title: NEPAL-DBS-187

description:
9422487018_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-196

status: Public on Jul 27 2016

type: RNA

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

country: USA

institute: UCLA School of Medicine

description:
9422487045_B.AVG_Signal
Illumina Human HT-12 BeadArray

hyb_protocol: Standard Illumina hybridization protocol for NuGEN target (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All probe and gene values are provided, with no additional filtering.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood (PAXgene RNA)

label_protocol: NuGEN PicoSL target synthesis for gene expression profiling (carried out UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from primary peripheral blood samples (DBS) using Qiagen RNEasy reagents.

tag: childsoldier

tag: female

tag: age

tag: ethnicminority

tag: castelow

tag: educationlevel

tag: pts

tag: resilience

tag: tissue

value: whole blood


title: NEPAL-DBS-190

description:
9422487018_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-181

description:
9408455003_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-193

description:
9422487018_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-204

description:
9422487045_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-174

description:
9408455003_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-194

description:
9422487018_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-192

description:
9422487018_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-182

description:
9408455003_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-177

description:
9408455003_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-173

description:
9408455003_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-176

description:
9408455003_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-172

description:
9408455003_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-180

description:
9408455003_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-163

description:
9408455015_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-153

description:
9388254108_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-157

description:
9388254108_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-150

description:
9388254108_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-165

description:
9408455015_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-164

description:
9408455015_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-188

description:
9422487018_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-168

description:
9408455015_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-170

description:
9408455015_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-159

description:
9408455015_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-167

description:
9408455015_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-169

description:
9408455015_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-148

description:
9388254108_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-166

description:
9408455015_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-189

description:
9422487018_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-171

description:
9408455003_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-151

description:
9388254108_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-154

description:
9388254108_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-152

description:
9388254108_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-162

description:
9408455015_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-161

description:
9408455015_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-156

description:
9388254108_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-149

description:
9388254108_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-160

description:
9408455015_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-146

description:
9388254093_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-158

description:
9388254108_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-147

description:
9388254108_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-155

description:
9388254108_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-144

description:
9388254093_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-134

description:
9421898030_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-145

description:
9388254093_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-130

description:
9421898030_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-143

description:
9388254093_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-129

description:
9421898030_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-123

description:
9421898030_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-132

description:
9421898030_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-126

description:
9421898030_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-117

description:
9421898036_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-120

description:
9421898036_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-118

description:
9421898036_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-138

description:
9388254093_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-139

description:
9388254093_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-122

description:
9421898036_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-140

description:
9388254093_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-142

description:
9388254093_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-136

description:
9388254093_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-137

description:
9388254093_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-125

description:
9421898030_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-135

description:
9388254093_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-127

description:
9421898030_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-128

description:
9421898030_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-119

description:
9421898036_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-114

description:
9421898036_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-115

description:
9421898036_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-121

description:
9421898036_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-133

description:
9421898030_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-112

description:
9421898036_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-109

description:
9421898020_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-110

description:
9421898020_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-104

description:
9421898020_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-105

description:
9421898020_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-113

description:
9421898036_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-100

description:
9421898020_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-95

description:
9421742102_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-94

description:
9421742102_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-106

description:
9421898020_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-102

description:
9421898020_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-91

description:
9421742102_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-107

description:
9421898020_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-101

description:
9421898020_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-108

description:
9421898020_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-99

description:
9421898020_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-111

description:
9421898036_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-103

description:
9421898020_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-98

description:
9421742102_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-81

description:
9407205097_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-73

description:
9407205098_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-93

description:
9421742102_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-70

description:
9407205098_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-87

description:
9421742102_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-72

description:
9407205098_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-80

description:
9407205097_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-89

description:
9421742102_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-88

description:
9421742102_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-92

description:
9421742102_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-116

description:
9421898036_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-78

description:
9407205097_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-67

description:
9407205098_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-61

description:
9388254115_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-65

description:
9407205098_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-62

description:
9407205098_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-68

description:
9407205098_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-64

description:
9407205098_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-66

description:
9407205098_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-55

description:
9388254115_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-50

description:
9388254115_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-49

description:
9388254106_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-58

description:
9388254115_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-57

description:
9388254115_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-51

description:
9388254115_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-60

description:
9388254115_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-54

description:
9388254115_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-59

description:
9388254115_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-36

description:
9408455018_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-41

description:
9388254106_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-37

description:
9388254106_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-34

description:
9408455018_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-45

description:
9388254106_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-40

description:
9388254106_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-35

description:
9408455018_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-38

description:
9388254106_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-52

description:
9388254115_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-47

description:
9388254106_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-42

description:
9388254106_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-33

description:
9408455018_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-48

description:
9388254106_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-43

description:
9388254106_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-39

description:
9388254106_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-44

description:
9388254106_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-29

description:
9408455018_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-31

description:
9408455018_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-30

description:
9408455018_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-24

description:
9408455004_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-18

description:
9408455004_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-19

description:
9408455004_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-22

description:
9408455004_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-21

description:
9408455004_I.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-16

description:
9408455004_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-23

description:
9408455004_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-28

description:
9408455018_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-32

description:
9408455018_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-17

description:
9408455004_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-10

description:
9443362089_J.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-20

description:
9408455004_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-12

description:
9443362089_L.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-15

description:
9408455004_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-11

description:
9443362089_K.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-7

description:
9443362089_G.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-14

description:
9408455004_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-8

description:
9443362089_H.AVG_Signal
Illumina Human HT-12 BeadArray


title: LUC replicate 2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description:
expression data from whole heart from black 6 animals receiving TAC surgery and AAV-Luc virus
TAC_AAV_Luc_9_2

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Mogene-1_0-st-type from Affymetrix. A Custom CDF Version 14 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

organism: Mus musculus

source_name: LUC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Animals received Adenoassociated virus containing a indicated coding sequence with age of 8 weeks. After 4 weeks, animals received transaortic constriction.

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

treatment_protocol: After 4 weeks, animals were sacrificed and hearts were collected in liquid nitrogen

tag: strain

tag: surgery

value: TAC

tag: treatment

value: AAV-Luc

value: heart


title: NEPAL-DBS-6

description:
9443362089_F.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-3

description:
9443362089_C.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-5

description:
9443362089_E.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-13

description:
9408455004_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-2

description:
9443362089_B.AVG_Signal
Illumina Human HT-12 BeadArray


title: NEPAL-DBS-4

description:
9443362089_D.AVG_Signal
Illumina Human HT-12 BeadArray


title: LUC replicate 1

description:
expression data from whole heart from black 6 animals receiving TAC surgery and AAV-Luc virus
TAC_AAV_Luc_8_1


title: NT replicate 2

description:
expression data from whole heart from black 6 animals receiving TAC surgery and AAV-HDAC4 aimnoacids 1-201 virus
TAC_HDAC_NT_4_1

source_name: NT

value: HDAC-NT


title: NEPAL-DBS-1

description:
9443362089_A.AVG_Signal
Illumina Human HT-12 BeadArray


title: LUC replicate 3

description:
expression data from whole heart from black 6 animals receiving TAC surgery and AAV-Luc virus
TAC_AAV_Luc_9_3


title: sham replicate 3

description:
expression data from whole heart from black 6 animals receiving sham TAC surgery and AAV-Luc virus
sham_AAV_Luc_12_5

source_name: sham

value: sham


title: J8.72.NK#1

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

tag: strain background

value: 6 Weeks Old

tag: gender

value: male

tag: number of treatments

tag: compound name

tag: hours since last treatment

value: Spleen

tag: cell type

value: NK

tag: exclusion markers

tag: phenotype markers

tag: separation method

value: dissection/trimming


title: J8.72.MF#1

tag: age

value: MF


title: sham replicate 1

description:
expression data from whole heart from black 6 animals receiving sham TAC surgery and AAV-Luc virus
sham_AAV_Luc_12_2


title: wild-type, rep2

city: Seoul

first: Ok Bin

last: Kim

address: Ewhayeodae-gil 52

department: Department of Life Science

country: South Korea

institute: Ewha University

description: Gene expression data from exponential growth phase

hyb_protocol: 10 μg biotinylated cDNA was hybridized on microarray chip E. coli Genome 2.0 (using Hybridization oven 645), and then washed and stained using hybridization, wach and stain kit (Affymetrix) in the Affymetrix Fluidics Station 450.

scan_protocol: The array was analyzed by GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were analyzed with Robust Multi-array Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array were arbitrarily set to 100.

organism: Escherichia coli

label_protocol: The cDNA was labelled by biotin using GeneChip IVT labeling kit (Affymetrix).

growth_protocol: E. coli strains were aerobically grown in LB medium at 37 C.

extract_protocol: The total RNA was isolated from the cells using RNeasy minikit (Qiagen) and RNase-free DNase (Qiagen), and transcribed in cDNA with SuperScript II reverse transcriptase (Invitrogen).

treatment_protocol: At OD=0.8, the culture was treated with RNA Protect Bacterial Reagenz (Qiagen) and harvested.

tag: genotype/variation

value: wild-type


title: NT replicate 3

description:
expression data from whole heart from black 6 animals receiving TAC surgery and AAV-HDAC4 aimnoacids 1-201 virus
TAC_HDAC_NT_4_3


title: J8.74.T4#1

source_name: Veh 0.5 %MC pH=3_14_Spleen_T4

value: Veh 0.5% MC pH=3


title: ΔacrR mutant, rep1

value: {delta}acrR mutant


title: ΔacrR mutant, rep2


title: J8.71.T4#1


title: J8.70.T4#1


title: NT replicate 1

description:
expression data from whole heart from black 6 animals receiving TAC surgery and AAV-HDAC4 aimnoacids 1-201 virus
TAC_HDAC_NT_3_5


title: J8.73.NK#1


title: J8.69.T4#1


title: wild-type, rep1


title: J8.71.NK#1


title: J8.72.T4#1


title: sham replicate 2

description:
expression data from whole heart from black 6 animals receiving sham TAC surgery and AAV-Luc virus
sham_AAV_Luc_12_3


title: J8.68.NK#1


title: WARM MIX

city: Dallas

first: Yi

last: Zhu

state: Texas

address: 5323 Harry Hines Boulevard, L5.210

department: Internal Medicine

institute: UT Southwestern

description: RNA extracted from 3-4 mice was pooled into one sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: mice housed in thermal neutrality (30-degree celsius)

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

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. Quality control was performed with Agilent Bioanalyser.

value: subcutaneous adipose


title: J8.73.T4#1


title: J8.68.MF#1


title: J8.71.MF#1


title: J8.70.MF#1

source_name: Veh 0.5 %MC pH=3_14_Spleen_MF


title: J8.67.T4#1


title: J8.68.T4#1


title: J8.67.NK#1


title: J8.69.MF#1


title: J8.65.NK#1


title: J8.66.MF#1

source_name: Veh 0.5 % MC_14_Spleen_MF

value: Veh 0.5% MC


title: J8.65.T4#1


title: COLD MIX

source_name: mice housed in cold (6-degree Celsius)


title: J8.64.T4#1

source_name: Veh 0.5 % MC_14_Spleen_T4


title: J8.63.NK#1


title: J8.63.T4#1


title: J6.58.MF#1

source_name: Veh 0.5 % MC_15_Spleen_MF


title: J8.61.MF#1


title: J8.61.NK#1


title: J6.57.GN#1

value: GN


title: J6.57.NK#1


title: J8.62.MF#1


title: J6.57.DC#1

value: DC


title: J6.57.BB#1

value: B


title: J6.56.MF#1


title: J6.56.T4#1

source_name: Veh 0.5 % MC_15_Spleen_T4


title: J8.63.MF#1


title: J6.58.BB#1

source_name: Veh 0.5 % MC_15_Spleen_B


title: J6.58.GN#1

source_name: Veh 0.5 % MC_15_Spleen_GN


title: J6.57.MF#1


title: J6.56.DC#1

source_name: Veh 0.5 % MC_15_Spleen_DC


title: J6.55.MF#1


title: J6.56.BB#1


title: J6.55.DC#1


title: J6.54.NK#1

source_name: Veh 0.5 % MC_15_Spleen_NK


title: J6.53.T4#1


title: J6.54.GN#1


title: J6.54.DC#1


title: J6.55.BB#1


title: J6.53.NK#1


title: J6.53.MF#1


title: J6.56.GN#1


title: J6.53.BB#1


title: J6.53.DC#1


title: J3.36.GN#1

source_name: Veh 0.5 % MC_14_Spleen_GN


title: J3.33.NK#1


title: J3.36.BB#1

source_name: Veh 0.5 % MC_14_Spleen_B


title: J3.36.MF#1


title: J3.35.BB#1


title: J3.35.DC#1


title: J3.32.MF#1


title: J3.33.MF#1


title: J3.35.GN#1


title: J3.35.MF#1


title: J3.33.DC#1


title: J3.36.DC#1

source_name: Veh 0.5 % MC_14_Spleen_DC


title: J3.32.BB#1


title: J3.33.BB#1


title: J3.33.GN#1


title: J3.31.GN#1


title: J3.36.T4#1


title: J26.8.BB#1

value: TCRB-

value: FACSAria


title: J3.31.T4#1


title: J26.9.BB#1

source_name: Veh 0.5 % MC_1_Spleen_B


title: J3.31.DC#1


title: J3.31.MF#1


title: J3.31.BB#1


title: J3.31.NK#1


title: J26.6.BB#1


title: J26.15.BB#1


title: J26.14.BB#1


title: J25.8.BB#1


title: J25.7.BB#1


title: J25.6.MF#1

source_name: SB00513404_1_Peritoneal Cavity_MF

value: Peritoneal Cavity


title: J25.8.MF#1

source_name: SB00526222_1_Peritoneal Cavity_MF

value: 6 Weeks Old


title: J26.1.BB#1

value: male


title: J25.9.BB#1

value: Spleen


title: J25.9.MF#1

source_name: SB00526222_14_Peritoneal Cavity_MF


title: J26.7.BB#1


title: J25.7.MF#1


title: J25.6.T4#1


title: J26.12.BB#1


title: J26.10.BB#1


title: J25.5.T4#1


title: J25.7.T4#1


title: J25.3.MF#1

source_name: SB00513404_14_Peritoneal Cavity_MF


title: J25.5.MF#1


title: J25.4.T4#1


title: J25.4.MF#1


title: J25.4.BB#1


title: J25.3.BB#1


title: J25.3.T4#1


title: AML_1361

city: Berlin

first: Eva

middle: Kristin

last: von der Heide

address: Hindenburgdamm 30

department: Hematology

institute: Charite Berlin

hyb_protocol: Sample hybridisation was performed  according to standard Affymetrix protocols

scan_protocol: Samples were scanned using an Affymetrix GeneChip scanner

data_processing: Normalization was performed using the Robust Multichip Average (RMA) background correction method and quantile normalization

source_name: Bone marrow mesenchymal stromal cells

label_protocol: Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols

growth_protocol: Bone marrow aspirates were obtained from AML patients and healthy donors, mononuclear cells were isolated using density centrifugation and BM-MSC were generated using their plastic adherent probability and expanded up to passage four

extract_protocol: total RNA was extracted using AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Gemany). cDNA preparation and  in vitro transcription were performed according to standard Affymetrix protocols.

tag: sample type

value: AML BM-MSC


title: AML_1425


title: AML_1311


title: J25.16.MF#1

source_name: Veh 0.5 % MC_1_Peritoneal Cavity_MF


title: J25.16.T4#1

source_name: Veh 0.5 % MC_1_Spleen_T4

value: dissection/trimming


title: AML_1282


title: J25.2.BB#1


title: J25.16.BB#1


title: J25.15.MF#1

value: MF


title: J25.15.BB#1


title: AML_1016


title: J25.2.T4#1


title: J25.14.MF#1


title: J8.66.T4#1

source_name: Veh 0.5 % MC_14_Spleen_T4


title: J25.13.MF#1


title: J25.13.T4#1


title: J8.64.MF#1

source_name: Veh 0.5 % MC_14_Spleen_MF


title: J25.12.MF#1

source_name: Veh 0.5 % MC_14_Peritoneal Cavity_MF


title: AML_866


title: J25.11.T4#1


title: AML_898


title: J25.12.T4#1


title: AML_1169


title: J8.67.MF#1


title: J25.12.BB#1


title: AML_1013


title: J25.11.MF#1


title: J25.10.T4#1


title: J25.14.BB#1


title: J25.10.MF#1


title: AML_808


title: AML_806


title: AML_803


title: AML_771


title: J23.9.MF#1


title: J25.1.T4#1


title: J23.8.BB#1

value: TCRb-


title: J23.9.BB#1


title: J23.7.MF#1


title: J23.8.MF#1


title: J23.7.BB#1


title: AML_769


title: AML_749


title: J23.6.BB#1


title: J23.4.MF#1


title: J23.4.BB#1


title: J23.5.MF#1


title: J23.14.MF#1


title: AML_728


title: AML_725


title: J23.15.BB#1


title: AML_704


title: J23.6.MF#1


title: AML_734


title: J23.2.MF#1


title: J23.14.BB#1


title: J23.5.BB#1


title: J6.58.DC#1


title: J23.3.BB#1


title: HD_n0362

value: control


title: J23.12.MF#1


title: J23.10.MF#1


title: J23.11.BB#1


title: J2.29.GN#1


title: HD_n0358


title: HD_n0352


title: J23.12.BB#1


title: J2.29.T4#1


title: HD_n0355


title: J23.1.BB#1


title: J2.29.BB#1


title: J2.28.T4#1


title: J2.26.NK#1

value: NK


title: J2.28.NK#1


title: J2.28.DC#1


title: J2.29.NK#1


title: GS-5759-treated Replicate 4 18h

city: Calgary

first: Mark

last: Giembycz

state: Alberta

address: 3280 Hospital Drive NW

department: Physiology & Pharmacology

country: Canada

institute: University of Calgary

hyb_protocol: Standard Affymetrix procedures were used using U133plus2.0 human GeneChips.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: Data were processed (PLIER normalization) implemented in Expression Console (Affymetrix).

source_name: BEAS-2B cells following GS-5759 18h Replicate 4

label_protocol: Standard procedures were used where each RNA sample was converted into a biotinylated cRNA target using a 3' in vitro tranbscription express kit (Affymetrix).

growth_protocol: BEAS-2B cells were grown for three days in keratinocyte-containing, serum-free medium (KSFM) supplemented with epidermal growth factor, bovine piutuitary extract and antibiotics and for a further 24h in KSFM.

extract_protocol: BEAS-2B cells stored at -80° C were processed for RNA according to the RNeasy protocol (Qiagen).

treatment_protocol: BEAS-2B cells were treated with vehicle, indacaterol and GSK 256066 in combination (both 10nM) or GS-5759 (10nM) for 1h, 2h, 6h and 18h.

tag: cell line


title: J2.29.MF#1

tag: tissue


title: J2.26.T4#1


title: J2.30.NK#1


title: J2.28.GN#1


title: J2.29.DC#1


title: GS-5759-treated Replicate 4 2h

source_name: BEAS-2B cells following GS-5759 2h Replicate 4


title: J2.27.BB#1


title: GS-5759-treated Replicate 3 18h

source_name: BEAS-2B cells following GS-5759 18h Replicate 3


title: GS-5759-treated Replicate 4 6h

source_name: BEAS-2B cells following GS-5759 6h Replicate 4


title: GS-5759-treated Replicate 4 1h

source_name: BEAS-2B cells following GS-5759 1h Replicate 4


title: GS-5759-treated Replicate 3 6h

source_name: BEAS-2B cells following GS-5759 6h Replicate 3


title: GS-5759-treated Replicate 3 2h

source_name: BEAS-2B cells following GS-5759 2h Replicate 3


title: GS-5759-treated Replicate 3 1h

source_name: BEAS-2B cells following GS-5759 1h Replicate 3


title: J2.26.MF#1


title: GS-5759-treated Replicate 2 18h

source_name: BEAS-2B cells following GS-5759 18 Replicate 2


title: J2.27.GN#1


title: J2.28.BB#1


title: J2.26.BB#1


title: J2.25.MF#1


title: J2.26.DC#1


title: J2.26.GN#1


title: J2.25.T4#1


title: GS-5759-treated Replicate 2 2h

source_name: BEAS-2B cells following GS-5759 2h Replicate 2


title: J2.23.NK#1


title: J2.22.T4#1

source_name: Veh 0.5 %MC pH=3_14_Spleen_T4

value: Veh 0.5% MC pH=3


title: GS-5759-treated Replicate 1 6h

source_name: BEAS-2B cells following GS-5759 6h Replicate 1


title: J2.25.GN#1


title: J2.24.BB#1


title: J2.20.MF#1


title: J2.21.MF#1

source_name: Veh 0.5 %MC pH=3_14_Spleen_MF


title: J2.20.BB#1


title: J2.19.MF#1


title: Ind/GSK-treated Replicate 4 2h

source_name: BEAS-2B cells following Ind/GSK 2h Replicate 4

value: Ind/GSK 2h


title: J2.22.MF#1


title: J2.23.MF#1


title: J2.22.GN#1

source_name: Veh 0.5 %MC pH=3_14_Spleen_GN

value: GN


title: GS-5759-treated Replicate 1 1h

source_name: BEAS-2B cells following GS-5759 1h Replicate 1


title: GS-5759-treated Replicate 2 1h

source_name: BEAS-2B cells following GS-5759 1h Replicate 2


title: GS-5759-treated Replicate 1 2h

source_name: BEAS-2B cells following GS-5759 2h Replicate 1


title: Ind/GSK-treated Replicate 4 18h

source_name: BEAS-2B cells following Ind/GSK 18h Replicate 4

value: Ind/GSK 18h


title: J2.20.NK#1


title: J2.23.DC#1

value: DC


title: J2.24.NK#1


title: GS-5759-treated Replicate 2 6h

source_name: BEAS-2B cells following GS-5759 6h Replicate 2


title: GS-5759-treated Replicate 1 18h

source_name: BEAS-2B cells following GS-5759 18h Replicate 1


title: Ind/GSK-treated Replicate 4 6h

source_name: BEAS-2B cells following Ind/GSK 6h Replicate 4

value: Ind/GSK 6h


title: J2.19.DC#1


title: J2.18.T4#1


title: J2.18.NK#1


title: J2.18.DC#1


title: J2.15.T4#1


title: J2.16.NK#1


title: J2.17.MF#1


title: Ind/GSK-treated Replicate 3 2h

source_name: BEAS-2B cells following Ind/GSK 2h Replicate 3


title: Ind/GSK-treated Replicate 3 1h

source_name: BEAS-2B cells following Ind/GSK 1h Replicate 3

value: Ind/GSK 1h


title: J2.14.BB#1

value: B


title: J2.16.T4#1

value: 6 Weeks Old


title: J2.14.T4#1

value: male


title: Ind/GSK-treated Replicate 4 1h

source_name: BEAS-2B cells following Ind/GSK 1h Replicate 4


title: J2.15.GN#1

value: Spleen


title: Ind/GSK-treated Replicate 3 18h

source_name: BEAS-2B cells following Ind/GSK 18h Replicate 3


title: J2.16.BB#1


title: J2.19.BB#1


title: J2.14.DC#1


title: J2.15.MF#1


title: J2.13.T4#1


title: Ind/GSK-treated Replicate 2 18h

source_name: BEAS-2B cells following Ind/GSK 18h Replicate 2


title: J2.13.MF#1


title: J2.13.NK#1


title: J2.15.NK#1


title: Ind/GSK-treated Replicate 2 6h

source_name: BEAS-2B cells following Ind/GSK 6h Replicate 2


title: Ind/GSK-treated Replicate 2 1h

source_name: BEAS-2B cells following Ind/GSK 1h Replicate 2


title: Ind/GSK-treated Replicate 3 6h

source_name: BEAS-2B cells following Ind/GSK 6h Replicate 3


title: Ind/GSK-treated Replicate 2 2h

source_name: BEAS-2B cells following Ind/GSK 2h Replicate 2


title: x-MeWo-L1CAM_06

city: Moscow

first: Maxim

last: Shkurnikov

address: 2 bld. 85, Ugreshkaya st.

country: Russia

institute: SRC Bioclinicum

hyb_protocol: GeneChip® Human Transcriptome Array 2.0 (Affymetrix Inc., Santa Clara, CA, USA) for 16 h at 48°C.

scan_protocol: Arrays were washed to remove nonspecifically bound nucleic acids and stained on Fluidics Station 450 (Affymetrix) and then scanned on Gene- Chip Scanner 3000 7G system (Affymetrix).

data_processing: CEL-files were jointly preprocessed in Affymetrix Expression Console (build 1.4.1.46) using SST-RMA method.

label_protocol: The procedures for cDNA synthesis and labelling were carried out according to the GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc., Santa Clara, CA, USA) using 500 ng total RNA as starting material.

growth_protocol: 10^6 melanoma cells (MeWo and MV3 with and without L1CAM knockdown) were subcutaneously injected into scid mice. Mice were sacrificed when the resulting tumors ulcerated or exceeded approx. 10 % of the animals' weight.

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

tag: origin

value: Xenograft

tag: knockdown

value: MeWo


title: x-MeWo-L1CAM_05


title: J2.14.NK#1

value: dissection/trimming


title: J2.13.DC#1


title: J2.12.T4#1

source_name: Veh 0.5 % MC_14_Spleen_T4

value: Veh 0.5% MC


title: Ind/GSK-treated Replicate 1 6h

source_name: BEAS-2B cells following Ind/GSK 6h Replicate 1

tag: treatment


title: J2.12.NK#1

source_name: Veh 0.5 % MC_14_Spleen_NK

tag: strain background


title: J2.12.DC#1

source_name: Veh 0.5 % MC_14_Spleen_DC

tag: gender


title: Ind/GSK-treated Replicate 1 2h

source_name: BEAS-2B cells following Ind/GSK 2h Replicate 1


title: Vehicle-treated Replicate 4 6h

source_name: BEAS-2B cells following vehicle 6h Replicate 4

value: Vehicle 6h


title: Untreated control, rep 3

city: Barcelona

first: Carlos

middle: J

last: Ciudad

state: Barcelona

address: Av. Juan XXIII-27

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Barcelona

description: Gene expression data from untreated control

hyb_protocol: Hybridization was performed using GeneChip HT 3’IVT Express Kit

scan_protocol: GeneChips were scanned using Genechip scanner 3000(Affymetrix)

data_processing: Data was processed using Genespring v13 software, computing the RMA (Robust Multichip Average) expression measure in log2 base scale, using a baseline transformation to the median of control samples

source_name: LNCaP prostate adenocarcinoma cells_control

label_protocol: RNA samples were processed in the automated  Biomek FX System (Beckman Coulter), where  cRNA was produced, and labeled with Biotin

growth_protocol: LNCaP prostate adenocarcinoma cells were seeded in 35mm plates, grown in F12 + 7%FBS

extract_protocol: RNAeasy mini kit, extraction performed according to user's protocol.

treatment_protocol: 24 hours with either saline or  40µM UA

value: Prostate

value: LNCaP


title: x-MeWo-L1CAM_01


title: Incubated with Urolithin A for 24h -rep3

description: Gene expression data from treated control

source_name: LNCaP prostate adenocarcinoma cells_Urolithin_A


title: Ind/GSK-treated Replicate 1 1h

source_name: BEAS-2B cells following Ind/GSK 1h Replicate 1


title: x-MeWo-L1CAM_04


title: J2.12.GN#1

source_name: Veh 0.5 % MC_14_Spleen_GN

tag: number of treatments


title: Vehicle-treated Replicate 4 18h

source_name: BEAS-2B cells following vehicle 18h Replicate 4

value: Vehicle 18h


title: J2.11.MF#1

source_name: Veh 0.5 % MC_14_Spleen_MF

tag: compound name

value: MF


title: x-MeWo-L1CAM_02


title: J2.11.NK#1

tag: hours since last treatment

value: NK


title: Incubated with Urolithin A for 24h -rep1


title: x-MeWo-luc_08

value: luc


title: Incubated with Urolithin A for 24h -rep2


title: x-MeWo-L1CAM_03


title: x-MeWo-luc_05


title: Vehicle-treated Replicate 4 2h

source_name: BEAS-2B cells following vehicle 2h Replicate 4

value: Vehicle 2h


title: Vehicle-treated Replicate 4 1h

source_name: BEAS-2B cells following vehicle 1h Replicate 4

value: Vehicle 1h


title: Ind/GSK-treated Replicate 1 18h

source_name: BEAS-2B cells following Ind/GSK 18h Replicate 1

value: Ind/GSK 18h


title: J2.11.DC#1

value: 6 Weeks Old

tag: cell type

value: DC


title: x-MeWo-luc_06


title: Untreated control, rep 1


title: Untreated control, rep 2


title: x-MeWo-luc_07


title: J2.11.BB#1

source_name: Veh 0.5 % MC_14_Spleen_B

value: male

value: Spleen

value: B

tag: exclusion markers

value: CD19+ Igm+


title: J16.79.MF#1

source_name: SB00526226_12_Peritoneal Cavity_MF

value: Peritoneal Cavity

tag: phenotype markers

value: dissection/trimming


title: Vehicle-treated Replicate 3 18h

source_name: BEAS-2B cells following vehicle 18h Replicate 3


title: Vehicle-treated Replicate 3 6h

source_name: BEAS-2B cells following vehicle 6h Replicate 3

value: Vehicle 6h


title: Vehicle-treated Replicate 3 2h

source_name: BEAS-2B cells following vehicle 2h Replicate 3


title: Vehicle-treated Replicate 3 1h

source_name: BEAS-2B cells following vehicle 1h Replicate 3


title: J16.75.MF#1

source_name: Veh 0.5 % MC_12_Peritoneal Cavity_MF

value: Veh 0.5% MC

tag: separation method


title: x-MeWo-luc_03

value: Xenograft

value: MeWo


title: J16.80.MF#1

tag: age

value: MF


title: J16.76.MF#1

source_name: SB00513404_12_Peritoneal Cavity_MF


title: Vehicle-treated Replicate 2 18h

source_name: BEAS-2B cells following vehicle 18h Replicate 2

value: Vehicle 18h


title: x-MeWo-luc_04

value: luc


title: x-MeWo-luc_01


title: x-MeWo-luc_02


title: J16.74.MF#1


title: J16.77.MF#1

source_name: SB00526221_12_Peritoneal Cavity_MF


title: J16.72.MF#1


title: J16.78.MF#1

source_name: SB00526222_12_Peritoneal Cavity_MF


title: Vehicle-treated Replicate 2 2h

source_name: BEAS-2B cells following vehicle 2h Replicate 2

value: Vehicle 2h


title: Vehicle-treated Replicate 1 18h

source_name: BEAS-2B cells following vehicle 18h Replicate 1


title: J16.73.MF#1


title: x-MV3-luc_04


title: x-MV3-luc_02


title: x-MV3-luc_01


title: Vehicle-treated Replicate 2 6h

source_name: BEAS-2B cells following vehicle 6h Replicate 2


title: x-MV3-L1CAM_03


title: Vehicle-treated Replicate 1 6h

source_name: BEAS-2B cells following vehicle 6h Replicate 1


title: x-MV3-L1CAM_04


title: x-MV3-luc_03


title: Vehicle-treated Replicate 2 1h

source_name: BEAS-2B cells following vehicle 1h Replicate 2

value: Vehicle 1h


title: J16.71.MF#1

value: 6 Weeks Old


title: J12.25.MF#1

source_name: Veh 0.5 % MC_1_Peritoneal Cavity_MF


title: Vehicle-treated Replicate 1 2h

source_name: BEAS-2B cells following vehicle 2h Replicate 1


title: J12.23.BB#1


title: x-MV3-L1CAM_02


title: J12.23.MF#1

source_name: SB00526222_1_Peritoneal Cavity_MF


title: J12.24.MF#1

source_name: SB00513404_1_Peritoneal Cavity_MF


title: J12.24.BB#1


title: J12.25.BB#1

source_name: Veh 0.5 % MC_1_Spleen_B


title: J12.22.MF#1

source_name: SB00526221_1_Peritoneal Cavity_MF


title: J12.22.BB#1


title: xenograft tissue_PC9_Sh KDM1A, biological rep3

city: Shanghai

first: FAN

last: ZHANG

state: Shanghai

address: 507 Zhengmin Road

country: China

institute: Clinical Translational Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Transcriptome Array 2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Array data was analysed using Affymetrix Expression Console Software and Transcriptome Analysis Console (TAC) Software.

source_name: Mouse xenograft derived from human PC9 cells expressing stable ShRNA KDM1A

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 3, Affymetrix).

growth_protocol: A total of 2×10^6 cells suspended in 100 μL PBS was injected subcutaneously into the right axillary part of 5-week old nude mice

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

treatment_protocol: After 5 weeks, xenograft tumor tissues were isolated, photographed, and stored in liquid nitrogen for gene expression microarray analysis

value: NSCLC cells

tag: mouse strain

value: BALB/C

tag: injection position

value: the right axillary

tag: shRNA


title: xenograft tissue_PC9_Sh control, biological rep2

source_name: Mouse xenograft derived from human PC9 cells expressing stable ShRNA control

value: control


title: J12.21.MF#1

value: male

tag: tissue


title: J12.20.MF#1

value: Peritoneal Cavity


title: Vehicle-treated Replicate 1 1h

source_name: BEAS-2B cells following vehicle 1h Replicate 1

tag: cell line


title: xenograft tissue_PC9_Sh KDM1A, biological rep2


title: J12.21.BB#1

value: Spleen

value: B

value: dissection/trimming


title: xenograft tissue_PC9_Sh control, biological rep3


title: J12.19.BB#1


title: J12.18.MF#1


title: J12.18.BB#1


title: J12.20.BB#1

value: Veh 0.5% MC


title: J12.17.BB#1


title: x-MV3-L1CAM_01

tag: origin

value: Xenograft

tag: knockdown


title: xenograft tissue_PC9_Sh KDM1A, biological rep1


title: xenograft tissue_PC9_Sh control, biological rep1


title: J12.17.MF#1

tag: strain background

value: MF


title: J12.19.MF#1

tag: gender


title: OPM2 VS-5584(SB2343) treated, biological rep1

city: Singapore

first: Nurulhuda

last: Mustafa

address: 14 Medical Drive, Level 12

department: Yong Loo Lin School of Medicine

country: Singapore

institute: National University of Singapore

hyb_protocol: Following fragmentation, 12.5µg of cDNA was hybridised for 16h at 45degC on Affymetrix GeneChip HG.1.0STarray. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data was analysed by Genespring GX (Agilent Technologies) Raw signals were converted to expression value using RMA algorithm.

source_name: OPM2, Human Multiple Myeloma Cell Line

label_protocol: Biotinylated cDNA was prepared using Nugen Applause WT kit and Encore biotin module (Nugen, USA) according to manufacturer's instruction from 100ng of total RNA.

growth_protocol: Human Multiple Myeloma Cell Line OPM2 was maintained in RPMI 1640 supplemented with 10% FBS. Cells were grown in 37deg C in a humidified atmosphere with 5% CO2.

extract_protocol: RNA was extracted using the Qiagen Rneasy Mini Kit according to manufacturer's instructions.

treatment_protocol: DMSO control or 123nM of VS-5584(SB2343) for 24h.

tag: treatment


title: OPM2 Control, biological rep1

value: DMSO control for 24h


title: Knockout_rep2

city: Tsukuba

first: Shogo

last: Matoba

state: Ibaraki

address: 3-1-1, Koyadai

country: Japan

institute: RIKEN BioResource Research Center

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse Gene Expression v2 8x60K Microarray (G4852B) at 65°C for 17 h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: The scanned images of microarray slides were processed using Feature Extraction software version 10.5.1.1 (Agilent Technologies). All raw data were loaded into Gene Spring GX 13.1.1 (Agilent Technologies) and signal intensities were normalized by shift to 75 percentile. Baseline was set to the median of all samples. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus molossinus

source_name: midbrain, adult (8-9 weeks), agouti homozygous mutant, MSM background

label_protocol: cRNA was amplified from 0.1 ug of RNA and labeled with Cy3 using Low-Input QuickAmp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy MinElute kit (QIAGEN).. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: MSM/Ms mice were derived from the colony maintained at RIKEN BioResource Center. The mutant mice for agouti (a) allele were generated by using CRISPR/Cas9 system. They were housed under controlled lighting conditions (daily light period 07:00 to 21:00).

extract_protocol: Total RNA was purified from isolated midbrain tissues with Trizol (Life technologies). The concentration of RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The midbrain tissues were manually isolated from 8-9 weeks old mice under dissecting microscope.

value: midbrain

tag: developmental stage

value: adult (8-9 weeks)

tag: strain

value: MSM/Ms

tag: agouti (a) allele

value: homzygous mutant


title: Knockout_rep3

value: female


title: FAC-sorted 20d beta cells, biological rep3

city: Distrito Federal

middle: Alfonso

last: Larqué Velázquez

state: Distrito Federal

address: Circuito Exterior s/n Ciudad Universitaria. Del. Coyoacán. Mexico City

department: Neurodevelopment and Physiology

country: Mexico

institute: Instituto de Fisiología Celular UNAM

description: Gene expression data from immature pancretic beta cells

hyb_protocol: GeneChip® Expression Wash, Stain  and ScanProtocol (2006-2015) on GeneChip GeneChip® Rat Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 G7

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling.  Quantile normalization method in R project .

organism: Rattus norvegicus

source_name: FACS sorted pancreatic beta cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ug total RNA (The Ambion® WT Expression Kit).

value: Wistar

value: suckling (postnatal 20d)


title: FAC-sorted 20d beta cells, biological rep2


title: Knockout_rep1


title: Wildtype_control_rep2

source_name: midbrain, adult (8-9 weeks), wildtype, MSM background

value: wildtype


title: Knockout_rep4

value: male


title: Knockout_rep5


title: scalp_androgenic alopecia_C_rep1

city: Shenyang

first: Lin

middle: Lin

last: Bao

state: Liaoning

address: 155N. Nanjing Street, Heping district

department: Dermatology Department

institute: First Hospital of China Medical University

description: Gene expression of androgenic alopecia scalp tissue of person C

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Arraystar Human LncRNA Microarray V4.0 for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Androgenic alopecia scalp tissue of person C

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA cleanup including a DNase I digestion step was performed using RNeasy spin columns (Qiagen,Valencia, CA). The integrity of the RNA was evaluated by using a NanoDrop ND-1000 spectrophotometer and standard denaturing agarose gel electrophoresis.

tag: ethnic group

value: Chinese

tag: subject id

value: C

tag: age (yrs)

value: scalp tissue

tag: tissue subtype

value: Androgenic alopecia scalp tissue


title: scalp_normal_A_rep1

description: Gene expression of normal scalp tissue of person A

source_name: Adjacent normal scalp tissue of person A

value: A

value: Adjacent normal scalp tissue


title: scalp_normal_D_rep1

description: Gene expression of normal scalp tissue of person D

source_name: Adjacent normal scalp tissue of person D

value: D


title: scalp_androgenic alopecia_D_rep1

description: Gene expression of androgenic alopecia scalp tissue of person D

source_name: Androgenic alopecia scalp tissue of person D


title: FAC-sorted adult beta cells, biological rep3

description: Gene expression data from fully mature pancretic beta cells

tag: age

value: young adult (250-280g)


title: FAC-sorted 20d beta cells, biological rep1


title: FAC-sorted adult beta cells, biological rep1


title: FAC-sorted adult beta cells, biological rep2


title: Petal

status: Public on Jul 26 2016

city: Miyazaki

first: Yasuko

last: Ito-Inaba

address: 1-1 Gakuenkibanadai-nishi

department: Organization for Promotion of Tenure Track

institute: University of Miyazaki

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Symplocarpus renifolius custom microarray 4x44K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

organism: Symplocarpus renifolius

source_name: Petal, female stage

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: status

value: inflorescence

tag: Stage

value: female stage

value: Petal


title: Wildtype_control_rep1

tag: tissue

value: midbrain

value: adult (8-9 weeks)

value: MSM/Ms


title: scalp_androgenic alopecia_A_rep1

description: Gene expression of androgenic alopecia scalp tissue of person A

source_name: Androgenic alopecia scalp tissue of person A


title: scalp_normal_C_rep1

description: Gene expression of normal scalp tissue of person C

source_name: Adjacent normal scalp tissue of person C


title: Pistil

source_name: Pistil, female stage

value: Pistil


title: Stamen

source_name: Stamen, female stage

value: Stamen


title: OPM2 Control, biological rep2

tag: cell line

value: DMSO control for 24h


title: D3

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
Gene expression in DRG neurons stimulated with 90 actions potentials every 5 min (90/5) delivered by a 6 V, 0.2 ms biphasic pulse for 5hr
Raw data file:
D3D4_US83000181_252665510919_S01_GE2_107_Sep09_1_3.txt

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two biological replicas were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) mouse (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction vs.11 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
Data table contains normalized log2 ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because is a control featrure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Neurons were dissociated from spinal cords of 13.5-day old mouse embryos and plated at a density of 0.5 x 106 cells per ml into each side compartment in Eagle’s MEM containing 5% horse serum and 100 ng/ml nerve growth factor.  Non-neuronal cell proliferation was inhibited by treatment with 13 μg/ml fluoro-2-deoxyurindine (Sigma, St. Louis, MO) by one day following plating for 5 days.  Cultures were subsequently used for experiments 3- 4 weeks after which axons extend from the side compartments into the central compartment and could be electrically stimulated.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a Thermo Scientific NanoDrop ND-2000 and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: DRG cultures were stimulated through platinum electrodes in contact with media on opposite sides of the barrier.  Stimulation parameters and responses to stimulation have been reported previously (Eshete and Fields, 2001 and Fields et al, 1992).  For this study, either 18 actions potentials every min (18/1) or 90 action potentials every 5 min (90/5) was delivered by a 6 V, 0.2 ms biphasic pulse for either 2hr or 5hr.

value: NIH Swiss

tag: cell type

value: DRG neurons

tag: stimulation pattern

tag: time


title: D4

source_name: DRG neurons stimulated with 90 actions potentials every 5 min (90/5) delivered by a 6 V, 0.2 ms biphasic pulse for 5hr


title: D2

description:
Gene expression in DRG neurons stimulated with 90 actions potentials every 5 min (90/5) delivered by a 6 V, 0.2 ms biphasic pulse for 5hr
Raw data file:
D1D2_US83000181_252665510919_S01_GE2_107_Sep09_1_4.txt


title: Pith

source_name: Pith, female stage

value: Pith


title: B3

description:
Gene expression in DRG neurons stimulated with 18 actions potentials every min (18/1) delivered by a 6 V, 0.2 ms biphasic pulse for 5hr
Raw data file:
B1B3_US83000181_252665510920_S01_GE2_107_Sep09_1_2.txt


title: C1

description:
Gene expression in DRG neurons stimulated with 90 actions potentials every 5 min (90/5) delivered by a 6 V, 0.2 ms biphasic pulse for 2hr
Raw data file:
C1C3_US83000181_252665510920_S01_GE2_107_Sep09_1_4.txt


title: B4

description:
Gene expression in DRG neurons stimulated with 18 actions potentials every min (18/1) delivered by a 6 V, 0.2 ms biphasic pulse for 5hr
Raw data file:
B2B4_US83000181_252665510920_S01_GE2_107_Sep09_1_1.txt


title: C4

description:
Gene expression in DRG neurons stimulated with 90 actions potentials every 5 min (90/5) delivered by a 6 V, 0.2 ms biphasic pulse for 2hr
Raw data file:
C2C4_US83000181_252665510920_S01_GE2_107_Sep09_1_3.txt


title: C2

source_name: DRG neurons stimulated with 90 actions potentials every 5 min (90/5) delivered by a 6 V, 0.2 ms biphasic pulse for 2hr


title: B2

source_name: DRG neurons stimulated with 18 actions potentials every min (18/1) delivered by a 6 V, 0.2 ms biphasic pulse for 5hr


title: A3

description:
Gene expression in DRG neurons stimulated with 18 actions potentials every min (18/1) delivered by a 6 V, 0.2 ms biphasic pulse for 2hr
Raw data file:
A3A4_US83000181_252665510921_S01_GE2_107_Sep09_1_3.txt


title: B1

value: 18 actions potentials every min (18/1) delivered by a 6 V, 0.2 ms biphasic pulse


title: A4

source_name: DRG neurons stimulated with 18 actions potentials every min (18/1) delivered by a 6 V, 0.2 ms biphasic pulse for 2hr


title: A2

description:
Gene expression in DRG neurons stimulated with 18 actions potentials every min (18/1) delivered by a 6 V, 0.2 ms biphasic pulse for 2hr
Raw data file:
A1A2_US83000181_252665510921_S01_GE2_107_Sep09_1_4.txt


title: C3

value: 90 actions potentials every 5 min (90/5) delivered by a 6 V, 0.2 ms biphasic pulse


title: X3

description:
Gene expression in Not stimulated DRG neurons
Raw data file:
X3X4_US83000181_252665510921_S01_GE2_107_Sep09_1_1.txt

source_name: Not stimulated DRG neurons

value: not stimulated


title: A1


title: X2

description:
Gene expression in Not stimulated DRG neurons
Raw data file:
X1X2_US83000181_252665510921_S01_GE2_107_Sep09_1_2.txt


title: X1


title: MHCh-F480-4x-2

city: Freiburg im Breisgau

first: David

middle: E

last: Sanin

address: Stübeweg 51

department: Immunometabolism

institute: Max-Planck-Institute für Immunbiologie und Epigenetik

hyb_protocol: Staff at the Technology Facility at the University of York, York, UK, prepared and carried out microarray analysis of purified RNA, including sample labelling and hybridisation, using the Agilent SurePrint system (Agilent Technologies).

scan_protocol: Agilent Technologies Scanner G2505C US83103526 - grid name 028005_D_F_20120201

data_processing: Data was processed using GeneSpring

source_name: Skin

extract_protocol: RNA extracted from sorted DEC populations using TRIzol (Life Technologies). RNA was quantified using a Nanodrop (Thermo Scientific, Waltham, USA) and quality checked using a Bioanalyzer (Agilent Technologies, Santa Clara, USA).

treatment_protocol: Dermal exudate cell obtained from infected pinnae in three independent experiments (12-18 mice each) recovered on day 4 after infection with S. mansoni cercariae were pooled and labelled with anti-MHC-II (IA-IE) (clone # M5/114) and anti-F4/80 (clone # BM8) mAbs. Cell populations which were F4/80+MHC-IIhigh, F4/80+MHC-IIlo, or F4/80-MHC-IIhigh were recovered by FACS (MoFlo Astrios, Beckman Coulter).

tag: gender

value: female

tag: agent

value: Schistosoma mansoni cercariae


title: X4


title: MO-1x-2

label_protocol: Staff at the Technology Facility at the University of York, York, UK, prepared and carried out microarray analysis of purified RNA, including sample labelling and hybridisation, using the Agilent SurePrint system (Agilent Technologies).


title: MO-4x-3


title: MO-1x-3


title: Knockout_rep6

source_name: midbrain, adult (8-9 weeks), agouti homozygous mutant, MSM background

tag: developmental stage

value: male

value: homzygous mutant


title: MO-1x-1

tag: strain


title: MO-4x-2


title: D1


title: MO-4x-1


title: MHCh-F480-4x-3


title: MO-4x-4


title: MHCh-F480-1x-2


title: MHCh-F480-1x-3


title: MHCh-F480-4x-1


title: DC-1x-3


title: DC-1x-1


title: DC-4x-2


title: DC-4x-1


title: OPM2 VS-5584(SB2343) treated, biological rep2

source_name: OPM2, Human Multiple Myeloma Cell Line

tag: treatment


title: R-K 24hDx3 biological rep-3 (3 pooled mice)

city: stanford

first: Gerlinde

last: Wernig

address: 265 Campus Drive

department: Pathology

institute: Stanford

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430_2 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) 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: c-Jun inducible mice after c-Jun induction

label_protocol: 10 ug RNA input were amplified & fragmented and biotinylated cDNA were submitted using NUGEN- OVATION SYSTEM#3100&#4200

growth_protocol: Time course experiments of c-Jun protein expression in vivo were performed as previously described by harvesting bone marrow from mice exposed to doxycycline on day 0 and day 1 and applied to standard affymetrix mouse arrays.

treatment_protocol: 8 week old mice were treated with doxycycline administered in the drinking water (1mg/ml) for 24 hours.

tag: protocol

value: c-Jun induction

value: bone marrow


title: CXB13 Male H1 20-Jul-05

city: Memphis

first: Robert

middle: W.

last: Williams

state: TN

address: 71 Manassas St.

department: Department of Genetics, Genomics and Informatics

institute: University of Tennessee

hyb_protocol: Samples were processed in the INIA Bioanalytical Core at the W. Harry Feinstone Center for Genomic Research, The University of Memphis, led by Thomas R. Sutter. All processing steps were performed by Shirlean Goodwin. In brief, RNA purity was evaluated using the 260/280 nm absorbance ratio, and values had to be greater than 1.8. The majority of samples were 1.9 to 2.1. RNA integrity was assessed using the Agilent Bioanalyzer 2100. We required an RNA integrity number (RIN) of greater than 8. This RIN value is based on the intensity ratio and amplitude of 18S and 28S rRNA signals. The standard Eberwine T7 polymerase method was used to catalyze the synthesis of cDNA template from polyA-tailed RNA using Superscript II reverse transcriptase (Invitrogen Inc.). The Enzo Life Sciences, Inc., BioArray High Yield RNA Transcript Labeling Kit (T7, Part No. 42655) was used to synthesize labeled cRNA. The cRNA was evaluated using both the 260/280 ratio (values of 2.0 or 2.1 are acceptable) and the Bioanalyzer output (a dark cRNA smear on the 2100 output centered roughly between 600 and 2000 nucleotides is required). Those samples that passed both QC steps (10% usually failed and new RNA samples had to be acquired and processed) were then sheared using a fragmentation buffer included in the Affymetrix GeneChip Sample Cleanup Module (Part No. 900371). Fragmented cRNA samples were either stored at -80°C until use or were immediately injected onto the array. The arrays were hybridized and washed following standard Affymetrix protocols.

scan_protocol: All samples in a group were labeled on one day, except for a few cases that failed QC on their first pass. The hybridization station accommodates up to 20 samples, and for this reason each group was split into a large first set of 20 samples and a second set of 12 to 14 samples. Samples were washed in groups of four and then held in at 4°C until all 20 (or 12-14) arrays were ready to scan. The last four samples out of the wash stations were scanned directly. Samples were scanned in sets of four.

data_processing: The expression values were generated using PDNN. The same simple steps described above were also applied to these values. Every microarray data set therefore has a mean expression of 8 with a standard deviation of 2. A 1 unit difference represents roughly a two-fold difference in expression level. Expression levels below 5 are usually close to background noise levels.

label_protocol: The BXD genetic reference panel of recombinant inbred strains consists of just over 80 strains. The BXDs in this data set include 27 of the BXD strains made by Benjamin Taylor at the Jackson Laboratory in the 1970s and 1990s (BXD1 through BXD42). All of these strains are fully inbred, many well beyond the 100th filial (F) generation of inbreeding. We have also included 39 inbred (25 strains at F20+) and nearly inbred (14 strains between F14 and F20) BXD lines generated by Lu and Peirce. All of these strains, including those between F14 and F20, have been genotyped at 13,377 SNPs. Mouse Diversity Panel (MDP). We have profiled a MDP consisting 16 inbred strains and a pair of reciprocal F1 hybrids; B6D2F1 and D2B6F1.

growth_protocol: Cells grown in mono layer are lysed directly in a culture dish by adding the RNA STAT-60TM (1 ml/3.5 cm petri dish) and passing the cell lysate several times through a pipette. Cells grown in suspension are sediment then lysed in the RNA STAT-60TM (1 ml per 5-10 x 106 cells) by repetitive pipetting. Washing calls before addition of the RNA STAT-60TM should be avoided as this increases the possibility of mRNA degradation.

extract_protocol: RNA Extraction: In brief, we used the RNA STAT-60 protocol (TEL-TEST B Bulletin No. 1), steps 5.1A (homogenization of tissue), 5.2 (RNA extraction), 5.3 (RNA precipitation), and 5.4 (RNA wash). In Step 5.4 we stopped after adding 75% ethanol (1 ml per 1 ml RNA STAT-60) and stored the mix at -80°C until further use. Before RNA labeling we thawed samples and proceeded with the remainder of Step 5.4; pelleting, drying, and redissolving the pellet in RNase-free water.

treatment_protocol: BXD animals were obtained from UTHSC, UAB, or directly from The Jackson Laboratory (see Table 1 below). Animals were housed at UTHSC, Beth Israel Deaconess, or the Jackson Laboratory before sacrifice. Virtually all CXB animals were obtained directly at the Jackson Laboratory by Lu Lu. We thank Muriel Davisson for making it possible to collect these cases on site. Standard inbred strain stock was from The Jackson Laboratory, but most animals were housed or reared at UTHSC. Mice were euthanized and killed by cervical dislocation and brains were removed and placed in RNAlater prior to dissection. Cerebella and olfactory bulbs were removed; brains were hemisected, and both hippocampi were dissected whole by Hong Tao Zhang in the Lu lab. Hippocampal samples are very close to complete (see Lu et al., 2001) but probably include variable amounts of subiculum and fimbria. A great majority of animals used in this study were between 45 and 90 days of age (average of 66 days, maximum range from 41 to 196 days). All animals were sacrifice between 9 AM and 5 PM during the light phase.

value: hippocampus

tag: Sex

value: Male

tag: age (days)

tag: batch id

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: scale factor

tag: background average

tag: present

tag: absent

tag: marginal

tag: affx-b-actinmur (3'/5')

tag: affx-gapdhmur (3'/5')

tag: source

value: JAX


title: R-K 24hDx2 biological rep-2 (3 pooled mice)

tag: tissue


title: R-K 24hDx1 biological rep-1 (3 pooled mice)


title: CXB13 Female H1 6-Dec-05

tag: strain

value: Female


title: CXB12 Female H1 20-Jul-05


title: R-K NoDx3 biological rep-3 (3 pooled mice)

source_name: c-Jun inducible mice before c-Jun induction

value: control


title: R-K NoDx2 biological rep-2 (3 pooled mice)


title: MHCh-F480-1x-1

tag: gender

tag: agent


title: DC-1x-2


title: CXB10 Male H1 6-Dec-05

tag: Sex


title: CXB12 Male H1 15-Jul-05

tag: age (days)


title: CXB10 Female H1 20-Jul-05

tag: batch id


title: CXB11 Female H1 15-Jul-05

tag: pool size (n of cases used per rna sample)


title: CXB9 Male H1 19-Jul-05

tag: rma outlier


title: CXB8 Male H1 20-Jul-05

tag: scale factor


title: CXB6 Female H1 6-Dec-05

tag: background average


title: CXB9 Female H1 15-Jul-05

tag: present


title: CXB6 Male H1 19-Jul-05

tag: absent


title: CXB7 Female H1 19-Jul-05

tag: marginal


title: CXB8 Female H1 15-Jul-05

tag: affx-b-actinmur (3'/5')


title: CXB7 Male H2 15-Jul-05

tag: affx-gapdhmur (3'/5')


title: CXB5 Male H2 13-Jul-05

tag: source

value: UTM RW


title: CXB11 Male H1 19-Jul-05

tag: tissue


title: CXB5 Male H1 19-Jul-05

tag: strain


title: CXB3 Male H1 19-Jul-05


title: CXB4 Male H1 15-Jul-05


title: CXB3 Female H1 14-Jul-05


title: CXB5 Female H1 26-Sep-05


title: CXB4 Female H1 19-Jul-05


title: R-K NoDx1 biological rep-1 (3 pooled mice)

tag: protocol


title: WSB/EiJ Female H2 26-Sep-05

value: WSB/EiJ


title: PWK/PhJ Male H1 23-Sep-05

value: PWK/PhJ


title: CXB2 Female H2 10-Aug-05


title: CXB1 Female H1 14-Jul-05


title: PWK/PhJ Female H1 9-Aug-05


title: CXB2 Male H1 14-Jul-05


title: PWD/PhJ Male H1 6-Dec-05

value: PWD/PhJ


title: CXB1 Male H1 19-Jul-05


title: NZO/HlLtJ Female H1 9-Aug-05

value: NZO/HlLtJ


title: KK/HIJ Female H1 26-Sep-05

value: KK/HIJ


title: NOD/LtJ Male H1 10-Aug-05

value: NOD/LtJ


title: LG/J Male H2 22-Sep-05

value: LG/J


title: C3H/HeJ Male H1 9-Aug-05


title: KK/HIJ Female H3 10-Aug-05


title: PWD/PhJ Male H3 10-Aug-05


title: BALB/cJ Male H1 9-Aug-05

value: BALB/cJ


title: NOD/LtJ Female H1 26-Sep-05


title: C57BL/6ByJ Female H1 9-Aug-05


title: CAST/EiJ Female H1 22-Sep-05

value: CAST/EiJ


title: C57BL/6ByJ Male H1 6-Dec-05


title: C3H/HeJ Female H3 23-Sep-05


title: NZO/HlLtJ Male H1 23-Sep-05


title: BALB/cByJ Male H1 6-Dec-05

value: BALB/cByJ


title: A/J Male H1 9-Aug-05

value: A/J


title: BALB/cJ Male H2 22-Sep-05

value: hippocampus


title: A/J Female H1 6-Dec-05


title: 129S1/SvImJ Male H2 10-Aug-05

value: Male


title: AKR/J Male H1 22-Sep-05

value: AKR/J

value: JAX


title: BXD98 Male H2 14-Jul-05


title: 129S1/SvImJ Female H2 9-Aug-05

value: Female


title: BXD65a Female H1 6-Dec-05

value: UTM RW


title: BXD98 Female H1 10-Aug-05


title: BXD99 Female H1 14-Jul-05


title: BXD94 Female H1 15-Jul-05


title: WSB/EiJ Male H1 10-Aug-05

value: WSB/EiJ


title: BXD65a Male H2 9-Jun-05


title: BXD99 Male H1 9-Aug-05


title: BXD48a Female H1 9-Aug-05


title: BXD65b Female H2 14-Jul-05


title: BXD65b Male H1 20-Jul-05


title: BXD48a Male H2 9-Jun-05


title: BXD89 Male H3 20-Jul-05


title: BXD90 Male H2 6-Dec-05

value: Glenn


title: BXD87 Male H1 14-Jul-05


title: BXD87 Female H2 13-Dec-05


title: BXD90 Female H1 14-Jul-05


title: BXD93 Male H1 9-Jun-05


title: BXD89 Female H2 14-Jul-05


title: BXD93 Female H1 9-Aug-05


title: BXD86 Female H1 20-Jul-05


title: BXD85 Female H1 14-Jul-05


title: BXD85 Male H1 13-Jun-05


title: 24hrs with Scutellaria baicalensis

city: Daejeon

first: Bu-Yeo

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

institute: Korea Institute of Oriental Medicine

description: 24hrs treatment with Scutellaria baicalensis

hyb_protocol: The labelled RNA were hybridized to a microarray (Agilent Human whole genome 44K, Agilent Technologies) containing approximately 44,000 probes (~26,600 unique genes) in accordance with the manufacturer's instructions.

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner.

data_processing: Signal intensities of genes were normalized by the quantile method.

source_name: Cell Line

label_protocol: The isolated RNA was amplified and labeled using a Low RNA Input Linear Amplification kit PLUS following manufacturer’s instructions (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: HepG2 cells were grown in Eagle's Minimum Essential Medium supplemented with 10% (v/v) fetal bovine serum, 100 U/mL penicillin, and 100 µg/mL streptomycin in a 5% CO2 humidified air at 37°C.

extract_protocol: Total RNA was purified from liver tissue of mice and HepG2 cells by using an RNeasy kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany). The quality of isolated RNA was measured using Agilent’s Bio-analyzer 2100 RNA Nano kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: One day before experiment, HepG2 cells were seeded on 100 mm dishes, after then cells were exposed to ESB of 100 µg/ml for 1 – 24 hours.

tag: cell line

value: HepG2 human hepatoma cells


title: BXD84 Male H3 14-Jul-05

tag: Sex


title: BXD84 Female H2 22-Sep-05

tag: age (days)


title: 3hrs with Scutellaria baicalensis

description: 3hrs treatment with Scutellaria baicalensis


title: 12hrs with Scutellaria baicalensis

description: 12hrs treatment with Scutellaria baicalensis


title: BXD83 Male H2 23-Sep-05

tag: batch id


title: BXD83 Female H1 14-Jul-05

tag: pool size (n of cases used per rna sample)


title: Control

description: Control


title: 6hsr with Scutellaria baicalensis

description: 6hsr treatment with Scutellaria baicalensis


title: BXD73a Male H2 13-Jul-05

tag: rma outlier


title: BXD73a Female H1 10-Aug-05

tag: scale factor


title: 1hr with Scutellaria baicalensis

description: 1hr treatment with Scutellaria baicalensis


title: BXD79 Male H1 10-Aug-05

tag: background average


title: EZH2 Y244A-2

first: Chong-Lei

last: Bi

address: #12-02, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive

institute: Cancer Science Institute Singapore

hyb_protocol: Following fragmentation, 12.5 ug of cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip HG1.0ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000 7G

data_processing: The data were analyzed with Genespring GX 11(Agilent Technologies)

source_name: NKYS cells

label_protocol: Biotinylated cDNA were prepared using Nugen Applause WT kit and Encore biotin module (Nugen, USA) according to the manufecturer's instructions from 100ng total RNA.

growth_protocol: NKYS cells were cultured in RPMI medium (Life Technologies) supplemented with heat-inactivated FBS (10%) and 100 IU/mL of recombinant human IL-2.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Invitrogen) and purified with the RNAeasyMini Kit (Qiagen).

treatment_protocol: Transfections of expressing siRNAs or plasmids on NKYS cells were performed using Neon® Transfection following the manufacturer's procedures.

value: NKYS

tag: transfection

value: MtCA


title: EZH2 SET∆


title: BXD79 Female H1 13-Jul-05

tag: present

tag: absent


title: EZH2 Y244D-2

value: EZH2 WT


title: EZH2 WT-1


title: BXD77 Male H1 13-Jul-05

tag: marginal

tag: affx-b-actinmur (3'/5')


title: BXD77 Female H1 15-Jul-05

tag: affx-gapdhmur (3'/5')

tag: source


title: EZH2 siRNA-2

value: EZH2 siRNA


title: EZH2 Y244A-1


title: Vector Control-2

value: vector control


title: BXD75 Male H2 9-Jun-05

tag: tissue

tag: strain


title: Vector Control-1

tag: cell line


title: Control siRNA-2 (for EZH2 siRNA-2)

value: control siRNA


title: EZH2 Y244D-1


title: EZH2 WT


title: BXD76 Male H1 10-Aug-05

tag: Sex


title: LG/J Female H1 9-Aug-05

value: LG/J

tag: age (days)


title: BXD76 Female H2 13-Jul-05

tag: batch id


title: EZH2 siRNA -1


title: BXD74 Male H1 9-Aug-05

tag: pool size (n of cases used per rna sample)


title: BXD74 Male H2 13-Jul-05

tag: rma outlier


title: BXD75 Female H1 13-Jul-05

tag: scale factor


title: Control siRNA-1 (for EZH2 siRNA-1)


title: BXD73 Male H2 13-Jul-05

tag: background average


title: Control siRNA-2 (for JAK3 KD)

tag: transfection


title: BXD85 Male H1 20-Jul-05

tag: present


title: Control siRNA-1 (for JAK3 KD)


title: Mouse liver tissue, organic sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 5

city: North Ryde

first: Megan

last: Osmond-McLeod

address: 11 Julius Avenue

country: Australia

institute: CSIRO

description:
Long-term sunscreen Group 8-5
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing only organic UVR filters with 29kJ/m2 UVR during 30 treatments over 36 weeks.

hyb_protocol: Following fragmentation, ~600-700 ng of single-stranded DNA were hybridised on Affymetrix 1.0 ST mouse gene arrays (17 h, 45˚C, 60 rpm) in an Affymetrix 640 GeneChip® Hybridization Oven. GeneChips were washed and stained in an Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix 7G GeneChip® Scanner.

data_processing: The data was processed and analysed using Matlab Bioinformatics and Statistical toolboxes. RMA was used as the normalisation method. In-house tools were used to remove batch effects and control for false discovery.

source_name: SKH:QS mouse liver tissue from organic sunscreen + 29kJ/m2 UVR-treated mouse, week 36 (30 weekly treatments)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay User Manual, Affymetrix).

growth_protocol: Mice were individually housed in polycarbonate cages in an isolated temperature (~21˚C) and moisture (~55-65% relative humidity) controlled room with a 14-hr light/10-hr dark cycle, with ad libitum access to food and water.

extract_protocol: Total RNA was extracted from liver tissue using the NucleoSpin® RNA II kit (Macherey Nagel, Scientifix) following manufacturer’s instructions.

treatment_protocol: Topical applications of commercially-available sunscreens containing either ZnO nanoparticles, a mixture of TiO2 nanoparticles and organic UVR filters, organic UVR filters only, or no sunscreen were delivered each week to SKH:QS mice. During each treatment, mice were fitted with Elizabethan collars to minimise oral ingestion of sunscreens. Half of the mice in each group were exposed to 29 kJ/m2 UVR 20 min after sunscreen application, and the other half received no UVR treatment. After two hours, the sunscreen was washed from the mice using mild soapy water, and mice were dried before being returned to their cages. Mice received 30 weekly treatments over 36 weeks. Mice were sacrificed at week 36 by intraperitoneal injection of Xylase (50mg/kg)/ketamine (50mg/kg) followed by cervical dislocation.

tag: strain/background

value: liver

tag: sunscreen treatment

value: sunscreen containing organic UVR filters

tag: uvr treatment

value: 29kJ/m2 UVR

tag: time point

value: 36 weeks (30 treatments)


title: BXD67 Male H1 13-Jun-05

value: hippocampus

value: Male

tag: absent

tag: marginal

tag: affx-b-actinmur (3'/5')

tag: affx-gapdhmur (3'/5')

tag: source


title: BXD69 Male H1 15-Jul-05

tag: tissue

tag: strain

tag: Sex

tag: age (days)

value: UTM RW


title: Mouse liver tissue, organic sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 4

description:
Long-term sunscreen Group 8-4
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing only organic UVR filters with 29kJ/m2 UVR during 30 treatments over 36 weeks.


title: BXD73 Female H1 9-Jun-05

value: Female

tag: batch id

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: scale factor


title: BXD70 Male H1 13-Jul-05

tag: background average

tag: present


title: BXD67 Female H1 23-Sep-05


title: Mouse liver tissue, organic sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 6

description:
Long-term sunscreen Group 8-6
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing only organic UVR filters with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: strain/background

tag: sunscreen treatment

tag: uvr treatment


title: NKTL-JS70

first: Siok-Bian

last: Ng

address: National University Hospital, 5 Lower Kent Ridge Road, Main Building, level 3

department: Department of Pathology

institute: National University Health System, Singapore

description:
45027F
Illumina DASL protocol
Normal

hyb_protocol: Illumina DASL protocol

scan_protocol: not provided

data_processing: Illumina BeadStudio version 3.3.8. No normalization was performed. Raw data were analyzed and used to draw conclusions.

label_protocol: Illumina DASL protocol

extract_protocol: For FFPE tissues, total RNA was extracted using High Pure RNA Paraffin Kit (Roche Applied Science, Mannheim, Germany) according to the manufacturer's instruction. For freshly isolated cells, total RNA was extracted using miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) with DNase I treatment protocol by the manufacturer's instruction.

tag: disease

value: Normal


title: JAK3 siRNA-2

tag: cell line

tag: transfection

value: JAK3 siRNA


title: Mouse liver tissue, organic sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 2

description:
Long-term sunscreen Group 8-2
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing only organic UVR filters with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: time point


title: Mouse liver tissue, organic sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 3

description:
Long-term sunscreen Group 8-3
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing only organic UVR filters with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: tissue


title: BXD68 Female H1 9-Aug-05

tag: strain

tag: absent

tag: marginal

tag: affx-b-actinmur (3'/5')

tag: affx-gapdhmur (3'/5')

tag: source


title: BXD66 Female H2 13-Jun-05

tag: Sex

tag: age (days)

tag: batch id

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: scale factor


title: JAK3 siRNA-1

value: NKYS


title: BXD68 Male H1 13-Jul-05

tag: background average

tag: present


title: BXD65 Female H2 13-Jun-05


title: NKTL-JS69

description:
45027E
Illumina DASL protocol
Normal

tag: disease


title: NKTL-JS71

description:
45027G
Illumina DASL protocol
Normal


title: BXD65 Male H2 26-Sep-05


title: BXD70 Female H1 9-Aug-05


title: BXD64 Female H2 13-Jun-05


title: BXD69 Female H3 13-Jul-05


title: NKTL-JS72

description:
45027H
Illumina DASL protocol
Normal


title: BALB/cJ Female H3 9-Aug-05

value: BALB/cJ


title: BXD64 Male H1 13-Jul-05


title: BXD66 Male H2 20-Jul-05


title: NKTL-JS68

description:
45027D
Illumina DASL protocol
NKTL Patient

value: NKTL


title: AKR/J Female H3 9-Aug-05

value: AKR/J

value: JAX


title: Mouse liver tissue, organic sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 1

description:
Long-term sunscreen Group 8-1
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing only organic UVR filters with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: strain/background

tag: sunscreen treatment

tag: uvr treatment

tag: time point


title: Mouse liver tissue, organic sunscreen, no UVR, 30 treatments, biological rep 6

description:
Long-term sunscreen Group 7-6
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing only organic filters with no UVR during 30 treatments over 36 weeks.

source_name: SKH:QS mouse liver tissue from organic sunscreen no UVR-treated mouse, week 36 (30 treatments)

tag: tissue

value: no UVR


title: BXD63 Male H3 26-Sep-05

tag: strain

tag: absent

tag: marginal

tag: affx-b-actinmur (3'/5')


title: Mouse liver tissue, organic sunscreen, no UVR, 30 treatments, biological rep 5

description:
Long-term sunscreen Group 7-5
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing only organic filters with no UVR during 30 treatments over 36 weeks.


title: NKTL-JS67

description:
45027C
Illumina DASL protocol
NKTL Patient


title: BXD62 Male H2 26-Sep-05

tag: Sex

tag: age (days)

tag: affx-gapdhmur (3'/5')

tag: source


title: Mouse liver tissue, organic sunscreen, no UVR, 30 treatments, biological rep 4

description:
Long-term sunscreen Group 7-4
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing only organic filters with no UVR during 30 treatments over 36 weeks.


title: BXD51 Male H1 23-Sep-05

tag: batch id

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: scale factor


title: BXD63 Female H1 9-Jun-05

tag: background average

tag: present


title: NKTL-JS62

description:
45026F
Illumina DASL protocol
NKTL Patient

tag: disease


title: NKTL-JS66

description:
45027B
Illumina DASL protocol
NKTL Patient


title: BXD61 Female H1 6-Dec-05


title: BXD62 Female H1 13-Jun-05


title: NKTL-JS64

description:
45026H
Illumina DASL protocol
NKTL Patient


title: BXD61 Male H2 13-Jun-05


title: Mouse liver tissue, organic sunscreen, no UVR, 30 treatments, biological rep 3

description:
Long-term sunscreen Group 7-3
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing only organic filters with no UVR during 30 treatments over 36 weeks.

tag: strain/background

tag: sunscreen treatment

tag: uvr treatment

tag: time point


title: Mouse liver tissue, organic sunscreen, no UVR, 30 treatments, biological rep 2

description:
Long-term sunscreen Group 7-2
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing only organic filters with no UVR during 30 treatments over 36 weeks.

tag: tissue


title: BXD60 Female H1 19-Jul-05

tag: strain

tag: absent

tag: marginal

tag: affx-b-actinmur (3'/5')


title: NKTL-JS61

description:
45026E
Illumina DASL protocol
NKTL Patient


title: Mouse liver tissue, organic sunscreen, no UVR, 30 treatments, biological rep 1

description:
Long-term sunscreen Group 7-1
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing only organic filters with no UVR during 30 treatments over 36 weeks.


title: NKTL-JS58

description:
45026B
Illumina DASL protocol
NKTL Patient


title: NKTL-JS63

description:
45026G
Illumina DASL protocol
NKTL Patient


title: BXD50 Male H2 9-Jun-05

tag: Sex

tag: age (days)

tag: affx-gapdhmur (3'/5')

tag: source


title: BXD60 Male H2 13-Jun-05

tag: batch id

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: scale factor


title: BXD50 Female H1 22-Sep-05

tag: background average

tag: present


title: Mouse liver tissue, TiO2 sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 6

description:
Long-term sunscreen Group 6-6
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing TiO2 nanoparticles and organic UVR filters with 29kJ/m2 UVR during 30 treatments over 36 weeks.

source_name: SKH:QS mouse liver tissue from TiO2 sunscreen + 29kJ/m2 UVR-treated mouse, week 36 (30 weekly treatments)

tag: strain/background

tag: sunscreen treatment

tag: uvr treatment


title: BXD48 Male H3 15-Jul-05

tag: tissue

tag: strain


title: BXD48 Female H1 19-Jul-05

tag: absent

tag: marginal


title: BXD51 Female H1 14-Jul-05

tag: Sex

tag: affx-b-actinmur (3'/5')


title: NKTL-JS57

description:
45026A
Illumina DASL protocol
NKTL Patient

tag: disease


title: Mouse liver tissue, TiO2 sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 5

description:
Long-term sunscreen Group 6-5
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing TiO2 nanoparticles and organic UVR filters with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: time point


title: BXD55 Male H1 6-Dec-05

tag: age (days)

tag: batch id

tag: affx-gapdhmur (3'/5')

tag: source


title: BXD45 Male H1 6-Dec-05

tag: pool size (n of cases used per rna sample)

tag: rma outlier

tag: scale factor

tag: background average


title: Mouse liver tissue, TiO2 sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 3

description:
Long-term sunscreen Group 6-3
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing TiO2 nanoparticles and organic UVR filters with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: strain/background

tag: sunscreen treatment

tag: uvr treatment


title: NKTL-JS52

description:
45025D
Illumina DASL protocol
NKTL Patient


title: NKTL-JS51

description:
45025C
Illumina DASL protocol
NKTL Patient


title: Mouse liver tissue, TiO2 sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 4

description:
Long-term sunscreen Group 6-4
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing TiO2 nanoparticles and organic UVR filters with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: tissue


title: NKTL-JS49

description:
45025A
Illumina DASL protocol
NKTL Patient


title: BXD45 Female H2 6-Dec-05

tag: strain

tag: present

tag: absent

tag: marginal

value: Glenn


title: NKTL-JS48

description:
45017H
Illumina DASL protocol
DLBCL with EBV

tag: disease

value: DLB CL+EBV


title: BXD44 Female H1 14-Jul-05

tag: Sex

tag: age (days)

tag: affx-b-actinmur (3'/5')


title: NKTL-JS50

description:
45025B
Illumina DASL protocol
NKTL Patient


title: NKTL-JS47

description:
45017G
Illumina DASL protocol
EBV-Associated Lymphoid Proliferation

value: EALP


title: Mouse liver tissue, TiO2 sunscreen, no UVR, 30 treatments, biological rep 6

description:
Long-term sunscreen Group 5-6
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing TiO2 nanoparticles and organic filters with no UVR during 30 treatments over 36 weeks.

source_name: SKH:QS mouse liver tissue from TiO2 sunscreen no UVR-treated mouse, week 36 (30 treatments)

value: liver

value: sunscreen containing TiO2 nanoparticles and organic UVR filters

tag: time point


title: BXD38 Male H1 14-Jul-05

value: hippocampus

tag: batch id

tag: pool size (n of cases used per rna sample)

tag: affx-gapdhmur (3'/5')

tag: source


title: Mouse liver tissue, TiO2 sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 2

description:
Long-term sunscreen Group 6-2
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing TiO2 nanoparticles and organic UVR filters with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: strain/background

value: 29kJ/m2 UVR

value: 36 weeks (30 treatments)


title: BXD43 Male H1 15-Jul-05

value: Male

tag: rma outlier

tag: scale factor

tag: background average

value: UTM RW


title: BXD39 Male H1 15-Jul-05

tag: tissue

tag: strain


title: BXD40 Male H1 14-Jul-05

tag: present

tag: absent

value: UMemphis


title: BXD39 Female H2 14-Jul-05

value: Female

tag: marginal


title: BXD42 Male H1 6-Dec-05

tag: Sex


title: BXD44 Male H2 9-Jun-05

tag: age (days)


title: Mouse liver tissue, TiO2 sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 1

description:
Long-term sunscreen Group 6-1
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing TiO2 nanoparticles and organic UVR filters with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: sunscreen treatment

tag: uvr treatment


title: Mouse liver tissue, TiO2 sunscreen, no UVR, 30 treatments, biological rep 5

description:
Long-term sunscreen Group 5-5
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing TiO2 nanoparticles and organic filters with no UVR during 30 treatments over 36 weeks.

tag: time point


title: NKTL-JS46

description:
45017F
Illumina DASL protocol
EBV-Associated Lymphoid Proliferation

tag: disease


title: BXD38 Female H1 13-Jul-05

tag: batch id

tag: pool size (n of cases used per rna sample)

tag: affx-b-actinmur (3'/5')

tag: affx-gapdhmur (3'/5')


title: BXD43 Female H2 9-Jun-05

tag: rma outlier

tag: scale factor

tag: source


title: BXD40 Female H1 19-Jul-05

tag: tissue

tag: strain

tag: background average


title: BXD42 Female H2 6-Dec-05

tag: present

tag: absent

tag: marginal


title: Mouse liver tissue, TiO2 sunscreen, no UVR, 30 treatments, biological rep 4

description:
Long-term sunscreen Group 5-4
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing TiO2 nanoparticles and organic filters with no UVR during 30 treatments over 36 weeks.

tag: strain/background

tag: sunscreen treatment


title: NKTL-JS45

description:
45017E
Illumina DASL protocol
EBV-Associated Lymphoid Proliferation


title: BXD34 Female H1 13-Jul-05

tag: Sex

tag: age (days)


title: BXD34 Male H3 10-Aug-05

tag: batch id


title: Mouse liver tissue, TiO2 sunscreen, no UVR, 30 treatments, biological rep 3

description:
Long-term sunscreen Group 5-3
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing TiO2 nanoparticles and organic filters with no UVR during 30 treatments over 36 weeks.

tag: uvr treatment

tag: time point


title: BXD32 Male H2 13-Jul-05

tag: pool size (n of cases used per rna sample)

tag: affx-b-actinmur (3'/5')

tag: affx-gapdhmur (3'/5')


title: BXD32 Female H1 6-Dec-05

tag: rma outlier

tag: scale factor

tag: source


title: Mouse liver tissue, ZnO sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 4

description:
Long-term sunscreen Group 4-4
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing ZnO nanoparticles with 29kJ/m2 UVR during 30 treatments over 36 weeks.

source_name: SKH:QS mouse liver tissue from ZnO sunscreen + 29kJ/m2 UVR-treated mouse, week 36 (30 weekly treatments)

tag: tissue

value: sunscreen containing ZnO nanoparticles


title: Mouse liver tissue, TiO2 sunscreen, no UVR, 30 treatments, biological rep 2

description:
Long-term sunscreen Group 5-2
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing TiO2 nanoparticles and organic filters with no UVR during 30 treatments over 36 weeks.


title: Mouse liver tissue, TiO2 sunscreen, no UVR, 30 treatments, biological rep 1

description:
Long-term sunscreen Group 5-1
Gene expression data from liver tissue harvested from SKH:QS mouse receiving weekly topical applications of sunscreen containing TiO2 nanoparticles and organic filters with no UVR during 30 treatments over 36 weeks.


title: Mouse liver tissue, ZnO sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 3

description:
Long-term sunscreen Group 4-3
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing ZnO nanoparticles with 29kJ/m2 UVR during 30 treatments over 36 weeks.


title: NKTL-JS41

description:
45017A
Illumina DASL protocol
EBV-Associated Lymphoid Proliferation

tag: disease


title: Mouse liver tissue, ZnO sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 5

description:
Long-term sunscreen Group 4-5
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing ZnO nanoparticles with 29kJ/m2 UVR during 30 treatments over 36 weeks.


title: BXD31 Male H2 13-Jul-05

tag: strain

tag: background average

tag: present

tag: absent


title: NKTL-JS40

description:
25009H
Illumina DASL protocol
EBV-Associated Lymphoid Proliferation


title: NKTL-JS37

description:
25009E
Illumina DASL protocol
Normal

value: Normal


title: BXD33 Male H1 15-Jul-05

tag: Sex

tag: marginal


title: BXD33 Female H3 13-Jul-05

tag: age (days)

tag: batch id


title: NKTL-JS44

description:
45017D
Illumina DASL protocol
EBV-Associated Lymphoid Proliferation


title: BXD31 Female H2 6-Dec-05


title: BXD28 Male H1 13-Jul-05


title: BXD28 Female H1 15-Jul-05


title: BXD24 Male H1 15-Jul-05


title: NKTL-JS42

description:
45017B
Illumina DASL protocol
EBV-Associated Lymphoid Proliferation


title: BXD27 Male H1 10-Aug-05

value: UAB


title: NKTL-JS31

description:
25008G
Illumina DASL protocol
NKTL Patient

value: NKTL


title: Mouse liver tissue, ZnO sunscreen, 29 kJ/m2/treatment UVR, 30 treatments, biological rep 2

description:
Long-term sunscreen Group 4-2
Gene expression data from liver tissue harvested from SKH:QS mouse weekly topical applications of sunscreen containing ZnO nanoparticles with 29kJ/m2 UVR during 30 treatments over 36 weeks.

tag: strain/background

tag: sunscreen treatment

tag: uvr treatment

tag: time point