spherule form

label_protocol: Double-stranded cDNA was synthesized from isolated RNA and labeled with Cy3 dye.

growth_protocol: C. immitis RS strain directly isolated from infected mice was grown on Mycosel agar (3.6% Mycosel agar, 0.5% yeast extract, and 50 µg/ml gentamicin). The plates were incubated at 30ºC until the mycelia covered the surface of the agar.

extract_protocol: Arthroconidia were harvested from the plate after 6 weeks of incubation at 25°C by adding 25 ml of saline. The plate was gently scraped using cell scraper and the fluid transferred to a 50 ml tube that was then vigorously mixed for 10 sec and centrifuged at 3000 rpm for 10 min. at 4 ºC.

value: spherule

tag: developmental stage

value: pathogenic


title: 26.7 mg/kg BW Csa 11d 101253-42

description: quality control: approved


title: Spherules at day 8 biological replicate 4

value: 8 days post-inocculation with arthroconidia of C. immitis


title: 26.7 mg/kg BW Csa 1d 101253-43

description: quality control: outlier

source_name: CsA high 1d


title: 26.7 mg/kg BW Csa 4d 101253-40

description: quality control: approved

source_name: CsA high 4d


title: Spherules at day 8 biological replicate 1


title: 3 mg/kg BW Csa 11d 101253-41

description: quality control: approved

source_name: CsA low 11d


title: Nom-tum_control_32w_rep3


title: Spherules at day 2 biological replicate 3

description: Gene expression data from spherule form 2 days post-inocculation with arthroconidia of C. immitis


title: Nom-tum_control_32w_rep2


title: olive oil 11d 101253-39

description: quality control: approved

source_name: 11d con


title: M. plumulosa-400 ppb Nickel- 5

city: Bangor

first: Sharon

middle: E.

last: Hook

state: NSW

address: Private Mail Bag 7

department: Centre for Environmental Contaminants Research

country: Australia

institute: CSIRO

hyb_protocol: Microarray hybridizations were performed at the Ramaciotti Centre for Gene Function analysis (University of New South Wales, Sydney, Australia) following Agilent’s protocols.

scan_protocol: Data files were generated using Agilent’s feature extraction software

data_processing: Data were uploaded into GeneSpring 12.1 (Agilent) for subsequent analysis.

label: Cy 3

organism: Melita plumulosa

source_name: 400 ppb Nickel exposed

growth_protocol: As described in Simpson, S.L., Spadaro, D.A. (2011) Performance and sensitivity of rapid sublethal sediment toxicity tests with the amphipod Melita plumulosa and copepod Nitocra spinipes. Environ Toxicol Chem 30, 2326–2334.

extract_protocol: Organisms are homogenized in Trizol in MoBio's lysing matrix E with a fast prep system.  Extraction proceeded following the Trizol protocol, except that the aqueous phase was cleaned up using an Rneasy kit.

value: 10 pooled individual organisms

label: Cy 5

source_name: time matched unexposed reference organisms


title: 3 mg/kg BW Csa 4d 101253-45

description: quality control: approved


title: M. plumulosa-0.6% Diesel - 2

source_name: 0.6% Diesel exposed

label_protocol: Microarray hybridizations were performed at the Ramaciotti Centre for Gene Function analysis (University of New South Wales, Sydney, Australia) following Agilent’s protocols.

treatment_protocol: As described in Simpson, S.L., Spadaro, D.A. (2011) Performance and sensitivity of rapid sublethal sediment toxicity tests with the amphipod Melita plumulosa and copepod Nitocra spinipes. Environ Toxicol Chem 30, 2326–2334.


title: 8.9 mg/kg BW Csa 11d 101253-38

description: quality control: approved

source_name: CsA mid 11d


title: M. plumulosa-50 ppt Fipronil-4

source_name: 50 ppt Fipronil exposed


title: M. plumulosa-30 mg L-1 pw Ammonia- 4

source_name: 30 mg L-1 pw Ammonia exposed


title: M. plumulosa-0.3% Crude Oil - 1

source_name: 0.3% Crude Oil exposed


title: 3 mg/kg BW Csa 4d 101253-37

description: quality control: approved


title: Mycelium biological replicate 4

description: Gene expression data from mycelial form of C. immitis

source_name: C. immitis RS strain mycelium form

value: mycelium

value: dormant

value: baseline


title: Spherules at day 2 biological replicate 1

value: 2 days post-inocculation with arthroconidia of C. immitis


title: Spherules at day 2 biological replicate 2


title: Spherules at day 2 biological replicate 4


title: olive oil 1d 101253-36

description: quality control: approved

source_name: CsA v 1d

value: liver


title: olive oil 4d 101253-35

description: quality control: approved

source_name: CsA v 4d

value: male


title: Spherules at day 8 biological replicate 2


title: 8.9 mg/kg BW Csa 1d 101253-34

description: quality control: approved

source_name: CsA mid 1d

value: 10 weeks


title: Mycelium biological replicate 2


title: Liver-AHCYmut-6

city: Philadelphia

first: Randolph

last: Matthews

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics/GI

institute: The Children's Hospital of Philadelphia Research Institute

description:
Gene expression data from liver of 4 dpf ahcy mutant larva
M6

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45 °C on GeneChip Zebrafish Genome arrays.  GeneChips were washed and stained in the Affymetrix Fludics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000, 7G

data_processing: Probe-level data in CEL files was normalized using GCRMA method implemented in Partek Genomics Suite to get gene-level expression measurements

organism: Danio rerio

source_name: liver of 4 dpf ahcy mutant larva

label_protocol: RNA was amplified twice and then labeled with Cy3 in accordance with Affymetrix standard protocol

growth_protocol: Embryos/larvae were grown at 28 °C in E3 as per standard practice

extract_protocol: At 4 dpf, larvae were treated with tricaine and livers were removed using thin forceps, and then placed into RNAlater

treatment_protocol: At 2 dpf, azacytidine (1 mM) or vehicle was injected into the yolk

value: ahcy -/-

tag: agent

value: vehicle

value: 4 dpf larva


title: M. plumulosa-400 ppb Zinc- 5

source_name: 400 ppb Zinc exposed

tag: tissue


title: Mycelium biological replicate 3


title: Liver-Azacytidine-6

description:
Gene expression data from liver of 4 dpf larva treated with azacytidine
A6

tag: genotype/variation

value: ahcy +/+

value: azacytidine


title: M. plumulosa-400 ppb Nickel- 3


title: M. plumulosa-50 ppt Fipronil- 3


title: Liver-AHCYmut-4

description:
Gene expression data from liver of 4 dpf ahcy mutant larva
M4


title: 26.7 mg/kg BW Csa 1d 101253-31

description: quality control: approved

source_name: CsA high 1d

value: 26.7 mg/kg BW Csa


title: Liver-AHCYmut-3

description:
Gene expression data from liver of 4 dpf ahcy mutant larva
M3


title: 8.9 mg/kg BW Csa 4d 101253-32

description: quality control: approved

source_name: CsA mid 4d

value: 8.9 mg/kg BW Csa


title: 26.7 mg/kg BW Csa 4d 101253-29

description: quality control: approved

source_name: CsA high 4d


title: Mycelium biological replicate 1


title: M. plumulosa-30 mg L-1 pw Ammonia- 3,2


title: M. plumulosa-0.3% Crude Oil - 4


title: M. plumulosa-250 ppb copper - 3

source_name: 250 ppb copper exposed


title: M. plumulosa-400 ppb Zinc- 1


title: Liver-Azacytidine-5

description:
Gene expression data from liver of 4 dpf larva treated with azacytidine
A5


title: M. plumulosa-400 ppb Zinc- 4


title: 3 mg/kg BW Csa 11d 101253-27

description: quality control: approved

source_name: CsA low 11d

value: 3 mg/kg BW Csa


title: M. plumulosa-100 ppt bifenthrin- 1,2

source_name: 100 ppt Bifentrhin exposed

source_name: time matched unexposed reference organisms


title: Liver-Azacytidine-2

description:
Gene expression data from liver of 4 dpf larva treated with azacytidine
A2


title: M. plumulosa-50 ppt Fipronil-1


title: Liver-Azacytidine-1

description:
Gene expression data from liver of 4 dpf larva treated with azacytidine
A1


title: M. plumulosa-0.6% Diesel - 4

source_name: 0.6% Diesel exposed


title: olive oil 11d 101253-28

description: quality control: approved

source_name: CsA v 11d

value: olive oil


title: M. plumulosa-250 ppb copper - 1

value: 10 pooled individual organisms


title: olive oil 1d 101253-25

description: quality control: approved


title: 3 mg/kg BW Csa 11d 101253-26

description: quality control: approved

source_name: 11d low


title: Liver-Control-4

description:
Gene expression data from liver of 4 dpf control larva
C4

source_name: liver of 4 dpf control larva


title: Liver-Control-8

description:
Gene expression data from liver of 4 dpf control larva
C8


title: 26.7 mg/kg BW Csa 11d 101253-30

description: quality control: approved

source_name: CsA high 11d


title: Liver-Control-2

description:
Gene expression data from liver of 4 dpf control larva
C2


title: MYC in Ph+ ALL (MIG2)

source_name: Total RNA from Ph+ ALL (C57Bl6)

value: 4 weeks

tag: cell type

value: BCR-ABL1 transformed pre-B cells

value: BCR-ABL1-driven ALL

value: Conditional Myc Knockout

value: pMIG


title: M. plumulosa-0.3% Crude Oil - 5

source_name: 0.3% Crude Oil exposed


title: Liver-Control-1

description:
Gene expression data from liver of 4 dpf control larva
C1

value: liver


title: M. plumulosa-30 mg L-1 pw Ammonia- 3

source_name: 30 mg L-1 pw Ammonia exposed


title: 8.9 mg/kg BW Csa 11d 101253-23

description: quality control: approved

source_name: CsA mid 11d

value: male

value: 10 weeks


title: 3 mg/kg BW Csa 1d 101253-22

description: quality control: approved

source_name: CsA low 1d


title: M. plumulosa-400 ppb Zinc- 3

source_name: 400 ppb Zinc exposed


title: M. plumulosa-100 ppt bifenthrin- 2


title: 26.7 mg/kg BW Csa 11d 101253-21

description: quality control: approved


title: olive oil 4d 101253-24

description: quality control: approved

source_name: CsA v 4d


title: M. plumulosa-50 ppt Fipronil- 2

source_name: 50 ppt Fipronil exposed


title: 3 mg/kg BW Csa 4d 101253-20

description: quality control: approved

source_name: CsA low 4d


title: M. plumulosa-250 ppb copper - 2

source_name: 250 ppb copper exposed


title: 8.9 mg/kg BW Csa 4d 101253-17

description: quality control: approved

source_name: CsA mid 4d


title: Leaf local, biological rep2

city: Rehovot

first: Robert

last: Fluhr

address: Hertzel st. 234

department: Plant science

country: Israel

institute: Weizmann institute of science

description: Gene expression data from from wounded leaves (local) or neighboring unwounded leaves (systemic) subsequently (10 min) after wounding .

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 5 minutes (N.B. this deviates from Affy SOP). • Transfer 200 μl of hyb solution to each array, then tape holes with parafilm. Hybridize 16 hours at 45° at 60rpm• Fluidics washing protocol is FS450_0004.

scan_protocol: GeneChips were scanned using the Affymetrix Gene ChIP Scanner 3000 7G.

data_processing: Analyzed with Affymetrix Expression Console, algorithm used for analysis- RMA, program-version = 1.1.2800.19935

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf 10 min after wounding (local)

label_protocol: Synthesis of cDNA was performed using the GeneChip Expression 3'-Amplification One-Cycle cDNA Synthesis Kit (Affymetrix, #900431). A starting amount of 6 ug total RNA was used for each sample. Purification of double-stranded cDNA was performed using the GeneChip Sample Clean-up Module (Affymetrix, #900371). Purified cRNA was enzymatically fragmented and biotinylated using GeneChip IVT Labeling Kit (Affymetrix, #900449).

growth_protocol: Arabidopsis ( 5 weeks old plants) were grown in soil  under white light illumination in a 10-h-light/14-h-dark cycle at 21°C.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen,7 4904) according to manufacturer's instructions.

treatment_protocol: Three rosette leaves of 5 weeks old plants were wounded by clamping them with tweezers across the midvein. 10 min after wounding a pool of local leaves (L) (wounded leaves from 3 plants ), a pool of systemic leaves (S) (unwounded leaves from 3 wounded plants) and a pool of control leaves (C) (a pool of leaves from 3 unwounded plants) were harvested and immersed in liquid nitrogen for subsequant RNA extraction and hybridization on Affymetrix microarrays.

value: vegetative leaf

tag: ecotype

value: Colombia

tag: growth condition

value: plants were grown in a 10-h-light/14-h-dark cycle at 21°C for 5 weeks


title: Leaf systemic, biological rep1

source_name: Arabidopsis leaf 10 min after wounding of a neighbor leaf (systemic)


title: 8.9 mg/kg BW Csa 1d 101253-18

description: quality control: approved

source_name: CsA mid 1d

tag: age


title: 26.7 mg/kg BW Csa 4d 101253-19

description: quality control: approved

source_name: CsA high 4d

tag: strain


title: Leaf systemic, biological rep2


title: M. plumulosa-30 mg L-1 pw Ammonia- 1

source_name: time matched unexposed reference organisms


title: M. plumulosa-100 ppt bifenthrin- 4

source_name: 100 ppt Bifentrhin exposed


title: olive oil 11d 101253-14

description: quality control: approved

source_name: CsA v 11d


title: 3 mg/kg BW Csa 11d 101253-15

description: quality control: approved

source_name: CsA low 11d


title: M. plumulosa-100 ppt bifenthrin- 4,2


title: Leaf control, biological rep2

source_name: Arabidopsis leaf control


title: Leaf local, biological rep1


title: M. plumulosa-0.3% Crude Oil - 3

source_name: 0.3% Crude Oil exposed


title: M. plumulosa-400 ppb Zinc-2


title: M. plumulosa-100 ppt bifenthrin- 1


title: 26.7 mg/kg BW Csa 1d 101253-16

description: quality control: approved

source_name: CsA high 1d


title: 26.7 mg/kg BW Csa 11d 101253-11

description: quality control: approved

source_name: CsA high 11d


title: M. plumulosa-250 ppb copper -5


title: M. plumulosa-50 ppt Fipronil- 5


title: 8.9 mg/kg BW Csa 11d 101253-13

description: quality control: approved

source_name: CsA mid 11d


title: 26.7 mg/kg BW Csa 4d 101253-10

description: quality control: approved


title: olive oil 1d 101253-12

description: quality control: approved

source_name: CsA v 1d


title: 26.7 mg/kg BW Csa 1d 101253-08

description: quality control: approved


title: 3 mg/kg BW Csa 4d 101253-09

description: quality control: approved

source_name: CsA low 4d


title: M. plumulosa-0.6% Diesel - 3

source_name: 0.6% Diesel exposed


title: olive oil 4d 101253-07

description: quality control: approved

source_name: CsA v 4d


title: Leaf control, biological rep1


title: M. plumulosa-0.6% Diesel - 1


title: M. plumulosa-400 ppb Nickel- 4

source_name: 400 ppb Nickel exposed


title: M. plumulosa-400 ppb Nickel- 1


title: 3 mg/kg BW Csa 1d 101253-05

description: quality control: approved

source_name: CsA low 1d


title: M. plumulosa-0.6% Diesel - 5


title: 3 mg/kg BW Csa 11d 101253-06

description: quality control: approved


title: 26.7 mg/kg BW Csa 11d 101253-04

description: quality control: approved

source_name: 11d high


title: M. plumulosa-0.3% Crude Oil - 2


title: DKD+ 4

city: Miami

first: Sandra

last: Merscher-Gomez

address: 1580 NW 10th Avenue

institute: University of Miami

description:
SAMPLE 6
replicate 2

data_processing: The data were normalised using quantile normalisation method and log2 transformed GeneSpring GX (v.11.02) and Batch Corrected in R/bioconductor (v.2.10.1) using Combat algorithm

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Normal human podocytes were differentiated for 14 days at 37C.

extract_protocol: RNA was isolated using the Nirvana kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Differentiated human podocytes were treated with the 4% serum of the patients for 24h.

tag: cell line

value: differentiated human podocytes

tag: treated with

value: serum from patients with diabetes and kidney disease (DKD+) for 24hr


title: M. plumulosa-400 ppb Nickel- 2


title: olive oil 11d 101253-02

description: quality control: approved


title: DKD- 4

description:
SAMPLE 4
replicate 2

value: serum from patients with diabetes and without kidney disease (DKD-) for 24hr


title: DKD+ 2

description:
SAMPLE 6
replicate 2


title: DKD- 2

description:
SAMPLE 4
replicate 2


title: 8.9 mg/kg BW Csa 4d 101253-03

description: quality control: approved

source_name: CsA mid 4d

value: 8.9 mg/kg BW Csa


title: M. plumulosa-250 ppb copper - 4

source_name: 250 ppb copper exposed

source_name: time matched unexposed reference organisms


title: C 2

description:
SAMPLE 2
replicate 2

source_name: podocytes_control serum

value: serum from patients without diabetes (C) for 24hr


title: KO TAM replicate 3

status: Public on Jul 10 2013

city: Columbus

first: Tsonwin

last: Hai

state: OH

address: 1060 Carmack Road #148

department: Molecular and Cellular Biochemistry

institute: Ohio State University

description: Gene expression of tumor macrophages isolated by FACS from tumors generated by orthotopic implantation of PyMT breast cancer cells.

hyb_protocol: After purification, Cy3-labeled cRNA was hybridized to the Whole Mouse Genome Oligo Microarray (G4122F; Agilent Technologies) per the manufacturers instructions.

scan_protocol: Microarray slides were washed and scanned with an Agilent G2505C Microarray Scanner.

data_processing: Images were analyzed with Feature Extraction 10.5 (Agilent Technologies), and median intensity values for each probe on the array were imported into the mathematical software package “R.”  The intensity values were corrected for scanner offset but not background corrected.  The dataset was then filtered to remove signals from positive control probes and any elements that have been flagged as outliers.  Using the negative controls on the arrays, the background threshold was determined and all values less than this value were set to the threshold value.  Finally, the data were normalized using the Quantile Normalization package in “R.”

source_name: ATF3 knockout tumor-associated macrophage replicate 3

label_protocol: 250 ng of total RNA was amplified and labeled with cyanine-3 (Cy3) using the Low Linear Amplification Kit (Agilent Technologies) according to the manufacturers instructions.

growth_protocol: Tumor-associated macrophages were isolated by FACS from breast tumors generated in C57BL/6 mice (WT or ATF3 KO) by orthotopic implantation of PyMT breast cancer cells.  The isolation was carried out ~21 days after tumor cell implantation.

extract_protocol: Total RNA was prepared from TRIzol-lysed cells by chloroform extraction according to the manufacturer instructions.  The upper aqueous phase was mixed with 1 volume of 70% ethanol and applied to an RNeasy column (Qiagen).  RNA was prepared according to the manufacturers instructions and quantitated.  The concentration of the samples provided was determined using the NanoDrop® ND-1000 UV-Vis Spectrophotometer. RNA samples were analyzed  using an Agilent 2100 Bioanalyzer Lab-On-A-Chip Agilent 6000 Series II chip to determine the integrity of the samples.

value: breast tumor-associated macrophage

tag: genotype

value: ATF3 knockout


title: KO TAM replicate 4

source_name: ATF3 knockout tumor-associated macrophage replicate 4


title: M. plumulosa-30 mg L-1 pw Ammonia- 2

source_name: 30 mg L-1 pw Ammonia exposed

value: 10 pooled individual organisms


title: C 4

description:
SAMPLE 2
replicate 2


title: DKD+ 3

description:
SAMPLE 5
replicate 1


title: KO TAM replicate 1

source_name: ATF3 knockout tumor-associated macrophage replicate 1


title: 8.9 mg/kg BW Csa 1d 101253-01

description: quality control: approved

source_name: CsA mid 1d


title: DKD+ 1

description:
SAMPLE 5
replicate 1


title: DKD- 1

description:
SAMPLE 3
replicate 1


title: DKD- 3

description:
SAMPLE 3
replicate 1


title: C 1

description:
SAMPLE 1
replicate 1


title: KO TAM replicate 2

source_name: ATF3 knockout tumor-associated macrophage replicate 2


title: WT TAM replicate 3

source_name: Wild type tumor-associated macrophage replicate 3

value: wild type


title: C 3

description:
SAMPLE 1
replicate 1


title: WT TAM replicate 4

source_name: Wild type tumor-associated macrophage replicate 4


title: WT TAM replicate 1

source_name: Wild type tumor-associated macrophage replicate 1


title: WT TAM replicate 2

source_name: Wild type tumor-associated macrophage replicate 2


title: Heart_BXD-5/TyJ ISO

first: Christoph

middle: Daniel

last: Rau

state: United States

address: 675 Charles E Young Drive S

institute: UCLA

data_processing:
GenomeStudio V2010.3 (Gene Expression 1.8.0 module).
Ddata was analyzed using the limma R package.

source_name: Left Ventricle, 10 wks

extract_protocol: total RNA was extracted using the Quiagen miRNAeasy 96-well kits using standard protocol.  RNA integrity was determined using an Agilent Bioanalyzer

treatment_protocol: Starting at 8-9 weeks, mice were treated for 3 weeks with 30 ug/g body weight/ day of Isoproterenol or were untreated controls for the same period of time

value: female

value: Isoproterenol

value: Left Ventricle


title: Heart_BXH-6/TyJ ISO


title: Heart_BXD-39/TyJ_2

value: untreated


title: control islets, e19, replicate 4

first: Lane

middle: Johanna

last: Jaeckle Santos

address: 421 Curie Blvd, BRB II/III 1341

department: CRRWH

institute: University of Pennsylvania School of Medicine

description: control sham surgery e19 rat islets, pooled from 1 litter

hyb_protocol: standard protocol for Rat Gene 1.0 ST

scan_protocol: standard protocol for Rat Gene 1.0 ST

data_processing: RMA, then samr v2.0

organism: Rattus norvegicus

source_name: control sham surgery rat islets, pooled from 1 litter

label_protocol: GeneChip WT terminal labeling kit

growth_protocol: 8 timed pregnant dams purchased from Charles River Laboratories

extract_protocol: Total RNA was isolated from pooled fetal islets at e19 (n=4 different litters per treatment) using RNAzol B.

treatment_protocol: 4 dams were underwent IUGR surgery, 4 dams underwent sham surgery on e18.

value: Sprague-Dawley

value: pancreatic islet


title: Heart_BXD-31/TyJ ISO


title: IUGR islets, e19, replicate 3

description: IUGR surgery e19 rat islets, pooled from 1 litter

source_name: IUGR surgery rat islets, pooled from 1 litter


title: IUGR islets, e19, replicate 1

value: IUGR surgery e19 rat islets, pooled from 1 litter


title: Heart_BXD-6/TyJ ISO


title: Heart_BXD-20/TyJ ISO


title: Heart_BXH-6/TyJ


title: control islets, e19, replicate 3

value: control sham surgery e19 rat islets, pooled from 1 litter


title: Heart_BXA-12/PgnJ


title: control islets, e19, replicate 2


title: IUGR islets, e19, replicate 4


title: Heart_BXD-5/TyJ


title: Heart_BXH-9/TyJ


title: Heart_BXD-1/TyJ


title: IUGR islets, e19, replicate 2


title: Heart_PL/J ISO_2

value: PL/J


title: control islets, e19, replicate 1


title: Heart_NOD/LtJ ISO_2

value: NOD/LtJ


title: Heart_FVB/NJ ISO_2

value: FVB/NJ


title: Heart_A/J ISO_2

value: A/J


title: Heart_BXHA1 ISO


title: Heart_MA/MyJ ISO

value: MA/MyJ


title: Heart_BXD-19/TyJ ISO


title: Heart_BXH-9/TyJ ISO


title: Heart_BXD-20/TyJ


title: Heart_AXB-12/PgnJ


title: Heart_BXD86


title: Heart_C58/J ISO


title: Heart_CXBH

value: CXBH


title: Heart_CXB-13/HiAJ


title: Heart_CXBH ISO


title: 009_179_045_neutro_D1

city: Dallas

first: Damien

last: Chaussabel

state: TX

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description:
Cell Subsets
5445279042_F

hyb_protocol: Hybridization to HumanHT-12 v3 Expression BeadChip as per Illumina protocol

scan_protocol: Illumina BeadStation 500 SentrixScanVersion 2.3.0.13

data_processing: Following background subtraction, the raw signal intensities extracted with Illumina Genome Studio v2010.1 Gene Expression 1.6.0 software were scaled to the mean intensity of the dataset.

source_name: Neutrophils

label_protocol: Biotinylated cRNA were generated following manufacturer protocols using the Illumina TotalPrep Amplification Kit from Ambion

extract_protocol: RNA was isolated using the MagMAX™-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion, Austin, TX, USA) according to the manufacturer's instructions

tag: subject id

tag: day

tag: vaccine

value: Pneumovax vaccine group

value: neutrophils

value: M

tag: race

value: Caucasian

tag: ethnicity

value: Not Hispanic or Latino


title: Heart_BXD-12/TyJ

tag: gender

value: female

value: Left Ventricle


title: Heart_BXD69

tag: agent

value: untreated


title: Heart_BXHB2

tag: tissue


title: 009_179_048_neutro_D1

description:
Cell Subsets
5445279040_J

value: F

value: Hispanic


title: Heart_CXB-12/HiAJ ISO

value: Isoproterenol


title: Heart_BXD-11/TyJ ISO


title: Heart_CXB-12/HiAJ


title: Heart_BXHB2 ISO


title: 009_179_045_neutro_D0

description:
Cell Subsets
5445279021_J


title: 009_179_040_neutro_D1

description:
Cell Subsets
5445279040_C

value: Influenza vaccine group

value: African American


title: 009_179_039_neutro_D0

description:
Cell Subsets
5445279042_I


title: Heart_BXA-8/PgnJ ISO


title: 009_179_039_neutro_D1

description:
Cell Subsets
5445279021_K


title: Heart_BXD-11/TyJ


title: Heart_BXD-12/TyJ ISO


title: 009_179_040_neutro_D0

description:
Cell Subsets
5445279042_C


title: brain 130 wks rep 2

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

institute: University of Amsterdam

hyb_protocol: The labeled cDNA was hybridized to the Mouse GeneChip 430 2.0 (Affymetrix, Santa Clara, CA, USA). The GeneChip Hybridization, Wash and Stain Kit (Affymetrix, CA) was used for the hybridizations according to the protocol of the manufacturer.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 HR GeneChip Scanner and GCOS

data_processing: The data were analyzed with the R statistical programming language (http://cran.r-project.org/) and the bioconductor affy package. The raw data were annotated according de Leeuw et al. (2008; BMC Res Notes. 19: 1-66 (hence the odd probeset identifiers)) and normalized using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003; Biostatistics 4: 249-264). Please note that we corrected the data for labelling-batch effects in the paper.

source_name: brain 130 wks

label_protocol: In short, biotin-labeled cRNA samples were prepared as described in the Affymetrix expression analysis technical manual (Affymetrix) using 3 μg of purified total RNA as template for the reaction. For this the One-Cycle cDNA Synthesis Kit (Affymetrix) was used.

growth_protocol: Female C57BL6/J mice were marked and randomized at the day of birth in different groups; i.e. longevity cohorts (previously described in Wijnhoven et al. (2005; DNA Repair (Amst) 4: 1314-1324.), or cross-sectional cohorts in which the mice were sacrificed at fixed time points. Cross-sectional cohorts C57BL6/J mice were sacrificed at a fixed age of 13, 26, 52, 78, 104 and 130 weeks. During the entire experiment, animals were kept in the same stringently controlled pathogen free (spf) environment, fed ad libitum and kept under a normal day/night rhythm. The microbiological status of the cohorts was monitored every 3 months.

extract_protocol: Total RNA was isolated from liver, kidney, spleen, lung and brain, using the RNeasy Midi Kit (Qiagen, Valencia, CA, USA;). RNA quality was tested using automated gel electrophoresis (Bioanalyzer 2100; Agilent technologies, Amstelveen, the Netherlands). Only RIN > 7 were processed further.

value: brain

value: 130 wks


title: brain 130 wks rep 3


title: Heart_BXA-8/PgnJ


title: brain 104 wks rep 3

source_name: brain 104 wks

value: 104 wks


title: brain 130 wks rep 1


title: 009_179_044_neutro_D0

description:
Cell Subsets
5445279021_F


title: brain 104 wks rep 2


title: brain 104 wks rep 1


title: brain 78 wks rep 3

source_name: brain 78 wks

value: 78 wks


title: Heart_BXA-1/PgnJ ISO


title: 009_179_042_neutro_D1

description:
Cell Subsets
5445279019_I


title: 009_179_042_neutro_D0

description:
Cell Subsets
5445279021_I


title: 009_179_048_neutro_D0

description:
Cell Subsets
5445279019_A

value: Pneumovax vaccine group


title: Heart_BXA-1/PgnJ


title: Heart_AXB-8/PgnJ  ISO


title: brain 78 wks rep 1


title: brain 78 wks rep 2


title: Heart_BXA-11/PgnJ ISO


title: 009_179_046_neutro_D1

description:
Cell Subsets
5445279019_C

value: neutrophils


title: Heart_BXA-11/PgnJ


title: brain 52 wks rep 2

source_name: brain 52 wks

value: 52 wks


title: Heart_KK/HlJ

value: KK/HlJ


title: Heart_AXB-6/PgnJ


title: Heart_KK/HlJ ISO


title: 009_179_041_neutro_D0

description:
Cell Subsets
5376074057_L

value: M

value: Caucasian

value: Not Hispanic or Latino


title: Heart_AXB-6/PgnJ ISO

value: female

value: Left Ventricle


title: Heart_AXB-4/PgnJ  ISO


title: Heart_DBA/2J ISO_2


title: 009_179_047_neutro_D1

description:
Cell Subsets
5376074057_K


title: Heart_AXB-8/PgnJ_2

value: untreated


title: brain 52 wks rep 3


title: 009_179_041_neutro_D1

description:
Cell Subsets
5445279043_H


title: brain 52 wks rep 1


title: brain 26 wks rep 2

source_name: brain 26 wks

value: 26 wks


title: Heart_DBA/2J_2


title: 009_179_047_neutro_D0

description:
Cell Subsets
5376074057_I


title: brain 26 wks rep 3


title: Heart_CXB-7/ByJ ISO

value: Isoproterenol


title: Heart_BXD-34/TyJ


title: Heart_CXB-7/ByJ


title: Heart_CBA/J_2

value: CBA/J


title: Heart_CXB-6/ByJ


title: 009_179_046_neutro_D0

description:
Cell Subsets
5376074055_F

value: F


title: Heart_CXB-6/ByJ ISO


title: 009_179_043_neutro_D1

description:
Cell Subsets
5376074055_A

value: Influenza vaccine group


title: brain 26 wks rep 1

value: brain


title: brain 13 wks rep 3

source_name: brain 13 wks

value: 13 wks


title: Heart_BXA-14/PgnJ_2


title: 009_179_043_neutro_D0

description:
Cell Subsets
5376074055_K


title: Heart_BUB/BnJ_2

value: BUB/BnJ


title: Heart_BXA-24/PgnJ_2


title: brain 13 wks rep 2


title: Heart_AXB-19/PgnJ_2


title: 009_179_044_neutro_D1

description:
Cell Subsets
5376074055_B

value: neutrophils


title: 009_179_040_CD8_D0

description:
Cell Subsets
5445279043_A

source_name: CD8 T lymphocytes

value: African American


title: lung 130 wks rep 3

source_name: lung 130 wks

value: lung

value: 130 wks


title: 009_179_040_CD8_D1

description:
Cell Subsets
5445279042_H


title: 009_179_043_CD8_D0

description:
Cell Subsets
5445279042_D

value: Caucasian


title: Heart_AXB-4/PgnJ


title: brain 13 wks rep 1


title: Heart_AXB-18/PgnJ_2


title: Heart_129X1/SvJ_2


title: Heart_NON/LtJ

value: NON/LtJ


title: 009_179_045_CD8_D0

description:
Cell Subsets
5445279042_B

value: Pneumovax vaccine group

value: M

value: Not Hispanic or Latino


title: lung 130 wks rep 2


title: Heart_NZB/BlNJ ISO

value: female

value: NZB/BlNJ

value: Left Ventricle


title: Heart_LG/J

value: LG/J

value: untreated


title: Heart_NZB/BlNJ


title: lung 130 wks rep 1


title: Heart_LP/J

value: LP/J


title: Heart_NON/LtJ ISO

value: Isoproterenol


title: 009_179_042_CD8_D0

description:
Cell Subsets
5445279040_G

value: Influenza vaccine group


title: Heart_CXB-3/ByJ


title: Heart_CXB-13/HiAJ ISO


title: Heart_LP/J ISO


title: Heart_LG/J ISO


title: 009_179_041_CD8_D0

description:
Cell Subsets
5445279040_B


title: 009_179_048_CD8_D0

description:
Cell Subsets
5445279040_L

value: F

value: Hispanic


title: Heart_CXB-3/ByJ ISO


title: 009_179_046_CD8_D1

description:
Cell Subsets
5445279040_D


title: Heart_CXB-11/HiAJ ISO


title: lung 104 wks rep 1

source_name: lung 104 wks

value: lung

value: 104 wks


title: lung 104 wks rep 3


title: Heart_CE/J

value: CE/J


title: Heart_CE/J ISO


title: Heart_CXB-11/HiAJ


title: 009_179_046_CD8_D0

description:
Cell Subsets
5445279021_L

value: Caucasian


title: lung 104 wks rep 2


title: Heart_C57BLKS/J ISO


title: lung 78 wks rep 2

source_name: lung 78 wks

value: 78 wks


title: 009_179_047_CD8_D0

description:
Cell Subsets
5445279019_K

value: Pneumovax vaccine group

value: M


title: Heart_BXD84 ISO

value: female


title: Heart_C57BLKS/J


title: lung 52 wks rep 3

source_name: lung 52 wks

value: 52 wks


title: lung 78 wks rep 3


title: 009_179_044_CD8_D1

description:
Cell Subsets
5445279019_J

value: Not Hispanic or Latino


title: Heart_BXD84

value: Left Ventricle


title: Heart_BXD79 ISO


title: 009_179_047_CD8_D1

description:
Cell Subsets
5445279019_G


title: 009_179_045_CD8_D1

description:
Cell Subsets
5445279019_F


title: lung 52 wks rep 1


title: Heart_BXD79

value: untreated


title: Heart_BXD74 ISO


title: Heart_BXD75


title: 009_179_042_CD8_D1

description:
Cell Subsets
5445279021_B


title: lung 26 wks rep 3

source_name: lung 26 wks

value: 26 wks


title: 009_179_043_CD8_D1

description:
Cell Subsets
5376074057_G


title: Heart_BXD75 ISO

value: Isoproterenol


title: 009_179_044_CD8_D0

description:
Cell Subsets
5376074057_H

value: Influenza vaccine group


title: lung 78 wks rep 1


title: Heart_BXD74


title: Heart_BXD45 ISO


title: lung 52 wks rep 2


title: lung 26 wks rep 2


title: Heart_BXD48


title: 009_179_048_CD8_D1

description:
Cell Subsets
5376074057_D

value: F


title: lung 26 wks rep 1


title: Heart_BXD44


title: Heart_BXD48 ISO


title: 009_179_039_CD8_D0

description:
Cell Subsets
5376074055_J


title: 009_179_039_CD8_D1

description:
Cell Subsets
5376074055_C


title: 009_179_041_CD8_D1

description:
Cell Subsets
5376074055_E


title: lung 13 wks rep 3

source_name: lung 13 wks

value: 13 wks


title: Heart_BXD45

source_name: Left Ventricle, 10 wks


title: spleen 130 wks rep 3

source_name: spleen 130 wks

value: spleen

value: 130 wks


title: Heart_BXD43 ISO


title: Heart_C57BL/6J ISO_2


title: lung 13 wks rep 2

value: lung


title: Heart_BXD87 ISO


title: Heart_BXH-19/TyJ ISO


title: lung 13 wks rep 1


title: Heart_BXH-19/TyJ


title: Heart_BXD87


title: Heart_BXD43


title: Heart_C57BL/6J_2


title: 009_179_040_CD4_D1

description:
Cell Subsets
5445279043_D

source_name: CD4 T lymphocytes

value: African American


title: Heart_BXD44 ISO


title: Heart_BXD85 ISO


title: Heart_BXD-14/TyJ ISO


title: spleen 130 wks rep 2


title: 009_179_044_CD4_D0

description:
Cell Subsets
5445279042_A

value: Caucasian


title: spleen 130 wks rep 1


title: Heart_BXD85


title: 009_179_043_CD4_D1

description:
Cell Subsets
5445279043_C


title: Heart_BXD-14/TyJ


title: 009_179_040_CD4_D0

description:
Cell Subsets
5445279042_E


title: Heart_BXA-7/PgnJ ISO


title: spleen 104 wks rep 3

source_name: spleen 104 wks

value: 104 wks


title: Heart_BXA-7/PgnJ


title: Heart_BXA-4/PgnJ


title: Heart_BXA-4/PgnJ ISO


title: Heart_SEA/GnJ ISO

value: SEA/GnJ


title: 009_179_042_CD4_D0

description:
Cell Subsets
5445279040_F

value: M


title: spleen 104 wks rep 1


title: spleen 78 wks rep 1

source_name: spleen 78 wks

value: 78 wks


title: Heart_SWR/J ISO

value: female

value: SWR/J


title: Heart_BXA-2/PgnJ

value: untreated

value: Left Ventricle


title: 009_179_042_CD4_D1

description:
Cell Subsets
5445279040_H

value: Not Hispanic or Latino


title: 009_179_044_CD4_D1

description:
Cell Subsets
5445279021_C

value: Influenza vaccine group


title: spleen 104 wks rep 2


title: spleen 78 wks rep 2


title: Heart_SM/J

value: SM/J


title: 009_179_047_CD4_D0

description:
Cell Subsets
5445279021_G

value: Pneumovax vaccine group


title: 009_179_043_CD4_D0

description:
Cell Subsets
5445279040_I

value: F


title: Heart_BXA-2/PgnJ ISO

value: Isoproterenol


title: Heart_SWR/J


title: 009_179_047_CD4_D1

description:
Cell Subsets
5445279019_L


title: Heart_SM/J ISO


title: spleen 78 wks rep 3

value: spleen


title: spleen 52 wks rep 3

source_name: spleen 52 wks

value: 52 wks


title: 009_179_041_CD4_D1

description:
Cell Subsets
5445279019_B

value: Caucasian


title: Heart_SEA/GnJ


title: spleen 52 wks rep 2


title: spleen 26 wks rep 3

source_name: spleen 26 wks

value: 26 wks


title: 009_179_041_CD4_D0

description:
Cell Subsets
5376074057_A


title: Heart_BXD71 ISO


title: Heart_NZW/LacJ ISO

value: NZW/LacJ


title: Heart_BXD73


title: Heart_BXD73 ISO


title: Heart_BXD70


title: 009_179_043_CD14_D0

description:
Cell Subsets
5445279043_J

source_name: Monocytes


title: Heart_BXD71


title: 009_179_040_CD14_D1

description:
Cell Subsets
5445279043_F

value: African American


title: Heart_BXD-40/TyJ ISO_2


title: spleen 26 wks rep 2


title: 009_179_046_CD14_D1

description:
Cell Subsets
5445279043_B


title: Heart_BXD70 ISO


title: Heart_BXD68 ISO


title: spleen 52 wks rep 1


title: spleen 13 wks rep 3

source_name: spleen 13 wks

value: 13 wks


title: Heart_BXD68

value: female


title: 009_179_048_CD14_D0

description:
Cell Subsets
5445279042_L

value: Hispanic


title: Heart_BXD-38/TyJ

value: untreated


title: spleen 13 wks rep 2


title: Heart_BXD-38/TyJ ISO

value: Left Ventricle


title: Heart_BXD-32/TyJ ISO_2


title: 009_179_039_CD14_D0

description:
Cell Subsets
5445279042_K

value: M

value: Not Hispanic or Latino


title: Heart_BXD-40/TyJ_2


title: Heart_BXD-32/TyJ_2


title: Heart_NZW/LacJ


title: Heart_BXD-24/TyJ ISO


title: liver 130 wks rep 3

source_name: liver 130 wks

value: liver

value: 130 wks


title: Heart_BXD56


title: 009_179_042_CD14_D0

description:
Cell Subsets
5445279021_D

value: Influenza vaccine group


title: liver 104 wks rep 2

source_name: liver 104 wks

value: 104 wks


title: 009_179_044_CD14_D0

description:
Cell Subsets
5445279040_K

value: F


title: 009_179_042_CD14_D1

description:
Cell Subsets
5445279021_H


title: spleen 26 wks rep 1

value: spleen


title: liver 104 wks rep 3


title: Heart_BXD66


title: 009_179_041_CD14_D0

description:
Cell Subsets
5445279040_A

value: Caucasian


title: Heart_BXD66 ISO

value: Isoproterenol


title: 009_179_046_CD14_D0

description:
Cell Subsets
5445279021_E

value: Pneumovax vaccine group


title: Heart_BXD55


title: spleen 13 wks rep 1


title: 009_179_048_CD14_D1

description:
Cell Subsets
5445279019_E


title: Heart_BXD50


title: Heart_BXD62


title: Heart_BXD-24/TyJ


title: Heart_BXD55 ISO


title: Heart_BXD62 ISO


title: Heart_BXD50 ISO


title: Heart_BXD64 ISO


title: Heart_BXD56 ISO


title: 009_179_039_CD14_D1

description:
Cell Subsets
5445279042_G


title: Heart_BXD61


title: Heart_BXD49 ISO


title: liver 78 wks rep 1

source_name: liver 78 wks

value: 78 wks


title: Heart_BXD64


title: liver 104 wks rep 1


title: liver 78 wks rep 2


title: liver 52 wks rep 3

source_name: liver 52 wks

value: 52 wks


title: 009_179_047_CD14_D0

description:
Cell Subsets
5445279019_D


title: liver 130 wks rep 2


title: Heart_BALB/cJ

value: female

value: BALB/cJ


title: Heart_BXD49

value: untreated


title: Heart_BALB/cByJ ISO

value: BALB/cByJ

value: Left Ventricle


title: Heart_BTBRT<+>tf/J ISO

value: BTBRT<+>tf/J


title: 009_179_043_CD14_D1

description:
Cell Subsets
5376074057_F

value: Not Hispanic or Latino


title: liver 52 wks rep 1

value: liver


title: 009_179_047_CD14_D1

description:
Cell Subsets
5376074057_J

value: M


title: 009_179_040_CD14_D0

description:
Cell Subsets
5376074057_C

value: Influenza vaccine group

value: African American


title: Heart_BTBRT<+>tf/J


title: liver 26 wks rep 3

source_name: liver 26 wks

value: 26 wks


title: Heart_AXB-20/PgnJ


title: liver 130 wks rep 1

value: 130 wks


title: liver 13 wks rep 3

source_name: liver 13 wks

value: 13 wks


title: Heart_BXD61 ISO

value: Isoproterenol


title: 009_179_045_CD14_D1

description:
Cell Subsets
5376074057_E

value: Pneumovax vaccine group

value: Caucasian


title: Heart_AKR/J ISO

value: female

value: AKR/J


title: liver 26 wks rep 1


title: liver 52 wks rep 2

value: 52 wks


title: Heart_AXB10/PgnJ

value: untreated


title: liver 78 wks rep 3

value: 78 wks


title: Heart_BALB/cByJ

value: BALB/cByJ

value: Left Ventricle


title: Heart_AXB10/PgnJ ISO


title: Heart_BALB/cJ ISO

value: BALB/cJ


title: Heart_AXB-20/PgnJ ISO


title: 009_179_041_CD14_D1

description:
Cell Subsets
5376074055_H

value: M

value: Not Hispanic or Latino


title: 009_179_045_CD14_D0

description:
Cell Subsets
5376074055_G


title: Heart_129X1/SvJ


title: Heart_A/J

value: A/J


title: Heart_AKR/J


title: liver 26 wks rep 2

value: liver

value: 26 wks


title: 009_179_044_CD14_D1

description:
Cell Subsets
5376074057_B

value: Influenza vaccine group

value: F


title: kidney 130 wks rep 3

source_name: kidney 130 wks

value: kidney

value: 130 wks


title: liver 13 wks rep 1

value: 13 wks


title: Heart_129X1/SvJ ISO

value: female

value: Isoproterenol


title: Heart_A/J ISO


title: liver 13 wks rep 2


title: Heart_SJL/J

value: SJL/J

value: untreated


title: Heart_SJL/J ISO


title: Heart_RIIIS/J ISO

value: RIIIS/J