title: Chronic lymphocytic leukemia_Dataset 2_Specimen 256

description: DS2-256 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 254

status: Public on Sep 07 2013

type: genomic

city: Rutherford

first: Jane

last: Houldsworth

state: NJ

address: 201 Route 17 North

country: USA

institute: Cancer Genetics, Inc.

description: DS2-254 CLL specimen as test DNA and Promega normal DNA as reference

hyb_protocol: Oligoarray hybridization buffer, block (both from Agilent In Situ Hybridization Kit Plus), and Cot-1 DNA (Life Technologies) were added to each sample prior to application to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization for 24 hours, slides were washed sequentially as described by the manufacturer.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505B.

data_processing: Data extraction was performed using Feature Extraction Version 10.7.3.1 (Agilent Technologies).

molecule: genomic DNA

organism: Homo sapiens

source_name: Human CLL specimen

label_protocol: Genomic DNA samples were labeled using the Agilent Genomic DNA Enzymatic Labeling Kit, according to the manufacturer's protocol, except that 1μg of DNA was used per 25μl labeling reaction mix.

extract_protocol: Extraction of genomic DNA was performed using Qiagen DNeasy Blood and Tissue kit according to the manufacturer's instructions.

tag: disease state

value: chronic lymphocytic leukemia

source_name: Reference human genome DNA equimixture of normal male and normal female (Promega).

tag: sample type

value: reference

value: healthy


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 243

description: DS2-243 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 24

description: DS2-24 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 240

description: DS2-240 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 238

description: DS2-238 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 251

description: DS2-251 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 246

description: DS2-246 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 245

description: DS2-245 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 235

description: DS2-235 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 250

description: DS2-250 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 253

description: DS2-253 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 239

description: DS2-239 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 237

description: DS2-237 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 236

description: DS2-236 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 247

description: DS2-247 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 244

description: DS2-244 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 233

description: DS2-233 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 231

description: DS2-231 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 234

description: DS2-234 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 241

description: DS2-241 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 230

description: DS2-230 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 225

description: DS2-225 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 228

description: DS2-228 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 23

description: DS2-23 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 224

description: DS2-224 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 22

description: DS2-22 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 222

description: DS2-222 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 221

description: DS2-221 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 217

description: DS2-217 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 216

description: DS2-216 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 208

description: DS2-208 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 205

description: DS2-205 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 212

description: DS2-212 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 202

description: DS2-202 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 207

description: DS2-207 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 21

description: DS2-21 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 20

description: DS2-20 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 209

description: DS2-209 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 213

description: DS2-213 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 204

description: DS2-204 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 197

description: DS2-197 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 199

description: DS2-199 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 196

description: DS2-196 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 203

description: DS2-203 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 190

description: DS2-190 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 192

description: DS2-192 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 193

description: DS2-193 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 210

description: DS2-210 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 25

description: DS2-25 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 2

description: DS2-2 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 195

description: DS2-195 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 194

description: DS2-194 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 188

description: DS2-188 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 184

description: DS2-184 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 19

description: DS2-19 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 200

description: DS2-200 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 189

description: DS2-189 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 178

description: DS2-178 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 177

description: DS2-177 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 179

description: DS2-179 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 174

description: DS2-174 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 18

description: DS2-18 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 186

description: DS2-186 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 171

description: DS2-171 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 173

description: DS2-173 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 172

description: DS2-172 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 161

description: DS2-161 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 167

description: DS2-167 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 168

description: DS2-168 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 163

description: DS2-163 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 169

description: DS2-169 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 158

description: DS2-158 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 162

description: DS2-162 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 175

description: DS2-175 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 17

description: DS2-17 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 165

description: DS2-165 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 181

description: DS2-181 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 157

description: DS2-157 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 155

description: DS2-155 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 170

description: DS2-170 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 160

description: DS2-160 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 164

description: DS2-164 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 152

description: DS2-152 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 15

description: DS2-15 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 16

description: DS2-16 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 150

description: DS2-150 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 146

description: DS2-146 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 149

description: DS2-149 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 154

description: DS2-154 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 143

description: DS2-143 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 138

description: DS2-138 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 145

description: DS2-145 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 142

description: DS2-142 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 135

description: DS2-135 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 125

description: DS2-125 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 127

description: DS2-127 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 129

description: DS2-129 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 140

description: DS2-140 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 124

description: DS2-124 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 134

description: DS2-134 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 147

description: DS2-147 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 136

description: DS2-136 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 137

description: DS2-137 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 132

description: DS2-132 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 14

description: DS2-14 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 133

description: DS2-133 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 12

description: DS2-12 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 123

description: DS2-123 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 120

description: DS2-120 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 118

description: DS2-118 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 115

description: DS2-115 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 111

description: DS2-111 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 114

description: DS2-114 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 113

description: DS2-113 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 11

description: DS2-11 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 106

description: DS2-106 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 112

description: DS2-112 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 110

description: DS2-110 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 949

description: DS1-949 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 103

description: DS2-103 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 105

description: DS2-105 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 1

description: DS2-1 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 910

description: DS1-910 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 10

description: DS2-10 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 107

description: DS2-107 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 879

description: DS1-879 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 950

description: DS1-950 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 122

description: DS2-122 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 108

description: DS2-108 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 923

description: DS1-923 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 880

description: DS1-880 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 934

description: DS1-934 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 909

description: DS1-909 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 102

description: DS2-102 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 897

description: DS1-897 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 93

description: DS1-93 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 899

description: DS1-899 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 870

description: DS1-870 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 876

description: DS1-876 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 942

description: DS1-942 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 877

description: DS1-877 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 862

description: DS1-862 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 868

description: DS1-868 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 865

description: DS1-865 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 854

description: DS1-854 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 863

description: DS1-863 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 853

description: DS1-853 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 794

description: DS1-794 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 809

description: DS1-809 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 782

description: DS1-782 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 815

description: DS1-815 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 816

description: DS1-816 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 849

description: DS1-849 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 821

description: DS1-821 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 834

description: DS1-834 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 822

description: DS1-822 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 774

description: DS1-774 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 766

description: DS1-766 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 759

description: DS1-759 CLL specimen as test DNA and Promega normal DNA as reference


title: euESCb2 expression

type: RNA

city: Ube

first: Yoshiaki

last: Yamagata

state: Yamaguchi

address: Minamikogushi 1-1-1

department: Obstetrics and Gynecology

country: Japan

institute: Yamaguchi University School of Medicine

description:
ESC05
Eutopic endometrial stromal cells with endometriosis.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite 6.5 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

source_name: isolated endometrial stromal cells with endometriosis

label_protocol: Biotinylated cDNA were prepared from 200 ng total RNA with the Ambion WT Expression Kit (Ambion) and Affymetrix GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells were cultured in D-MEM supplemented with 10% FCS.

extract_protocol: Total RNA was isolated from tissues using RNeasy (QIAGEN).

tag: gender

value: female

tag: tissue

value: eutopic endometrium

tag: cell type

value: eutopic endometrial stromal cells

tag: disease status

value: endometriosis


title: choESC2 expression

description:
choESC03
Ectopic endometrial stromal cells from chocolate cyst.

source_name: isolated endometrial stromal cells from chocolate cyst

value: ovarian chocolate cyst

value: ectopic endometrial stromal cells


title: choESC3 expression

description:
choESC04
Ectopic endometrial stromal cells from chocolate cyst.


title: euESCb3 expression

description:
ESC07
Eutopic endometrial stromal cells with endometriosis.


title: euESCa3 expression

description:
ESC09
Control eutopic endometrial stromal cells without endometriosis to compare with ones with endometriosis or ones from chocolate cysts.

source_name: isolated endometrial stromal cells without endometriosis

value: non-endometriosis


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 758

description: DS1-758 CLL specimen as test DNA and Promega normal DNA as reference


title: choESC1 expression

description:
choESC01
Ectopic endometrial stromal cells from chocolate cyst.


title: euESCb1 expression

description:
ESC04
Eutopic endometrial stromal cells with endometriosis.


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 696

description: DS1-696 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 705

description: DS1-705 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 733

description: DS1-733 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 738

description: DS1-738 CLL specimen as test DNA and Promega normal DNA as reference


title: euESCa1 expression

description:
ESC01
Control eutopic endometrial stromal cells without endometriosis to compare with ones with endometriosis or ones from chocolate cysts.


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 767

description: DS1-767 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 717

description: DS1-717 CLL specimen as test DNA and Promega normal DNA as reference


title: euESCa2 expression

description:
ESC08
Control eutopic endometrial stromal cells without endometriosis to compare with ones with endometriosis or ones from chocolate cysts.


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 693

description: DS1-693 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 689

description: DS1-689 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 746

description: DS1-746 CLL specimen as test DNA and Promega normal DNA as reference


title: Spleen_saline_WT_rep8

city: Cincinnati

first: nupur

last: dasgupta

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hopital Medical Center

description: saline treated Spleen of WT mice

hyb_protocol: Biotinylated sense strand fragments were hybridized to Affymetrix Mouse Gene 1.0 ST GeneChips using the hybridisation control and hybridisation stain kits at 45degree for 18 hours

scan_protocol: Affymetrix GeneChip Scanner 3000 7G was used to scan the stained array

data_processing: All 55  RNA GeneChip data were normalized using the RMA (Robust multiarray average) algorithm.  Affymetrix CEL files were uploaded into the Partek Genomic Suite for downstream analyses

label: Biotin

organism: Mus musculus

label_protocol: Biotinylated cRNA was prepared using the WT Terminal labelling kit according to standard affymetrix protocol

extract_protocol: 9V/null mice were sacrificed one wk after the last injection along with WT mice, and lung, liver and spleen were collected for RNA analysis. Collected tissues were immediately immersed in Ambion RNA-Later thenextracted using the ToTALLY RNA kit(lung an dliver) or Trizol(Spleen). Th eRN Asamples were prepared by pooling of mRNA from 3 individual mice for each tissue type in a treatment cohort.`

treatment_protocol: 9V/null mice (Gaucher mouse model) were injected weekly via tail vein with 60U/kg/wk of imig or vela for 8 wks. Control 9V/null mice were injected with same volume of saline. Wt mice were untreated. Age and strain matched mice were used for the study.

tag: age

value: 28 wks at the time of RNA isolation

tag: background strain

tag: genotype

value: WT

value: Spleen

tag: treatment

value: saline


title: Spleen_saline_WT_rep6

description: saline treated Spleen of WT mice


title: Chronic lymphocytic leukemia_Dataset 2_Specimen 153

description: DS2-153 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 753

description: DS1-753 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 667

description: DS1-667 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 665

description: DS1-665 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 574

description: DS1-574 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 625

description: DS1-625 CLL specimen as test DNA and Promega normal DNA as reference


title: Spleen_saline_WT_rep4

description: saline treated Spleen of WT mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 739

description: DS1-739 CLL specimen as test DNA and Promega normal DNA as reference


title: Spleen_saline_WT_rep3

description: saline treated Spleen of WT mice


title: Spleen_saline_WT_rep7

description: saline treated Spleen of WT mice


title: Spleen_saline_WT_rep5

description: saline treated Spleen of WT mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 518

description: DS1-518 CLL specimen as test DNA and Promega normal DNA as reference


title: Lung_saline_WT_rep3

description: saline treated Lung of WT mice

value: Lung


title: Lung_saline_WT_rep4

description: saline treated Lung of WT mice


title: Spleen_saline_WT_rep1

description: saline treated Spleen of WT mice


title: Spleen_saline_WT_rep2

description: saline treated Spleen of WT mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 654

description: DS1-654 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 505

description: DS1-505 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 707

description: DS1-707 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 524

description: DS1-524 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 453

description: DS1-453 CLL specimen as test DNA and Promega normal DNA as reference


title: Lung_saline_WT_rep1

description: saline treated Lung of WT mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 487

description: DS1-487 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 659

description: DS1-659 CLL specimen as test DNA and Promega normal DNA as reference


title: Lung_saline_WT_rep2

description: saline treated Lung of WT mice


title: Liver_saline_WT_rep3

description: saline treated Liver of WT mice

value: Liver


title: Liver_saline_WT_rep2

description: saline treated Liver of WT mice


title: Liver_saline_WT_rep4

description: saline treated Liver of WT mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 435

description: DS1-435 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 606

description: DS1-606 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 499

description: DS1-499 CLL specimen as test DNA and Promega normal DNA as reference


title: Liver_saline_WT_rep1

description: saline treated Liver of WT mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 626

description: DS1-626 CLL specimen as test DNA and Promega normal DNA as reference


title: Lung_saline_KO_rep4

description: saline treated Lung of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 348

description: DS1-348 CLL specimen as test DNA and Promega normal DNA as reference


title: Lung_saline_KO_rep2

description: saline treated Lung of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 430

description: DS1-430 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 373

description: DS1-373 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 403

description: DS1-403 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 342

description: DS1-342 CLL specimen as test DNA and Promega normal DNA as reference


title: Liver_saline_KO_rep3

description: saline treated Liver of 9V/null mice


title: Lung_saline_KO_rep1

description: saline treated Lung of 9V/null mice


title: Lung_saline_KO_rep3

description: saline treated Lung of 9V/null mice


title: Liver_saline_KO_rep4

description: saline treated Liver of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 336

description: DS1-336 CLL specimen as test DNA and Promega normal DNA as reference


title: Spleen_saline_KO_rep4

description: saline treated Spleen of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 334

description: DS1-334 CLL specimen as test DNA and Promega normal DNA as reference


title: Spleen_saline_KO_rep6

description: saline treated Spleen of 9V/null mice


title: Spleen_saline_KO_rep1

description: saline treated Spleen of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 321

description: DS1-321 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 377

description: DS1-377 CLL specimen as test DNA and Promega normal DNA as reference


title: Spleen_saline_KO_rep3

description: saline treated Spleen of 9V/null mice


title: Spleen_saline_KO_rep5

description: saline treated Spleen of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 280

description: DS1-280 CLL specimen as test DNA and Promega normal DNA as reference


title: Spleen_saline_KO_rep2

description: saline treated Spleen of 9V/null mice


title: Liver_saline_KO_rep1

description: saline treated Liver of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 283

description: DS1-283 CLL specimen as test DNA and Promega normal DNA as reference


title: Spleen_saline_KO_rep7

description: saline treated Spleen of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 316

description: DS1-316 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 277

description: DS1-277 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 331

description: DS1-331 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 267

description: DS1-267 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 271

description: DS1-271 CLL specimen as test DNA and Promega normal DNA as reference


title: Liver_GCB_KO_rep3

description: vela treated Liver of 9V/null mice

data_processing: The data were loaded into Partek Genomics Suite 6.4 (Partek, Inc., St Louis, MO) and normalization was performed using the RMA (robust multiarray average) algorithm.

extract_protocol: 9V/null mice were sacrificed one wk after the last injection  and lung, liver an dspleen were collected for RNA analysis using ToTALLY RNA kit(lung and liver) or Trizol (Spleen). The RNA sample sets were prepared by pooling of mRNA from three individual mice for each tissue type in a treatment cohort

treatment_protocol: 9V/null mice were injected weekly via tail vein with 60U/kg/wk of imig or vela for 8 wks and were sacrificed one week after the injection  for RNA isolation from different tissues for transcriptome study

value: GCB (velaglucerase)


title: Liver_GCB_KO_rep2

description: vela treated Liver of 9V/null mice


title: Liver_GCB_KO_rep4

description: vela treated Liver of 9V/null mice


title: Lung_GCB_KO_rep4

description: vela treated Lung of 9V/null mice


title: Liver_GCB_KO_rep1

description: vela treated Liver of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 276

description: DS1-276 CLL specimen as test DNA and Promega normal DNA as reference

value: chronic lymphocytic leukemia


title: Lung_GCB_KO_rep3

description: vela treated Lung of 9V/null mice


title: wild type, chemostat, D = 0.3[1/hr], Pfeed = 0.3mM, steady state rep2.

city: rehovot

first: Noam

last: Vardi

address: herzel 235

department: molecular genetics

country: Israel

institute: Weizmann Institute of Science

description: chemostat, D=0.3[1/hr], Pfeed = 0.3mM Pi (cye 5), 7.3mM Pi (cy3, control), block 8

hyb_protocol: Agilent yeast dual color expression microarrays (8x15K, G2509F)

scan_protocol: Agilent microarray scanner

data_processing:
The scanned images were analyzed using SpotReader software (Niles Scientific). Problematic probes (flagged by SpotReader, or highly variable, with no signal, or at regions of spatial bias) were declared 'missing values'. Dye-dependent (Cy3 vs. Cy5) and array-dependent (same color in different arrays) biases were corrected by converting the samples distributions to their reference distribution using percentile normalization
Normalized log-2-ratio of the sample signal (cells at t>0 or cells in a chemostat with D=0.3[1/hr] and Pfeed=0.3mM Pi ) relative to the control sample (cells at t=0, growing in rich media (7.3mM Pi). Signal was averaged over 2 repeats.

organism: Saccharomyces cerevisiae

source_name: wild type, chemostat, steady state, D=0.1[1/hr], Pfeed = 0.3mM Pi

label_protocol: The samples were amplified, labeled with Agilent's Low Input Quick Amp Labeling Kit.

extract_protocol: Total RNA was extracted using MasterPure™ yeast RNA purification Kit (Epicentre).  Total RNA was extracted using MasterPure™ yeast RNA purification Kit (Epicentre).  Total RNA was extracted using MasterPure™ yeast RNA purification Kit (Epicentre).

source_name: wild type, t=0

value: wild type. 7.3mM, control


title: Lung_GCB_KO_rep2

description: vela treated Lung of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 263

description: DS1-263 CLL specimen as test DNA and Promega normal DNA as reference

value: reference

value: healthy


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 275

description: DS1-275 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 215

description: DS1-215 CLL specimen as test DNA and Promega normal DNA as reference


title: Lung_GCB_KO_rep1

description: vela treated Lung of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 257

description: DS1-257 CLL specimen as test DNA and Promega normal DNA as reference


title: Spleen_GCB_KO_rep4

description: vela treated Spleen of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 186

description: DS1-186 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 169

description: DS1-169 CLL specimen as test DNA and Promega normal DNA as reference


title: Spleen_GCB_KO_rep2

description: vela treated Spleen of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 171

description: DS1-171 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 156

description: DS1-156 CLL specimen as test DNA and Promega normal DNA as reference


title: Spleen_GCB_KO_rep1

description: vela treated Spleen of 9V/null mice


title: Spleen_GCB_KO_rep3

description: vela treated Spleen of 9V/null mice


title: Lung_CZ_KO_rep3

description: imig treated Lung of 9V/null mice

value: CZ (imiglucerase)


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 344

description: DS1-344 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1408

description: DS1-1408 CLL specimen as test DNA and Promega normal DNA as reference


title: Lung_CZ_KO_rep2

description: imig treated Lung of 9V/null mice


title: wild type, no Pi, t=8[h], rep2

description: no pi (cy5), 7.3mM Pi (cy3, control), block 4

source_name: wild type, t=8[h]

value: wild type, no Pi,  t=8[h]


title: wild type, no Pi, t=25[h], rep2

description: no pi (cy5), 7.3mM Pi (cy3, control), block 6

source_name: wild type, t=25[h]

value: wild type, no Pi,  t=25[h]


title: wild type, no Pi, t=4[h], rep2

description: no pi (cy5), 7.3mM Pi (cy3, control), block 2

source_name: wild type, t=4[h]

value: wild type, no Pi,  t=4[h]


title: wild type, no Pi, t=2[h], rep2

description: no pi (cy5), 7.3mM Pi (cy3, control), block 7

source_name: wild type, t=2[h]

value: wild type, no Pi,  t=2[h]


title: wild type, no Pi, t=1[h], rep2

description: no pi (cy5), 7.3mM Pi (cy3, control), block 5

source_name: wild type, t=1[h]

value: wild type, no Pi,  t=1[h]


title: Liver_CZ_KO_rep5

description: imig treated Lung of 9V/null mice

value: 28 wks at the time of RNA isolation


title: Liver_CZ_KO_rep4

description: imig treated Liver of 9V/null mice


title: wild type, no Pi, t=0.5[h], rep2

description: no pi (cy5), 7.3mM Pi (cy3, control), block 3

source_name: wild type, t=0.5[h]

value: wild type, no Pi,  t=0.5[h]


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1397

description: DS1-1397 CLL specimen as test DNA and Promega normal DNA as reference


title: Liver_CZ_KO_rep2

description: imig treated Liver of 9V/null mice


title: Lung_CZ_KO_rep1

description: imig treated Lung of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1388

description: DS1-1388 CLL specimen as test DNA and Promega normal DNA as reference


title: wild type, chemostat, D = 0.3[1/hr], Pfeed = 0.3mM, steady state rep1.

description: chemostat, D=0.3[1/hr], Pfeed = 0.3mM Pi (cye 5), 7.3mM Pi (cy3, control), block 8

value: wild type, chemostat, steady state, D=0.1[1/hr], Pfeed = 0.3mM Pi


title: wild type, no Pi, t=0.25[h], rep2

description: no pi (cy5), 7.3mM Pi (cy3, control), block 1

source_name: wild type, t=0.25[h]

value: wild type, no Pi,  t=0.25[h]


title: wild type, no Pi, t=8[h], rep1


title: wild type, no Pi, t=25[h], rep1


title: Liver_CZ_KO_rep1

description: imig treated Liver of 9V/null mice


title: wild type, no Pi, t=2[h], rep1


title: wild type, no Pi, t=1[h], rep1


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1344

description: DS1-1344 CLL specimen as test DNA and Promega normal DNA as reference


title: wild type, no Pi, t=0.5[h], rep1


title: Spleen_CZ_KO_rep1

description: imig treated Spleen of 9V/null mice

value: Spleen


title: wild type, no Pi, t=0.25[h], rep1


title: Liver_CZ_KO_rep3

description: imig treated Liver of 9V/null mice

value: Liver


title: wild type, D=0.1, P=0.1, rep2

description: chemostat, Pfeed=0.1mM Pi, D=0.1[1/hr], block 3 (cy3)

data_processing:
The scanned images were analyzed using SpotReader software (Niles Scientific). Problematic probes (flagged by SpotReader, or highly variable, with no signal, or at regions of spatial bias) were declared 'missing values'. Dye-dependent (Cy3 vs. Cy5) and array-dependent (same color in different arrays) biases were corrected by converting the samples distributions to their reference distribution using percentile normalization
Normalized log-2-ratio of the sample signal (steady state cultures at different dilution rates and Pi concentration), relative to the control signal (one repeat of steady state cultures at D=0.3[1/hr], Pfeed = 0.3mM). Signal is an average of 2 repeats for D= 0.1 [1/hr], Pfeed = 0.1mM and for D= 0.1 [1/hr], Pfeed = 0.3mM, and an average of 4 repeats for Pfeed = 0.3mM and for for D= 0.3 [1/hr]

source_name: wild type, D=0.1, Pi=0.1

value: wild type, chemostat steady state, Pfeed=0.1mM Pi, D=0.1[1/hr]


title: wild type, D=0.1, P=0.1, rep1

description: chemostat, Pfeed=0.1mM Pi, D=0.1[1/hr, block 1 (cy3)


title: Spleen_CZ_KO_rep4

description: imig treated Spleen of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1329

description: DS1-1329 CLL specimen as test DNA and Promega normal DNA as reference

value: chronic lymphocytic leukemia


title: Spleen_CZ_KO_rep2

description: imig treated Spleen of 9V/null mice


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1358

description: DS1-1358 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1333

description: DS1-1333 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1324

description: DS1-1324 CLL specimen as test DNA and Promega normal DNA as reference


title: wild type, no Pi, t=4[h], rep1

value: wild type. 7.3mM, control


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1326

description: DS1-1326 CLL specimen as test DNA and Promega normal DNA as reference

value: reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1301

description: DS1-1301 CLL specimen as test DNA and Promega normal DNA as reference

value: healthy


title: Spleen_CZ_KO_rep3

description: imig treated Spleen of 9V/null mice

value: CZ (imiglucerase)


title: wild type, D=0.1, P=0.3, rep2

description: chemostat, Pfeed=0.3mM Pi, D=0.1[1/hr],  block 8 (cy3)

source_name: wild type, D=0.1, Pi=0.3

value: wild type, chemostat steady state, Pfeed=0.3mM Pi, D=0.1[1/hr]


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1319

description: DS1-1319 CLL specimen as test DNA and Promega normal DNA as reference


title: wild type, D=0.1, P=0.3, rep1

description: chemostat, Pfeed=0.3mM Pi, D=0.1[1/hr], block 7 (cy3)


title: wild type, D=0.3, P=0.3, rep4

description: chemostat, Pfeed=0.3mM Pi, D=0.3[1/hr], block 2 (cy5)

source_name: wild type, D=0.3, Pi=0.3

value: wild type, chemostat steady state, Pfeed=0.3mM Pi, D=0.3[1/hr]


title: wild type, D=0.3, P=0.3, rep3

description: chemostat, Pfeed=0.3mM Pi, D=0.3[1/hr], block 1 (cy3)


title: wild type, D=0.3, P=0.3, rep1

description: chemostat, Pfeed=0.3mM Pi, D=0.3[1/hr], block 2 (cy3)


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1294

description: DS1-1294 CLL specimen as test DNA and Promega normal DNA as reference

source_name: Human CLL specimen


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1299

description: DS1-1299 CLL specimen as test DNA and Promega normal DNA as reference

source_name: Reference human genome DNA equimixture of normal male and normal female (Promega).


title: wild type, D=0.3, P=0.3, rep2

description: chemostat, Pfeed=0.3mM Pi, D=0.3[1/hr], block 4(cy3)


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1281

description: DS1-1281 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1330

description: DS1-1330 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1317

description: DS1-1317 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1241

description: DS1-1241 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1222

description: DS1-1222 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1168

description: DS1-1168 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1240

description: DS1-1240 CLL specimen as test DNA and Promega normal DNA as reference


title: Liver_saline_KO_rep2

description: saline treated Liver of 9V/null mice

value: saline


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1239

description: DS1-1239 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1271

description: DS1-1271 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1153

description: DS1-1153 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1156

description: DS1-1156 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1049

description: DS1-1049 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1058

description: DS1-1058 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1199

description: DS1-1199 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1150

description: DS1-1150 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1099

description: DS1-1099 CLL specimen as test DNA and Promega normal DNA as reference


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1140

description: DS1-1140 CLL specimen as test DNA and Promega normal DNA as reference


title: Lung_H-SWCNT, 754 days

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

description: Gene expression after 754 days in H-SWCNT-instilled in rat lungs

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Oligo Microarrays (G4131F) for 17 hours at 65°C 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan resolution 5um).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014879_D_F_20110906). Background detrend: On (Feat NCRange, LoPass). Multiplicative detrend: True. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Normalized data is the average of n=4 (CN200_004: N=3).

organism: Rattus norvegicus

source_name: Rat lungs, 754 days, H-SWCNT, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Tokyo, Japan). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Nine-week-old male Wistar rats purchased from Hokudo Co., Ltd (Sapporo, Japan) were divided into groups (n = 6 per group per time point). SWCNTs were intratracheally administered into rats as a single injection (0.2 mg, or 0.4 mg SWCNTs per rat). The vehicle control groups received 0.1% Triton X-100 per rat. After intratracheal instillation treatment, rats were housed within polycarbonate cages at a controlled temperature of 22 ◦C with a chow diet ad libitum, and were dissected at 3 days, 7 days, 30 days, 90 days, 180 days, 365 days, and 754 days post-instillation. Lungs of anesthetized rats were perfused with physiological saline, excised, and used for the morphological observation, histopathological findings and comprehensive gene expression analysis microarray analysis. All procedures and animal handling were performed according to the guidelines described in the Japanese Guide for the Care and Use of Laboratory Animals as approved by the Animal Care and Use Committee, National Institute of Advanced Industrial Science and Technology, Japan.

extract_protocol: The right lungs (n = 4 per group per time point) were homogenized using QIAzol lysis reagent with a Tissue Ruptor (Qiagen, Tokyo, Japan). Total RNA from the homogenates was extracted using the RNeasy Midi kit (Qiagen) following the manufacturer’s instructions. RNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, US) and the quality of the samples was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, US).

treatment_protocol: 0.2 mg or 0.4 mg of SWCNTs was suspended in 0.4 ml of distilled water including 0.1% Triton X-100. Each material suspension was intratracheally instilled once in rats. The animals were dissected at 3 days, 7 days, 30 days, 90 days, 180 days, 365 days, or 754 days after instillation.

value: male

tag: strain

value: Wistar

tag: post-instillation period

value: 754 days


title: LCC-2-P.24

city: Arlington

first: Jinghua

last: Gu

address: 900 N.Glebe Rd

institute: Virginia Tech

hyb_protocol: standard Affymetrix protocol

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

data_processing: The data were analyzed with Affymetrix expression console 1.2.0 using Affymetrix default analysis settings and plier as normalization method.

source_name: Epithelial cells derived from metastatic adenocarcinoma

label_protocol: Standard one-cycle Affymetrix protocol

growth_protocol: Cells were grown in phenol-red free IMEM media supplemented with 5% Charcoal-Stripped Calf Serum.   Both Control and Treated cells were kept in a 37C incubator with 5% C02 and regulated humidity.

extract_protocol: Total RNA was extracted from cell lines using TRIzol, cleaned using the QIAGEN Rneasy Mini Kit, and its quality confirmed using an Agilent 2100 Bioanalyzer and RNA 6000 LabChips

treatment_protocol: Stripped cells were grown over 96 hours (4 successive days) in phenol-red free IMEM media supplemented with 5% Charcoal-Stripped Calf Serum.  Every 24 hours the media was removed and replaced with fresh phenol-red free IMEM media supplemented with 5% Charcoal-Stripped Calf Serum (3 times total).

tag: cell line

value: Female

value: 69 years

tag: race

value: Caucasian


title: Lung_L-SWCNT, 754 days

institute: National Institute of Advanced Industrial Science and Technology

description: Gene expression after 754 days in L-SWCNT-instilled in rat lungs

source_name: Rat lungs, 754 days, L-SWCNT, replicate 4


title: LCC-2-P.21


title: Lung_L-SWCNT, 365 days

description: Gene expression after 365 days in L-SWCNT-instilled in rat lungs

source_name: Rat lungs, 365 days, L-SWCNT, replicate 3

value: 365 days


title: LCC-2-P.22


title: Lung_Control, 754 days

description: Gene expression after 754 days in vehicle control-instilled in rat lungs

source_name: Rat lungs, 754 days, Control for L-SWCNT or H-SWCNT, replicate 5


title: Lung_Control, 365 days

description: Gene expression after 365 days in vehicle control-instilled in rat lungs

source_name: Rat lungs, 365 days, Control for L-SWCNT or H-SWCNT, replicate 3


title: Lung_H-SWCNT, 180 days

description: Gene expression after 180 days in H-SWCNT-instilled in rat lungs

source_name: Rat lungs, 180 days, H-SWCNT, replicate 4

value: 180 days


title: Lung_H-SWCNT, 365 days

description: Gene expression after 365 days in H-SWCNT-instilled in rat lungs

source_name: Rat lungs, 365 days, H-SWCNT, replicate 4


title: LCC-1-P.8


title: LCC-1-P.9


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1158

description: DS1-1158 CLL specimen as test DNA and Promega normal DNA as reference


title: RR-STR-P39


title: RR-STR-P43


title: LCC-1-P.10


title: Lung_Control, 180 days

description: Gene expression after 180 days in vehicle control-instilled in rat lungs

source_name: Rat lungs, 180 days, Control for L-SWCNT or H-SWCNT, replicate 3


title: RR-STR-P38


title: Chronic lymphocytic leukemia_Dataset 1_Specimen 1118

description: DS1-1118 CLL specimen as test DNA and Promega normal DNA as reference


title: MCF7-2-STR-P60


title: SAE 12522955 L.h. Prep. 2 Cy3 t24 vs. L.p. Prep. 2 Cy5 t24

city: Cologne

first: Ludwig

last: Eichinger

address: Joseph-Stelzmann-Strasse 52

country: Germany

institute: Institute for Biochemistry 1

description: DNA microarrays cotainining 5,423 non-redundant ESTs from the D. discoideum cDNA project (Urushihara et al., 2004), partial sequences of 450 selected genes, probes of the SpotReport-10 Array Validation System (Stratagene, La Jolla, USA) and appropriate positive and negative controls were produced in-house using standard protocols (see also: http://www.uni-koeln.de/medfak/biochemie/transcriptomics/ production.e.shtml). Briefly, probes were amplified by two 100µl PCR reactions in 96-well microtiter plates using standard primers (M13F2: 5’-GTAAAACGACGGCCAGTG-3’, M13R2: 5’-C6-Aminolink-ACCATGATTACGCCAAGC-3’) for the cloned ESTs and gene-specific primers for the selected genes and the positive controls. After analysis by agarose gel electrophoresis (10µl of each reaction) the two reactions were combined, precipitated, solubilised in 11µl 25% DMSO, 1µl separated again by agarose gel electrophoresis and evaluated (Farbrother et al., 2002). Probes were transferred with the proteineer dp pipetting robot (Bruker, Germany) into 384-well microarray plates with cylindrical wells (Abgene, Hamburg, Germany) and printed onto UltraGaps slides (Corning, New York, USA) at 18°C and 45% humidity with a BioRobotics MicroGrid 600 microarray robot (Genomic Solutions, Huntingdon, UK) using MicroSpot 2500 microarraying pins. Each probe was spotted in duplicate, positive and negative controls were spotted 6, 24, 192 or 286 times and the SpotReport controls 96 times. The microarray is composed of three grids with 16 subarrays each and 14,620 spots in total. The complete microarray dataset is available at GEO, http://www.ncbi.nlm.nih.gov/geo; accession number GPL1972.

hyb_protocol: Cy3 and Cy5 labelled targets were mixed, ethanol precipitated and dissolved in 65 µl of hybridisation buffer (Noegel et al., 1985) with 500 µg/ml Fish sperm DNA (Roche, Mannheim, Germany) and 2 µM Oligo dA 18-mer. The hybridisation mix was heated to 80 °C for 10 min, applied to the microarray under a cover-slip and incubated in a hybridisation chamber (Corning, New York, USA) for 15 hours at 37°C. Post-hybridisation washes were performed twice with 2x SSC, 0.1% SDS and once with 0.1x SSC, 0.1% SDS for 5 min each, five times with 0.1x SSC and once with with 0.01x SSC for 5 sec each and dried by centrifugation at 235xg for 5 min. See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

scan_protocol: Signal detection was performed with the ScanArray 4000XL confocal laser scanner (PerkinElmer Life Sciences, Wellesley, USA). Images for Cy3 and Cy5 were obtained, spots were detected and quantified with ScanArray Express v2.2 (PerkinElmer Life Sciences), then manually inspected and if necessary corrected. See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

data_processing:
For each individual comparison four microarrays were hybridised and analysed. Two imagepairs were produced per microarray slide, one with high laser intensity so that signals for most probes and also some saturated signals were obtained and a second one with lower laser intensity so that none of the signals was saturated. This way the dynamic range of the measurement was expanded. To handle the import and export of microarray data to different analysis programs an Excel Add-In, Array tools (http://www.uni-koeln.de/med-fak/biochemie/ transcriptomics/tools-array.e.shtml), was programmed in Visual Basic. Upon import of two data files of the same microarray scanned with different laser powers the saturated spots of the high laser power scan were replaced by non-saturated spots from the low laser power scan. In addition the import also performed data filtering by flagging SpotReport controls, negative controls, empty spots, spots where only spotting solution was printed and spots whose intensities were below or equal to zero as "Bad". Fluorescence ratios were normalised by LOWESS-norma-lisation using R1.6.2 (BioConductor, http://www.bioconductor.org/). The normalized M values (M = log2 (Intensityexperiment/Intensitycontrol) were transferred into a new worksheet for significance analysis of microarrays (SAM) analysis (Tusher et al., 2001). At the transfer all probes spotted in higher replicates were reduced to double spots by averaging. Furthermore all probes that were flagged "Found" in less than half of the spots, were excluded from SAM analysis. Differentially regulated genes were identified using the one-class SAM method calculating 1000 permutations. The SAM program not only identifies the differentially regulated genes, but also predicts the number of false positives. These are the genes that are falsely reported as differentially expressed. This feature was used in all microarray experiments to set the significance level such, that the 90th percentile of the false discovery rate (FDR) was minimal.
See also Farbrother et al., Cell. Microbiol., 3:438-456, 2006.

organism: Dictyostelium discoideum

source_name: Prep. 2 - L. hackeliae t24

label_protocol: Fairplay indirect labelling kit

extract_protocol: RNA was isolated using the protocol for the isolation of cytoplasmic RNA of the RNAeasy mini kit (Qiagen AG)

value: AX2 cells treated with L. hackeliae. Total RNA was isolated 24h post infection.

source_name: Prep. 2 - L.p. JR32 t24

value: AX2 cells treated with L.p. JR32. Total RNA was isolated 24h post infection.


title: Lung_L-SWCNT, 180 days

description: Gene expression after 180 days in L-SWCNT-instilled in rat lungs

source_name: Rat lungs, 180 days, L-SWCNT, replicate 4


title: Lung_L-SWCNT, 90 days

description: Gene expression after 90 days in L-SWCNT-instilled in rat lungs

source_name: Rat lungs, 90 days, L-SWCNT, replicate 4

value: 90 days


title: SAE 12522954 L.h. Prep. 2 Cy5 t24 vs. L.p. Prep. 2 Cy3 t24


title: MCF7-2-STR-P59


title: Lung_H-SWCNT, 90 days

description: Gene expression after 90 days in H-SWCNT-instilled in rat lungs

source_name: Rat lungs, 90 days, H-SWCNT, replicate 4


title: SAE 12522953 L.h. Prep. 1 Cy3 t24 vs. L.p. Prep. 1 Cy5 t24

source_name: Prep. 1 - L. hackeliae t24

source_name: Prep. 1 - L.p. JR32 t24


title: SAE 12522952 L.h. Prep. 1 Cy5 t24 vs. L.p. Prep. 1 Cy3 t24


title: SAE 12650154 Prep. 2 Cy3 t24 vs. Prep. 4 Cy5 t24

source_name: Prep. 2 - L.p. delta DotA t24

value: cells treated with L.p. delta DotA

source_name: Prep. 4 - L.p. JR32 t24

value: cells treated with L.p. JR32


title: SAE 12650153 Prep. 2 Cy5 t24 vs. Prep. 4 Cy3 t24


title: choESC3 methylation

description:
choESC04
Ectopic endometrial stromal cells from chocolate cyst.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: GenomeStudio Methylation Module

label: Alexa555 and Alexa647

source_name: isolated endometrial stromal cells from chocolate cyst

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from cells using Qiagen DNeasy Kit according to standard instructions.

value: female

value: ovarian chocolate cyst

value: ectopic endometrial stromal cells

value: endometriosis


title: MCF7-2-STR-P58

source_name: Epithelial cells derived from metastatic adenocarcinoma


title: Lung_Control, 90 days

description: Gene expression after 90 days in vehicle control-instilled in rat lungs

source_name: Rat lungs, 90 days, Control for L-SWCNT or H-SWCNT, replicate 4

value: male


title: miR-146a 5dIL7BMC KO B

city: Freiburg

first: John

last: Lindner

address: Stübeweg 51

department: Reth

institute: MPI-IE Freiburg

hyb_protocol: standard manufacture protocol

scan_protocol: Scan_ScannerName = Agilent Technologies Scanner G2505C US91803681; Scan_NumChannels = 1; Scan_MicronsPerPixelX = 5; Scan_MicronsPerPixelY = 5; Grid_NumSubGridRows = 1; Grid_NumSubGridCols = 1; Grid_NumRows = 532; Grid_NumCols = 85; Grid_RowSpacing = 73.3235; Grid_ColSpacing = 63.5; Grid_OffsetX = 0; Grid_OffsetY = 36.6617; Grid_NomSpotWidth = 65; Grid_NomSpotHeight = 65; Grid_GenomicBuild = mm9:NCBI37:Jul2007

data_processing: Data were normalized using the R package 'limma'. Background normalization parameters were (method = normexp, offset = 16), between-array normalization parameters were (method = quantile), replicate features for each probe ID were averaged using avereps

source_name: 5d IL-7 culture, mir146a KO bone marrow, replicate B

label_protocol: oligo-dT primed synthesis of Cy3 labeled cRNA

growth_protocol: Mouse femurs were flushed with culture medium and seeded at 5 x 105 cells/ml. Culture conditions: Iscove's medium supplemented with 10% FCS, pen/strep, glutamine, and IL-7 at 37 ºC and 7% CO2.

extract_protocol: RNA extracted and purified using QIAzol

value: 5-day IL-7 supplemented bone marrow culture


title: Lung_L-SWCNT, 7 days

description: Gene expression after 7 days in L-SWCNT-instilled in rat lungs

source_name: Rat lungs, 7 days, L-SWCNT, replicate 4

value: Wistar

value: 7 days


title: Lung_H-SWCNT, 30 days

description: Gene expression after 30 days in H-SWCNT-instilled in rat lungs

source_name: Rat lungs, 30 days, H-SWCNT, replicate 4

value: 30 days


title: Lung_Control, 30 days

description: Gene expression after 30 days in vehicle control-instilled in rat lungs

source_name: Rat lungs, 30 days, Control for L-SWCNT or H-SWCNT, replicate 4


title: euESCb1 methylation

description:
ESC04
Eutopic endometrial stromal cells with endometriosis.

source_name: isolated endometrial stromal cells with endometriosis

value: eutopic endometrium

value: eutopic endometrial stromal cells


title: euESCb2 methylation

description:
ESC05
Eutopic endometrial stromal cells with endometriosis.


title: Lung_H-SWCNT, 7 days

description: Gene expression after 7 days in H-SWCNT-instilled in rat lungs

source_name: Rat lungs, 7 days, H-SWCNT, replicate 4


title: miR-146a 5dIL7BMC KO A

source_name: 5d IL-7 culture, mir146a KO bone marrow, replicate A


title: Bob1 KO 5dIL7BMC B

source_name: 5d IL-7 culture, Bob1 KO bone marrow, replicate B


title: euESCb3 methylation

description:
ESC07
Eutopic endometrial stromal cells with endometriosis.


title: choESC1 methylation

description:
choESC01
Ectopic endometrial stromal cells from chocolate cyst.


title: miR-146a 5dIL7BMC wt B

source_name: 5d IL-7 culture, BL/6 wt bone marrow, replicate B


title: Lung_H-SWCNT, 3 days

description: Gene expression after 3 days in H-SWCNT-instilled in rat lungs

source_name: Rat lungs, 3 days, H-SWCNT, replicate 4

value: 3 days


title: Lung_L-SWCNT, 30 days

description: Gene expression after 30 days in L-SWCNT-instilled in rat lungs

source_name: Rat lungs, 30 days, L-SWCNT, replicate 4


title: miR-146a 5dIL7BMC wt A

source_name: 5d IL-7 culture, BL/6 wt bone marrow, replicate A


title: euESCa3 methylation

description:
ESC09
Control eutopic endometrial stromal cells without endometriosis to compare with ones with endometriosis or ones from chocolate cysts.

source_name: isolated endometrial stromal cells without endometriosis

value: non-endometriosis


title: SAE 12650152 Prep. 1 Cy3 t24 vs. Prep. 3 Cy5 t24

description: DNA microarrays cotainining 5,423 non-redundant ESTs from the D. discoideum cDNA project (Urushihara et al., 2004), partial sequences of 450 selected genes, probes of the SpotReport-10 Array Validation System (Stratagene, La Jolla, USA) and appropriate positive and negative controls were produced in-house using standard protocols (see also: http://www.uni-koeln.de/medfak/biochemie/transcriptomics/ production.e.shtml). Briefly, probes were amplified by two 100µl PCR reactions in 96-well microtiter plates using standard primers (M13F2: 5’-GTAAAACGACGGCCAGTG-3’, M13R2: 5’-C6-Aminolink-ACCATGATTACGCCAAGC-3’) for the cloned ESTs and gene-specific primers for the selected genes and the positive controls. After analysis by agarose gel electrophoresis (10µl of each reaction) the two reactions were combined, precipitated, solubilised in 11µl 25% DMSO, 1µl separated again by agarose gel electrophoresis and evaluated (Farbrother et al., 2002). Probes were transferred with the proteineer dp pipetting robot (Bruker, Germany) into 384-well microarray plates with cylindrical wells (Abgene, Hamburg, Germany) and printed onto UltraGaps slides (Corning, New York, USA) at 18°C and 45% humidity with a BioRobotics MicroGrid 600 microarray robot (Genomic Solutions, Huntingdon, UK) using MicroSpot 2500 microarraying pins. Each probe was spotted in duplicate, positive and negative controls were spotted 6, 24, 192 or 286 times and the SpotReport controls 96 times. The microarray is composed of three grids with 16 subarrays each and 14,620 spots in total. The complete microarray dataset is available at GEO, http://www.ncbi.nlm.nih.gov/geo; accession number GPL1972.

source_name: Prep. 1 - L.p. delta DotA t24

source_name: Prep. 3 - L.p. JR32 t24


title: choESC2 methylation

description:
choESC03
Ectopic endometrial stromal cells from chocolate cyst.

source_name: isolated endometrial stromal cells from chocolate cyst


title: Lung_L-SWCNT, 3 days

description: Gene expression after 3 days in L-SWCNT-instilled in rat lungs

source_name: Rat lungs, 3 days, L-SWCNT, replicate 4


title: Lung_Control, 7 days

description: Gene expression after 7 days in vehicle control-instilled in rat lungs

source_name: Rat lungs, 7 days, Control for L-SWCNT or H-SWCNT, replicate 4


title: Bob1 KO 5dIL7BMC A

source_name: 5d IL-7 culture, Bob1 KO bone marrow, replicate A


title: Bob1 wt 5dIL7BMC A

source_name: 5d IL-7 culture, Bob1 wt bone marrow, replicate A


title: Bob1 wt 5dIL7BMC B

source_name: 5d IL-7 culture, Bob1 wt bone marrow, replicate B


title: SAE 12650151 Prep. 1 Cy5 t24 vs. Prep. 3 Cy3 t24


title: euESCa1 methylation

description:
ESC01
Control eutopic endometrial stromal cells without endometriosis to compare with ones with endometriosis or ones from chocolate cysts.


title: Lung_Control, 3 days

description: Gene expression after 3 days in vehicle control-instilled in rat lungs

source_name: Rat lungs, 3 days, Control for L-SWCNT or H-SWCNT, replicate 4


title: euESCa2 methylation

description:
ESC08
Control eutopic endometrial stromal cells without endometriosis to compare with ones with endometriosis or ones from chocolate cysts.


title: Time 35 replicate 3

status: Public on Sep 06 2013

city: Barcelona

first: Salvador

middle: Aznar

last: Benitah

address: Baldiri Reixac 10

department: Oncology

country: Spain

institute: Institute for Research in Biomedicine (IRB, Barcelona)

hyb_protocol: After fragmentation, 1650 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: Time 35

label_protocol: 500 ng of total RNA from each sample were amplified by Oligo-dT-T7 reverse transcription and labeled by in vitro transcription with T7 RNA polymerase in the presence of Cy3-CTP using the Quick Amp Labeling kit (Agilent) and purified using RNAeasy columns (Qiagen, Hilden, Germany)

extract_protocol: Total RNAs were prepared with Qiagen Rneasy minikit according to manufacturer’s protocol

value: epidermal stem cell


title: Time 25 replicate 3

source_name: Time 25


title: Time 35 replicate 1


title: Time 45 replicate 3

source_name: Time 45


title: Time 45 replicate 2


title: Time 45 replicate 1


title: Time 20 replicate 1

source_name: Time 20


title: Time 30 replicate 1

source_name: Time 30


title: Time 40 replicate 3

source_name: Time 40


title: Time 25 replicate 1


title: Time 40 replicate 2


title: Time 35 replicate 2


title: Time 15 replicate 2

source_name: Time 15


title: Time 15 replicate 1


title: Time 25 replicate 2


title: Time 20 replicate 3


title: Time 20 replicate 2


title: Time 15 replicate 3


title: Time 30 replicate 3


title: Time 30 replicate 2


title: Time 40 replicate 1


title: Time10 replicate 3


title: activated WT T-cells day 4 rep1

city: Bethesda

first: Seok-Joo

last: Kwon

state: MD

address: 37 Convent Dr.

institute: NCI/NIH

description: Gene expression data from WT Balb/C T-cells

hyb_protocol: All prepared samples were labeled and hybridized to Affymetrix mouse Gene ST 1.0 GeneChip.

scan_protocol: Affymetrix GeneChip scanner 3000 was used for scanning and Affymetrix GCOS software was used for data collection.

data_processing: RMA

source_name: Balb/c mouse WT1

label_protocol: 100 ng/ml total RNA was reverse transcribed with T7 oligo(dT) primer and amplified. After amplification, multiple copies of biotin-modified aRNA was generated by using Affymetrix GeneChip 3' IVT Express Kit according to manufacturer's protocol.

growth_protocol: Isolated CD3+ T-cells were cultured in RPMI supplemented with 10% FBS, 100 U/mL penicillin/streptomycin, and 55 mM 2-mercaptoethanol at 37°C in 95% humidity and 5% CO2.

extract_protocol: Total RNA was isolated using the RNeasy Kit from Qiagen. We followed company's instruction.

treatment_protocol: Isolated cells were cultured on tissue culture plates with 3 mg/ml of plate-coated anti-mouse CD3 antibody and 3 mg//ml of soluble anti-mouse CD28 antibody for 4 days.

value: CD3+ T-cells

value: WT

value: 12 wk

tag: genetic background

value: Balb/C

value: Male


title: activated KLF13 KO T-cells day 4 rep 3

description: Gene expression data from KLF13 KO Balb/C T-cells

source_name: Balb/c mouse KLF13 KO3

value: KLF13 KO


title: activated KLF13 KO T-cells day 4 rep 1

source_name: Balb/c mouse KLF13 KO1


title: Time 5 replicate 2

source_name: Time 5


title: Time 5 replicate 1


title: Time 5 replicate 3


title: Time 0 replicate 3

source_name: Time 0


title: Time 0 replicate 1


title: Time10 replicate 1


title: activated KLF13 KO T-cells day 4 rep 2

source_name: Balb/c mouse KLF13 KO2


title: activated KLF13 KO T-cells day 4 rep 4

source_name: Balb/c mouse KLF13 KO4


title: cKO.SHAM 2

city: London

first: Byambajav

last: Buyandelger

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

description: gene expression data from cKO mouse heart after 4 weeks SHAM

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

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: mouse heart after 4 weeks SHAM

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

growth_protocol: male mice were at 8-10 weeks old before TAC

extract_protocol: total RNA was extracted according to manufacturer's instructions using Qiagen RNeasy fibrous tissue kit

treatment_protocol: mice underwent to TAC surgery for 4 weeks

value: sham

value: zbtb17 cKO

value: heart


title: Control.SHAM 3

description: gene expression data from Control mouse heart after 4 weeks SHAM

value: control


title: activated WT T-cells day 4 rep3

source_name: Balb/c mouse WT3


title: Control.TAC 3

description: gene expression data from Control mouse heart after 4 weeks TAC

source_name: mouse heart after 4 weeks TAC

value: transverse aortic constriction


title: Control.TAC 1


title: cKO.SHAM 1


title: Control.SHAM 2


title: Control.TAC 4


title: Control.TAC 2


title: Control.SHAM 1


title: Control.SHAM 4


title: cKO.TAC 4

description: gene expression data from cKO mouse heart after 4 weeks TAC


title: cKO.TAC 2


title: cKO.SHAM 3


title: Time10 replicate 2


title: Time 0 replicate 2


title: activated KLF13 KO T-cells day 4 rep 5

source_name: Balb/c mouse KLF13 KO5


title: cKO.SHAM 4


title: cKO.TAC 1


title: cKO.TAC 3


title: activated WT T-cells day 4 rep5

source_name: Balb/c mouse WT5


title: activated WT T-cells day 4 rep4

source_name: Balb/c mouse WT4


title: PShTert-AR_16h_Cur

city: Adelaide

first: Lauren

last: Giorgio

state: SA

address: Basil Hetzel Institute, 28 Woodville Rd Woodville South

department: Medicine

country: Australia

institute: University of Adelaide

hyb_protocol: Standard Affymetrix hybridization protocol.

scan_protocol: Standard Affymetrix scanning protocol.

data_processing: Raw data was processed in R using Bioconductor and Limma. Array data was normalized using RMA, filtered by mapped probes and an arbitrary minimum threshold.

source_name: PShTert-AR, 16 h 30 uM curcumin

label_protocol: Biotinylated cRNA were prepared from 300ng RNA according to the standard Affymetrix protocol.

growth_protocol: PShTert-AR cells were maintained in RPMI 1640 medium containing 5% fetal bovine serum.

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: Plated 3x10E4 cells/well in 6-well dishes for 48 h in RPMI 1640 containing 5% fetal bovine serum. Cells were treated with 30 uM curcumin for 4, 8, 12 or 16 h or equivalent vehicle control for 16 h in phenol-red free RPMI 1640.

value: PShTert-AR

value: immortalized androgen-receptor-positive prostate fibroblasts

value: 16 h 30 uM curcumin


title: Baby tooth PDL tissue-2

city: Seoul

first: Seong-Oh

last: Kim

address: 250 Seongsanno, Seodaemun-gu

department: Pediatric dentistry

country: South Korea

institute: Yonsei University College of Dentistry

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.3.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

source_name: baby tooth PDL

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: PDL samples were obtained from permanent premolar (n=38; from 4 males and 10 females, aged 10-19 years) and anterior deciduous teeth (n=31; from 14 males and 12 females aged 5-13 years) from 40 healthy persons

extract_protocol: The PDL tissues were homogenized using a homogenizer. The Rneasy Fibrous Mini kit (Qiagen) was then used to extract total RNA from the PDL tissues, according to the manufacturer's instructions.

treatment_protocol: PDL samples were obtained from healthy permanent premolars extracted for orthodontic reasons and from anterior deciduous teeth extracted for space management in 40 healthy persons. The extracted teeth were immediately frozen and stored in liquid nitrogen. The PDL tissues were obtained carefully using sterile curettes, from the middle-third or the nonresorbed root surface in case of deciduous teeth.

value: baby tooth PDL


title: Baby tooth PDL tissue-1


title: Adult tooth PDL tissue-4

source_name: adult tooth PDL

value: adult tooth PDL


title: PShTert-AR_12h_Cur

source_name: PShTert-AR, 12 h 30 uM curcumin

value: 12 h 30 uM curcumin


title: Baby tooth PDL tissue-3


title: activated WT T-cells day 4 rep2

source_name: Balb/c mouse WT2

value: CD3+ T-cells


title: PShTert-AR_4h_Cur

source_name: PShTert-AR, 4 h 30 uM curcumin

value: 4 h 30 uM curcumin


title: PShTert-AR_8h_Cur

source_name: PShTert-AR, 8 h 30uM curcumin

value: 8 h 30uM curcumin


title: PShTert-AR_16h_VC

source_name: PShTert-AR, 16 h vehicle

value: 16 h vehicle (DMSO)


title: GMP_AP-CML, biorep_3

city: Glasgow

first: david

last: irvine

address: 21 shelly road

department: MVLS

institute: University of Glasgow

hyb_protocol: As per standard Afymetrix protocol using Ambion WT expression kit.

scan_protocol: As per standard Affymetrix protocol, with GeneChip Scanner 3000 7G.

data_processing: Following initial quality control, the raw CEL files were summarised and normalised using Partek GS bioinformatics platform on default settings.

source_name: Peripheral blood at diagnosis, AP CML, GMP

label_protocol: As per standard Affymetrix protocol using Ambion WT expression kit.

growth_protocol: Leukapheresis or PB specimens were obtained with written informed consent, in accordance with the declaration of Helsinki and with Greater Glasgow and Clyde NHS Trust Ethics Committee approval from patients newly diagnosed with CP, AP or BC CML. Each sample was determined to by Ph + by FISH and BCR-ABL + by PCR. Samples were assessed for viability and proportion of CD34 + cells. If suitable for further processing, small volume samples (50mL) were purified using Histopaque 1077 to enrich for MNC followed by CD34 + enrichment using CD34 + selection columns and larger volume samples (apheresis samples) were purified directly through the CliniMACS system. Normal CD34+ cells were obtained from consenting volunteers undergoing stem cell mobilization with GCSF for subsequent autologous stem cell transplant for myeloma or lymphoma. All cells were cryopreserved in liquid nitrogen until required.

extract_protocol: As above using Qiagen RNeasy mini or micro kits as appropriate to extract RNA which was quantified and assessed for quality prior to storage at -80oC.

treatment_protocol: Enriched CD34+ samples were thawed, viable cell count performed and cultured over night in growth factor supplemented media. The following day the cells were washed twice in DPBS / 2% FCS and a viable cell count performed. The cells were simultaneously stained with lineage (lin) cocktail-FITC, CD90-PE, CD34PerCP, CD38PE-Cy7, CD123-APC and CD45RA-Pacific Blue for 30min at RT in the dark. They were then washed twice in DPBS / 2% FCS prior to re-suspension in multiple FACS tubes placed on ice. This allowed sorting of the cells into HSC CD34 + 38 - lin - CD45RA - CD90 + ; MPP CD34 + 38 - lin - CD45RA - CD90 - ; CMP CD34 + 38 + lin - CD123 + CD45RA - ; [GMP] CD34 + 38 + lin - CD123 + CD45RA + and MEP CD34 + 38 + lin - CD123 - CD45RA - sub-populations on a FACS Aria cell sorter. This machine allows for the concurrent sorting of up to 4 populations, the fifth population (MPP) was swapped in when sufficient cells for one of the other populations had been collected. Following sorting the cells were counted and divided into aliquots either for cell culture (progenitor and proliferation assays) or for RNA purification using the RNEasy mini or micro kit. Isolated RNA was subsequently checked for purity and integrity. All samples were subject to FISH analysis to confirm the presence and the proportion of cells carrying BCR-ABL in each sample in each sub-population. RNA processing and microarray analysis were carried out at the Sir Henry Wellcome Functional Genomics Facility (SHWFGF, University of Glasgow) using the Affymetrix GeneChip Human Gene 1.0 ST arrays according to the manufacturer's instructions.

value: chronic myeloid leukaemia (CML)

tag: disease stage

value: accelerated phase (AP)

value: GMP

tag: patient identifier

value: AP-CML 3


title: CMP_AP-CML, biorep_4

source_name: Peripheral blood at diagnosis, AP CML, CMP

value: CMP

value: AP-CML 4


title: GMP_BC-CML, biorep_1

source_name: Peripheral blood at diagnosis, BC CML, GMP

value: blastic phase (BC)

value: BC-CML 1


title: HSC_BC-CML, biorep_1

source_name: Peripheral blood at diagnosis, BC CML, HSC

value: HSC


title: HSC_BC-CML, biorep_2

value: BC-CML 2


title: HSC_AP-CML, biorep_4

source_name: Peripheral blood at diagnosis, AP CML, HSC


title: MEP_BC-CML, biorep_2

source_name: Peripheral blood at diagnosis, BC CML, MEP

value: MEP


title: CMP_AP-CML, biorep_3


title: MPP_AP-CML, biorep_3

source_name: Peripheral blood at diagnosis, AP CML, MPP

value: MPP


title: MEP_AP-CML, biorep_4

source_name: Peripheral blood at diagnosis, AP CML, MEP


title: MEP_AP-CML, biorep_3


title: MEP_BC-CML, biorep_1


title: MPP_BC-CML, biorep_2

source_name: Peripheral blood at diagnosis, BC CML, MPP


title: GMP_AP-CML, biorep_2

value: AP-CML 2


title: MPP_BC-CML, biorep_1


title: CMP_AP-CML, biorep_1

value: AP-CML 1


title: MEP_AP-CML, biorep_2


title: CMP_AP-CML, biorep_2


title: GMP_AP-CML, biorep_4


title: CMP_BC-CML, biorep_2

source_name: Peripheral blood at diagnosis, BC CML, CMP


title: HSC_AP-CML, biorep_2


title: HSC_AP-CML, biorep_3


title: GMP_AP-CML, biorep_1


title: HSC_AP-CML, biorep_1


title: MEP_AP-CML, biorep_1


title: MEP_CP-CML, biorep_6

source_name: Peripheral blood at diagnosis, CP CML, MEP

value: chronic phase (CP)

value: CP-CML 6


title: MPP_AP-CML, biorep_4


title: CMP_BC-CML, biorep_1


title: GMP_CP-CML, biorep_6

source_name: Peripheral blood at diagnosis, CP CML, GMP


title: HSC_CP-CML, biorep_6

source_name: Peripheral blood at diagnosis, CP CML, HSC


title: CMP_CP-CML, biorep_6

source_name: Peripheral blood at diagnosis, CP CML, CMP


title: HSC_CP-CML, biorep_5

value: CP-CML 5


title: CMP_CP-CML, biorep_5

value: chronic myeloid leukaemia (CML)


title: GMP_CP-CML, biorep_4

value: CP-CML 4


title: GMP_BC-CML, biorep_2

value: GMP


title: CMP_CP-CML, biorep_3

value: CP-CML 3


title: MEP_CP-CML, biorep_3


title: MEP_CP-CML, biorep_4


title: GMP_CP-CML, biorep_2

value: CP-CML 2


title: MEP_CP-CML, biorep_1

value: CP-CML 1


title: CMP_CP-CML, biorep_2

value: CMP


title: HSC_CP-CML, biorep_4


title: HSC_CP-CML, biorep_3


title: CMP_normal, biorep_3

source_name: Peripheral blood, normal, CMP

value: normal

value: normal 3


title: GMP_CP-CML, biorep_1


title: MEP_CP-CML, biorep_5


title: GMP_normal, biorep_3

source_name: Peripheral blood, normal, GMP


title: MEP_CP-CML, biorep_2


title: GMP_CP-CML, biorep_3


title: GMP_CP-CML, biorep_5


title: CMP_CP-CML, biorep_1


title: CMP_CP-CML, biorep_4


title: HSC_normal, biorep_3

source_name: Peripheral blood, normal, HSC

value: HSC


title: CMP_normal, biorep_2

value: normal 2


title: GMP_normal, biorep_2


title: MPP_normal, biorep_3

source_name: Peripheral blood, normal, MPP

value: MPP


title: HSC_CP-CML, biorep_2


title: MEP_normal, biorep_2

source_name: Peripheral blood, normal, MEP

value: MEP


title: MPP_normal, biorep_2


title: MEP_normal, biorep_1

value: normal 1


title: HSC_CP-CML, biorep_1

value: chronic phase (CP)


title: HSC_normal, biorep_2


title: GMP_normal, biorep_1


title: CMP_normal, biorep_1


title: HSC_normal, biorep_1


title: MEP_normal, biorep_3


title: primary epithelial cells rep2

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

institute: Durham University

description: Total RNA from human tonsillar epithelial cells

hyb_protocol: 1μg of fragmented cRNA was hybridized onto Human gene 1.0 ST array using Affymetrix hybridization protocol.

scan_protocol: Affymetrix Standard protocol

data_processing: normalized using RMA-Sketch of Affymetrix Expression Console

source_name: Primary epithelial cell

label_protocol: Affymetrix labelling protocol

growth_protocol: Cells were cultured in serum-free keratinoctye growth medium, which selects for pure populations of keratinocytes.

extract_protocol: Total cellular RNA was isolated using RNeasy Mini Kit (Qiagen)

treatment_protocol: Primary tonsil epithelial cells were isolated form collagenase digests of lymphoid depleted tonsil epithelium by Claire Shannon-Low who holds ethical approval.

value: primary tonsil epithelial cells


title: OCM1A_shBAP1_2

city: Miami

last: Harbour

state: FL

address: 900 N.W. 17th Street

institute: University of Miami

description: SAMPLE 12

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw expression data were subjected to cubic spline normalization in GenomeStudio (version 2011.1)

source_name: Uveal Melanoma Cell Line

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

growth_protocol: Cells were grown under puromycin selection for 4 weeks after lentiviral infection

extract_protocol: RNA was extracted from cells using Qiagen's RNeasy Mini Kit according to manufacturers instructions

treatment_protocol: Cells were infected with lentivirus expressing either GFP (control) or BAP1 shRNA

tag: shRNA

tag: replicate

tag: length of selection

value: 4 weeks


title: MPP_normal, biorep_1


title: OCM1A_shBAP1_1

description: SAMPLE 10


title: OCM1A_shGFP_2

description: SAMPLE 11

value: shGFP


title: 92.1_shBAP1_2

description: SAMPLE 4


title: Mel290_shGFP_1

description: SAMPLE 5


title: Mel290_shGFP_2

description: SAMPLE 7


title: OCM1A_shGFP_1

description: SAMPLE 9


title: C666.1 rep3

description: Total RNA from C666.1 cell line

source_name: C666-1 cell line

growth_protocol: C666.1 cells were cultured in keratinocyte serum-free medium

extract_protocol: Total cellular RNA was isolated using RNAeasy Mini Kit (Qiagen)

treatment_protocol: C666.1 cell line is derived from an undifferentiated nasopharyngeal carcinoma xenograft of southern Chinese origin.

tag: source tissue

value: undifferentiated nasopharyngeal carcinoma xenograph


title: C666.1 rep1

description: Total RNA from C666.1 cell line


title: Mel290_shBAP1_1

description: SAMPLE 6


title: 92.1_shGFP_2

description: SAMPLE 3


title: C666.1 rep2

description: Total RNA from C666.1 cell line


title: Mel290_shBAP1_2

description: SAMPLE 8


title: 92.1_shGFP_1

description: SAMPLE 1


title: primary epithelial cells rep1

tag: cell type


title: Diabetic 2

city: Campinas

first: Flávia

middle: Gerelli

last: Ghiraldini

state: São Paulo

address: Av Bertrand Russel sno.

department: Structural and Functional Biology

country: Brazil

institute: Unicamp

description: Technical replicate 1

data_processing:
For the differential expression the data was normolised, background removed using software GenomeStudio (Illumina). The reference sample was Normoglycemic NOD for comparisons against diabetic NOD mice and Young-Adult Balb/c for comparisons aganst middle-aged Balb/c mice. LIMMA statistical test was applied for those samples using sorftware R.
It was considered differential expressed genes with P-values < 0.05 and Fold Change >2.0.

source_name: mouse liver

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA amplification kit (Ambion) for Illumina arrays

growth_protocol: Mice were maintained in climatized facility with 12-hour light cycle and fed extrused chow and water ad libitum.

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 (RIN>7.0).

treatment_protocol: The young-adult group and aged group were sacrificed only when mice reached the desired age. For the diabetic group, NOD glycemia was measured weekly by cauldal punction using Accu Chek Performa. Animals with glycemia higher than 500 mg/dl for 3 consecutive weeks were sacrificed and labeled as Diabetic. For the normoglycemic group, animals at the same age as diabetic animals and with glycemia between 90 - 190 mlg/dl were used.

value: NOD

value: 16 weeks old

tag: glycemia

value: Hyperglycemic


title: T47D_mCDPR_R5020_6h_rep3

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description:
TPK318_2
Replicate 3 of 3.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were filtered and any probes with a detection P value less than 0.05 were removed from the normalized dataset. The data was then normalized using log2 transformation and quantile normalization with R using the lumi bioconductor package.

source_name: T47D-Y cells stably expressing mutant CD domain PR-B, treated with 10nM R5020, for 6 hours

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

growth_protocol: Samples grown in complete medium (MEM, 5% FBS, 1% NEAA, 1% pen/strep, 6ng/ml insulin, 200 ug/ml G418) before 1 day starvation in IMEM medium, then treated in IMEM medium for 6 hr.

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.

treatment_protocol: Samples treated in IMEM medium, with or without 10e-8 M R5020 for 6 hr.

tag: parental cell line

value: breast cancer cells

tag: stable vector integration

tag: treatment duration

value: 6 hr


title: primary epithelial cells rep3


title: T47D_mCDPR_R5020_6h_rep1

description:
TPK316
Replicate 1 of 3.

tag: treatment


title: Diabetic 3

description: Biological replicate 2

tag: strain

tag: age


title: Normoglycemic 2

description: Technical replicate 1

value: Normoglycemic


title: Normoglycemic 1

description: Biological replicate 1


title: T47D_mCDPR_R5020_6h_rep2

description:
TPK317
Replicate 2 of 3.


title: T47D_mCDPR_vehicle_6h_rep3

description:
TPK315
Replicate 3 of 3.

source_name: T47D-Y cells stably expressing mutant CD domain PR-B, treated with ethanol vehicle, for 6 hours

value: ethanol vehicle


title: Diabetic 1

description: Biological replicate 1


title: 92.1_shBAP1_1

description: SAMPLE 2

tag: cell line


title: Normoglycemic 3

description: Biological replicate 2


title: T47D_WTPR_R5020_6h_rep3

description:
TPK312
Replicate 3 of 3.

source_name: T47D-Y cells stably expressing wild type PR-B, treated with 10nM R5020, for 6 hours


title: Aged 2

description: Biological replicate 2

value: Balb/c

value: 47 weeks old


title: T47D_WTPR_R5020_6h_rep2

description:
TPK311
Replicate 2 of 3.


title: T47D_WTPR_R5020_6h_rep1

description:
TPK310
Replicate 1 of 3.