title: Xba_277

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 79, status: 0


title: Xba_278

status: Public on May 05 2009

type: genomic

city: San Diego

first: Jack

last: Yu

state: CA

address: 3210 Merryfield Row

country: USA

institute: Veridex, LLC

description: Gene copy data from breast cancer

hyb_protocol: Biotinylated genomic DNA fragments were hybridized for 17 hr at 48C on Affy Human Mapping 100K Array sets.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip scanner

data_processing: The data were analyzed with Affy GTYPE and CCNT 3.0 software to generate copy numbers for the probes.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: human breast cancer, time: 50, status: 1

label_protocol: Biotinylated genomic DNA were prepared according to the standard Affymetrix protocol

extract_protocol: QIAamp DNA mini kit according to the manufacturer

tag: age

tag: differentiation

value: moderate

tag: er

value: Pos

tag: menopause

value: pre

tag: pr

value: Neg

tag: survival time (months)

tag: status (0=no relapse, 1=relapse)


title: Xba_272

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 83, status: 0

value: post


title: Xba_235

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 33, status: 1

value: poor


title: Xba_262

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 18, status: 1


title: Xba_605

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 57, status: 0


title: Xba_226

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 38, status: 1


title: Xba_249

description: Gene copy data from breast cancer


title: Xba_271

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 64, status: 1


title: Xba_253

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 19, status: 1


title: Xba_252

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 15, status: 1


title: Xba_270

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 59, status: 0


title: Xba_254

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 48, status: 1


title: Xba_250

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 14, status: 1


title: Xba_223

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 23, status: 1


title: Xba_217

description: Gene copy data from breast cancer


title: Xba_234

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 37, status: 1


title: Xba_222

description: Gene copy data from breast cancer


title: Xba_247

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 44, status: 1


title: Xba_246

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 47, status: 1


title: Xba_231

description: Gene copy data from breast cancer


title: Xba_546

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 62, status: 1


title: Xba_230

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 24, status: 1


title: Xba_140

description: Gene copy data from breast cancer


title: Xba_138

description: Gene copy data from breast cancer


title: Xba_31

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 30, status: 1


title: Xba_130

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 26, status: 1


title: Xba_134

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 28, status: 1


title: Xba_39

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 43, status: 1


title: Xba_126

description: Gene copy data from breast cancer


title: Xba_258

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 9, status: 1


title: Xba_81

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 11, status: 1


title: Xba_11

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 109, status: 0


title: Xba_200

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 108, status: 0


title: Xba_913

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 80, status: 1


title: Xba_49

description: Gene copy data from breast cancer


title: Xba_44

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 169, status: 0


title: Xba_5

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 118, status: 0


title: Xba_15

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 99, status: 0


title: Xba_125

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 93, status: 0


title: Xba_75

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 15, status: 1


title: Xba_205

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 23, status: 1


title: Xba_72

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 134, status: 0


title: Xba_416

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 60, status: 1


title: Xba_137

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 32, status: 1


title: Xba_33

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 7, status: 1


title: Xba_40

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 102, status: 0


title: Xba_899

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 86, status: 0


title: Xba_63

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 14, status: 1


title: Xba_62

description: Gene copy data from breast cancer


title: Xba_616

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 88, status: 0


title: Xba_19

description: Gene copy data from breast cancer


title: Xba_86

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 104, status: 0


title: Xba_614

description: Gene copy data from breast cancer


title: Xba_615

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 92, status: 0


title: Xba_239

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 35, status: 1


title: Xba_696

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 51, status: 1


title: Xba_606

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 66, status: 0


title: Xba_240

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 36, status: 1


title: Xba_241

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 17, status: 1


title: Xba_611

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 75, status: 0


title: Xba_9

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 125, status: 0


title: Xba_244

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 39, status: 1


title: Xba_540

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 49, status: 1


title: Xba_612

description: Gene copy data from breast cancer


title: Xba_550

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 58, status: 1


title: Xba_273

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 81, status: 0


title: Xba_613

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 93, status: 0


title: Xba_900

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 108, status: 0


title: Xba_237

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 19, status: 1


title: Xba_141

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 25, status: 1


title: Hind_JA.1563

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 103, status: 0


title: Xba_91

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 20, status: 1


title: Hind_JA.120

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 96, status: 0


title: Xba_843

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 110, status: 0


title: Hind_JA.2038

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 102, status: 0


title: Hind_JA.1222

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 7, status: 1


title: Hind_JA.2001

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 4, status: 1


title: Hind_JA.2007

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 91, status: 0


title: Hind_JA.2025

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 83, status: 0


title: Xba_856

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 88, status: 0


title: Hind_JA.1060

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 71, status: 0


title: Hind_JA.245

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 22, status: 1


title: Hind_JA.248

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 29, status: 1


title: Hind_JA.1978

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 69, status: 0


title: Hind_JA.632

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 61, status: 0


title: Hind_JA.1938

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 90, status: 0


title: Hind_JA.941

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 87, status: 0


title: Hind_JA.1650

description: Gene copy data from breast cancer


title: Hind_JA.1501

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 74, status: 0


title: Hind_JA.1455

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 64, status: 0


title: Hind_JA.1524

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 68, status: 0


title: Hind_JA.243

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 10, status: 1


title: Hind_JA.1967

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 80, status: 0


title: Hind_JA.076

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 136, status: 0


title: Hind_JA.1069

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 24, status: 1


title: Hind_JA.1482

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 86, status: 0


title: Hind_JA.1593

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 127, status: 0


title: Hind_JA.872

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 69, status: 1


title: Hind_JA.746

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 123, status: 0


title: Hind_JA.1939

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 152, status: 0


title: Hind_JA.1535

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 42, status: 1


title: Hind_JA.282

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 83, status: 0


title: Hind_JA.1853

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 63, status: 0


title: Hind_JA.1487

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 71, status: 0


title: Hind_JA.1568

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 115, status: 0


title: Hind_JA.1966

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 61, status: 0


title: Hind_JA.1571

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 76, status: 0


title: Hind_JA.1412

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 128, status: 0


title: Hind_JA.401

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 12, status: 1


title: Hind_JA.1858

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 89, status: 0


title: Hind_JA.812

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 117, status: 0


title: Hind_98

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 14, status: 1


title: Hind_621

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 80, status: 0

value: good


title: Hind_100

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 39, status: 1


title: Hind_216

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 13, status: 1


title: Hind_111

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 98, status: 0


title: Hind_107

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 94, status: 0


title: Hind_JA.1828

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 103, status: 0


title: Hind_94

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 109, status: 0


title: Hind_61

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 11, status: 1


title: Hind_3

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 101, status: 0


title: Hind_14

description: Gene copy data from breast cancer


title: Hind_37

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 7, status: 1


title: Hind_118

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 95, status: 0


title: Hind_121

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 23, status: 1


title: Hind_29

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 25, status: 1


title: Hind_879

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 108, status: 0


title: Hind_713

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 156, status: 0


title: Hind_862

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 87, status: 0


title: Hind_846

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 84, status: 0


title: Hind_864

description: Gene copy data from breast cancer


title: Hind_90

description: Gene copy data from breast cancer


title: Hind_20

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 128, status: 0


title: Hind_93

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 48, status: 1


title: Hind_855

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 88, status: 0


title: Hind_853

description: Gene copy data from breast cancer


title: Hind_857

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 98, status: 0


title: Hind_833

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 97, status: 0


title: Hind_JA.1821

description: Gene copy data from breast cancer


title: Hind_839

description: Gene copy data from breast cancer


title: Hind_777

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 153, status: 0


title: Hind_774

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 120, status: 0


title: Hind_805

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 103, status: 0


title: Hind_637

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 54, status: 0


title: Hind_844

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 114, status: 0


title: Hind_287

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 79, status: 0


title: Hind_894

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 123, status: 0


title: Hind_264

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 33, status: 1


title: Hind_780

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 124, status: 0


title: Hind_267

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 59, status: 0


title: Hind_265

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 66, status: 0


title: Hind_782

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 148, status: 0


title: Hind_806

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 85, status: 0


title: Hind_263

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 32, status: 1


title: Hind_65

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 9, status: 1


title: Hind_710

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 50, status: 0


title: Hind_293

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 56, status: 0


title: Hind_259

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 14, status: 1


title: Hind_813

description: Gene copy data from breast cancer


title: Hind_275

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 105, status: 0


title: Hind_55

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 11, status: 1


title: Hind_260

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 29, status: 1


title: Hind_136

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 25, status: 1


title: Hind_268

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 82, status: 0


title: Hind_261

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 18, status: 1


title: Hind_255

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 6, status: 1


title: Hind_633

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 76, status: 0


title: Xba_34

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 100, status: 0


title: Hind_215

description: Gene copy data from breast cancer


title: Hind_78

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 152, status: 0


title: Hind_74

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 90, status: 0


title: Hind_79

description: Gene copy data from breast cancer


title: Hind_84

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 114, status: 0


title: Hind_38

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 133, status: 0


title: Hind_96

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 30, status: 1


title: Hind_113

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 101, status: 0


title: Hind_8

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 37, status: 1

value: Tx


title: Hind_7

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 106, status: 0


title: Hind_6

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 9, status: 1


title: Hind_204

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 24, status: 1


title: Hind_48

description: Gene copy data from breast cancer


title: Hind_71

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 12, status: 1


title: Hind_707

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 98, status: 0


title: Hind_64

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 134, status: 0


title: Hind_609

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 79, status: 0


title: Hind_103

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 97, status: 0


title: Hind_236

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 16, status: 1


title: Hind_292

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 58, status: 0


title: Hind_213

description: Gene copy data from breast cancer


title: Hind_647

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 105, status: 0


title: Hind_737

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 123, status: 0


title: Hind_112

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 17, status: 1


title: Hind_115

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 15, status: 1


title: Hind_56

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 153, status: 0


title: Hind_68

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 112, status: 0


title: Hind_41

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 25, status: 1


title: Hind_106

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 40, status: 1


title: Hind_88

description: Gene copy data from breast cancer


title: Hind_110

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 8, status: 1


title: Hind_728

description: Gene copy data from breast cancer


title: Hind_139

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 111, status: 0


title: Hind_50

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 125, status: 0


title: Hind_104

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 11, status: 1


title: Hind_108

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 28, status: 1


title: Hind_54

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 144, status: 0


title: Hind_89

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 2, status: 1


title: Hind_233

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 5, status: 1


title: Hind_105

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 99, status: 0


title: Hind_18

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 34, status: 1


title: Hind_67

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 19, status: 1


title: Hind_122

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 104, status: 0


title: Hind_21

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 14, status: 1


title: Hind_114

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 86, status: 0


title: Hind_57

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 20, status: 1


title: Hind_80

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 97, status: 0


title: Hind_28

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 155, status: 0


title: Hind_124

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 8, status: 1


title: Hind_46

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 109, status: 0


title: Hind_99

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 107, status: 0


title: Hind_203

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 29, status: 1


title: Hind_133

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 87, status: 0


title: Hind_35

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 30, status: 1


title: Hind_66

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 152, status: 0


title: Hind_82

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 143, status: 0


title: Hind_17

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 137, status: 0


title: Hind_92

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 146, status: 0


title: Hind_32

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 84, status: 0


title: Hind_877

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 66, status: 1


title: Hind_876

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 60, status: 1


title: Hind_201

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 113, status: 0


title: Hind_874

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 70, status: 1


title: Hind_873

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 59, status: 1


title: Hind_871

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 71, status: 1


title: Hind_870

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 56, status: 1


title: Hind_712

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 86, status: 0


title: Hind_714

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 157, status: 0


title: Hind_867

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 55, status: 1


title: Hind_861

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 95, status: 0


title: Hind_865

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 92, status: 0


title: Hind_868

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 77, status: 1


title: Hind_863

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 107, status: 0


title: Hind_847

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 105, status: 0


title: Hind_845

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 109, status: 0


title: Hind_852

description: Gene copy data from breast cancer


title: Hind_909

description: Gene copy data from breast cancer


title: Hind_836

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 84, status: 0


title: Hind_841

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 96, status: 0


title: Hind_808

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 110, status: 0


title: Hind_849

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 88, status: 0


title: Hind_851

description: Gene copy data from breast cancer


title: Hind_820

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 116, status: 0


title: Hind_809

description: Gene copy data from breast cancer


title: Hind_804

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 121, status: 0


title: Hind_866

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 75, status: 1


title: Hind_810

description: Gene copy data from breast cancer


title: Hind_817

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 108, status: 0


title: Hind_797

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 122, status: 0


title: Hind_903

description: Gene copy data from breast cancer


title: Hind_798

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 132, status: 0


title: Hind_848

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 86, status: 0


title: Hind_785

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 138, status: 0


title: Hind_794

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 101, status: 0


title: Hind_789

description: Gene copy data from breast cancer


title: Hind_787

description: Gene copy data from breast cancer


title: Hind_793

description: Gene copy data from breast cancer


title: Hind_791

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 87, status: 0


title: Hind_765

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 147, status: 0


title: Hind_772

description: Gene copy data from breast cancer


title: Hind_768

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 129, status: 0


title: Hind_815

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 107, status: 0


title: Hind_754

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 109, status: 0


title: Hind_796

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 143, status: 0


title: Hind_891

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 112, status: 0


title: Hind_749

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 141, status: 0


title: Hind_751

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 125, status: 0


title: Hind_887

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 161, status: 0


title: Hind_762

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 116, status: 0


title: Hind_778

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 104, status: 0


title: Hind_795

description: Gene copy data from breast cancer


title: Hind_741

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 124, status: 0


title: Hind_779

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 137, status: 0


title: Hind_760

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 98, status: 0


title: Hind_747

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 96, status: 0


title: Hind_648

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 95, status: 0


title: Hind_729

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 86, status: 0


title: Hind_727

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 121, status: 0


title: Hind_767

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 134, status: 0


title: Hind_726

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 105, status: 0


title: Hind_738

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 126, status: 0


title: Hind_646

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 100, status: 0


title: Hind_631

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 99, status: 0


title: Hind_635

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 119, status: 0


title: Hind_641

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 77, status: 0


title: Hind_642

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 54, status: 0


title: Hind_769

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 84, status: 0


title: Hind_629

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 131, status: 0


title: Hind_627

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 113, status: 0


title: Hind_703

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 61, status: 1


title: Hind_630

description: Gene copy data from breast cancer


title: Hind_625

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 72, status: 1


title: Hind_600

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 66, status: 0


title: Hind_602

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 57, status: 1


title: Hind_601

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 52, status: 0


title: Hind_620

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 62, status: 1


title: Hind_605

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 57, status: 0


title: Hind_288

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 71, status: 1


title: Hind_284

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 72, status: 0


title: Hind_290

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 100, status: 0


title: Hind_286

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 107, status: 0


title: Hind_277

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 79, status: 0


title: Hind_271

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 64, status: 1


title: Hind_278

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 50, status: 1


title: Hind_262

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 18, status: 1


title: Hind_272

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 83, status: 0


title: Hind_249

description: Gene copy data from breast cancer


title: Hind_696

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 51, status: 1


title: Hind_285

description: Gene copy data from breast cancer


title: Hind_276

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 54, status: 0


title: Hind_270

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 59, status: 0


title: Hind_250

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 14, status: 1


title: Hind_254

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 48, status: 1


title: Hind_246

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 47, status: 1


title: Hind_252

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 15, status: 1


title: Hind_247

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 44, status: 1


title: Hind_231

description: Gene copy data from breast cancer


title: Hind_253

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 19, status: 1


title: Hind_235

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 33, status: 1


title: Hind_640

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 81, status: 0


title: Hind_223

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 23, status: 1


title: Hind_234

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 37, status: 1


title: Hind_222

description: Gene copy data from breast cancer


title: Hind_138

description: Gene copy data from breast cancer


title: Hind_226

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 38, status: 1


title: Hind_546

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 62, status: 1


title: Hind_258

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 9, status: 1


title: Hind_130

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 26, status: 1


title: Hind_134

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 28, status: 1


title: Hind_416

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 60, status: 1


title: Hind_913

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 80, status: 1


title: Hind_31

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 30, status: 1


title: Hind_126

description: Gene copy data from breast cancer


title: Hind_230

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 24, status: 1


title: Hind_125

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 93, status: 0


title: Hind_49

description: Gene copy data from breast cancer


title: Hind_899

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 86, status: 0


title: Hind_137

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 32, status: 1


title: Hind_9

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 125, status: 0


title: Hind_11

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 109, status: 0


title: Hind_33

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 7, status: 1


title: Hind_86

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 104, status: 0


title: Hind_140

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 19, status: 1


title: Hind_217

description: Gene copy data from breast cancer


title: Hind_75

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 15, status: 1


title: Hind_200

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 108, status: 0


title: Hind_81

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 11, status: 1


title: Hind_39

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 43, status: 1


title: Hind_19

description: Gene copy data from breast cancer


title: Hind_44

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 169, status: 0


title: Hind_616

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 88, status: 0


title: Hind_62

description: Gene copy data from breast cancer


title: Hind_15

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 99, status: 0


title: Hind_205

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 23, status: 1


title: Hind_613

description: Gene copy data from breast cancer


title: Hind_611

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 75, status: 0


title: Hind_606

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 66, status: 0


title: Hind_5

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 118, status: 0


title: Hind_244

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 39, status: 1


title: Hind_612

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 92, status: 0


title: Hind_239

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 35, status: 1


title: Hind_141

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 25, status: 1


title: Hind_550

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 58, status: 1


title: Hind_634

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 117, status: 0


title: Hind_900

description: Gene copy data from breast cancer


title: Hind_237

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 19, status: 1


title: Hind_240

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 36, status: 1


title: Hind_91

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 20, status: 1


title: Hind_241

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 17, status: 1


title: Hind_540

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 49, status: 1


title: Hind_843

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 110, status: 0


title: iPS cells from episomal vectors (Defined Factor sub-clone) DF6_9_9T (set of 12)

status: Public on Mar 27 2009

type: RNA

city: Madison

first: Victor

last: Ruotti

state: WI

address: 425 Henry Mall

department: Biotechnology

institute: UW Madison

hyb_protocol: All arrays were hybridized at 45ºC for 16 hours and scanned using an AFX GC3000 G7 scanner

scan_protocol: AFX GC3000 G7 scanner

data_processing: RMA

molecule: total RNA

label_protocol: Approximately 3 µg of RNA from each sample was labeled using the MessageAmp™ Biotin II-Enhanced IVT kit (Ambion) following manufacturer’s instructions.

growth_protocol: iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion or Tri-Reagent (Sigma).

treatment_protocol: IPS cells treated with episomal vectors

tag: cell type


title: Hind_856

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 88, status: 0


title: Hind_34

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 100, status: 0


title: iPS cells from episomal vectors (Defined Factor) DF6_9 (set of 12)


title: iPS cells from episomal vectors (Defined Factor sub-clone) DF19_9_7T (set of 12)


title: H14A ESC (set of 12)

description: Human Embryonic Stem Cell line

hyb_protocol: All arrays were hybridized at 45ºC for 16 hours and scanned using an AFX GC3000 G7 scanner.

source_name: Human Embryonic Stem Cells

growth_protocol: iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells (GM03813 and GM03814, Coriell Inst.) were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).

treatment_protocol: Lentiviral transduction of fibroblast cells was performed as previously described.

value: H14B passage 61 Human Embryonic Stem Cells


title: iPS cells from episomal vectors (Defined Factor sub-clone) DF19_9_11T (set of 12)


title: iPS cells from episomal vectors (Defined Factor) DF19_9 (set of 12)


title: 800ml mimimal glucose chemostat, replicate 1

status: Public on Nov 21 2008

city: Ann Arbor

first: Eric

middle: Charles

last: Martens

state: MI

address: 1150 West Medical Center Drive

department: Dept. of Microbiology and Immunology

institute: University of Michigan Medical School

description: 800ml minimal glucose (0.5%) medium chemostat culture of B. thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 1 of 3

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Data normalized to 500 in Affymetrix MAS5 software

label: Biotin

organism: Bacteroides thetaiotaomicron

source_name: bacterial

label_protocol: Enzo Biochemicals Bioarray terminal labeling kit

extract_protocol: Qiagen RNeasy mini column extraction; Ambion DNA free treatment

tag: strain VPI-5482


title: Foreskin Cells Parental Foreskin (set of 16)

source_name: Foreskin Cells Parental

value: Foreskin Cells Parental


title: 800ml minimal medium glucose chemostat 2

description: 800ml minimal glucose (0.5%) medium chemostat culture of B. thetaiotaomicron VPI-5482; grown to mid-log phase; replicate 2 of 3


title: H13B ESC (set of 12)

description: Human Embryonic Stem Cell line

value: H13B passage 43 Human Embryonic Stem Cells


title: H9 ESC (set of 12)

description: Human Embryonic Stem Cell line

value: H9 passage 50 Human Embryonic Stem Cells


title: H7 ESC (set of 12)

description: Human Embryonic Stem Cell line

value: H7 passage 73 Human Embryonic Stem Cells


title: IGF-treated cells (3hr), biological rep2

status: Public on Nov 20 2008

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: cells from primary breast cancers were flow sorted to select for CD44+/CD24- cells and compare with the rest of the cells

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized on Human Genome U133 A_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-ws2v5 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Affymetrix).

data_processing: The data were analyzed with dChip version2006 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10%. of intensity values

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

extract_protocol: Trizol extraction of total RNA was carried out using EZ1 RNA universal tissue kit with BioRobot EZ1 workstation according to the manufacturer's instructions.

tag: IGF


title: IGF-treated cells (24hr), biological rep2


title: SFM control cells (24hr), biological rep2

tag: SFM


title: IGF-treated cells (3hr), biological rep3


title: SFM control cells (3hr), biological rep1


title: IGF-treated cells (3hr), biological rep1


title: IGF-treated cells (24hr), biological rep3


title: IGF-treated cells (24hr), biological rep1


title: SFM control cells (3hr), biological rep2


title: s-shaped body - 1s03

status: Public on Nov 18 2006

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7074

hyb_protocol: Amount labeled  target hybridization to array: 15 ug Hybridization/Wash/Stain protocol: EukGE-WS2v4

scan_protocol: Affymetrix standard protocol

data_processing: Analysis method: Affymetrix GCOS and Rosetta Resolver GCOS Tgt value: 500

organism: Mus musculus

source_name: s-shaped body

label_protocol: Affymetrix standard protocol

extract_protocol: Total RNA extracted using TRIzol.  Two round amplification using the Arcturus kit according to the manufacturer protocol.

treatment_protocol:
pool size: 1 S-shaped body
Pooled sample: No
Dissection Method: Whole organ excision
Two early nephron structures, the renal vesicle and the s-shaped body, and the collecting duct system were micro-dissected from E14.5 kidneys based on morphological criteria.  Antibody and lectin staining together with RT-PCR were used for identity verification and for exclusion of contamination by other tissues.  Samples are minimally pooled for amplification.  A biological replicate is a single minimally pooled sample.  RNA isolated from the collected structures was put through two rounds of T7-driven amplification to obtain the microgram quantities of cRNA needed for hybridization to Affymetrix microarrays.

tag: gene reported

value: wild-type

tag: strain

value: Swiss Webster

tag: sex

value: unknown

tag: developmental stage

tag: theiler stage

tag: somite count

tag: developmental landmark


title: s-shaped body - 1s04

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7075

hyb_protocol: Amount labeled target hybridization to array: 15 ug Hybridization/Wash/Stain protocol: EukGE-WS2v4


title: SFM control cells (24hr), biological rep1


title: Hind_72

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 134, status: 0

tag: age

tag: differentiation


title: collecting duct - UR03

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7073

source_name: collecting duct

treatment_protocol:
pool size: 1 collecting duct
Pooled sample: No
Dissection Method: Whole organ excision
Two early nephron structures, the renal vesicle and the s-shaped body, and the collecting duct system were micro-dissected from E14.5 kidneys based on morphological criteria.  Antibody and lectin staining together with RT-PCR were used for identity verification and for exclusion of contamination by other tissues.  Samples are minimally pooled for amplification.  A biological replicate is a single minimally pooled sample.  RNA isolated from the collected structures was put through two rounds of T7-driven amplification to obtain the microgram quantities of cRNA needed for hybridization to Affymetrix microarrays.


title: s-shaped body - 1s05

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7076


title: s-shaped body - 20s01

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7068

treatment_protocol:
pool size: 20 s-shaped bodies
Pooled sample: Yes
Dissection Method: Whole organ excision
Two early nephron structures, the renal vesicle and the s-shaped body, and the collecting duct system were micro-dissected from E14.5 kidneys based on morphological criteria.  Antibody and lectin staining together with RT-PCR were used for identity verification and for exclusion of contamination by other tissues.  Samples are minimally pooled for amplification.  A biological replicate is a single minimally pooled sample.  RNA isolated from the collected structures was put through two rounds of T7-driven amplification to obtain the microgram quantities of cRNA needed for hybridization to Affymetrix microarrays.


title: Hind_273

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 81, status: 0

tag: er

tag: menopause


title: renal vesicle - 20v03

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7066

source_name: renal vesicle

treatment_protocol:
pool size: 20 renal vesicles
Pooled sample: Yes
Dissection Method: Whole organ excision
Two early nephron structures, the renal vesicle and the s-shaped body, and the collecting duct system were micro-dissected from E14.5 kidneys based on morphological criteria.  Antibody and lectin staining together with RT-PCR were used for identity verification and for exclusion of contamination by other tissues.  Samples are minimally pooled for amplification.  A biological replicate is a single minimally pooled sample.  RNA isolated from the collected structures was put through two rounds of T7-driven amplification to obtain the microgram quantities of cRNA needed for hybridization to Affymetrix microarrays.


title: renal vesicle - 20v04

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7067


title: collecting duct - UR02

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7072


title: Hind_63

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 14, status: 1

tag: pr

tag: survival time (months)


title: s-shaped body - 20s03

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7070


title: collecting duct - UR01

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7071


title: SFM control cells (24hr), biological rep3


title: Hind_615

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 92, status: 0

tag: status (0=no relapse, 1=relapse)


title: Hind_614

description: Gene copy data from breast cancer


title: J1 EB 14d 1, chip MOE430A

status: Public on Dec 06 2005

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S249
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_216
Short description:			14 days of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL

data_processing: Calculated using the MAS5 algorithm where sc=1500, tau=0.015, alpha1=0.04, and alpla2=0.06

source_name: J1, Fetal cells

growth_protocol:
Growth medium:				ES Cell Medium - DMEM (high glucose)
Media supplements:			Hyclone FCS, non-essential amino acids, Glutamax, Penicillin/Streptomycin, sodium pyruvate, beta-mercaptoethanol
Culture conditions:			37 C, 5% CO2

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Culturing
Contaminating cell type:			None
Method for estimating purity:		By eye

treatment_protocol: Assays to confirm viability:		Stratagene mycoplasma PCR test

tag: Strain:					129/Sv

tag: Gender:					Male


title: Neuro2A Differentiation RA1h Replicate 3

status: Public on Apr 29 2005

city: Kisarazu

first: Kazuhide

last: Imai

state: Chiba

address: 2-6-7 Kazusa-Kamatari

country: Japan

institute: Chiba Industry Advancement Center

description:
Murine neuroblastoma cell line Neuro2A was cultured in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% FBS at 37°C under 5% CO2 To induce neuronal differentiation, the cells were plated at a density of 3.8 x 10e3 cells/cm2. After 48 h, the medium was replaced with 2% FBS-DMEM containing 20 uM all-trans-retinoic acid , and the incubation was continued to 1 h ,then cells were harvested and RNA was extracted, 4-6 plates per replicate.Total RNAs were isolated from the Neuro2A cells using TRIZOL (Invitrogen) reagent. The poly (A)+ RNAs were isolated from the total RNAs using the uMACS mRNA Isolation Kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) according to the manufacturer's protocol.mRNAs (1 ug) were labeled with Cy5 dye using the BD PowerScript Fluorescent Labeling Kit (BD Biosciences Clontech, Palo Alto, CA) according to the manufacturer's protocol (except for a partial modification of the priming procedure, in which we annealed 0.36 ug random nonamer at 42°C for 90 min). The labeled cDNAs were purified by using a QIAquick PCR Purification Kit (Qiagen Inc., Valencia, CA).  After the cDNAs were mixed with 2 ug mouse Cot-1 DNA and 2 ug poly dA, they were precipitated by ethanol. The precipitant was dissolved in 40 ul hybridization buffer (50% formamide, 5 x SSC, 0.5% SDS), denatured at 100°C for 5 min, and incubated at 42°C for 15 min.Before hybridization, mKIAA oligonucleotide microarrays were treated with blocking buffer (1% BSA, 4 x SSC, 0.5% SDS) at 42°C for 45 min, washed twice with sterile water, and then immediately dried by blown air. Hybridization was carried out at 42°C for 16 h using the Array Booster (Advalytix AG, Brunnthal, Germany). After hybridization, the arrays were washed twice with 2 x SSC/0.1% SDS buffer at 60°C for 10 min and then twice with 0.2 x SSC/0.1% SDS buffer at 60°C for 10 min. After further soaking at RT in 0.05 x SSC buffer, the slides were immediately desiccated by blown air and scanned on the FLA-8000 Fluorescent Image Analyzer (Fujifilm, Tokyo, Japan). The fluorescence intensities were quantified by Phoretix Array software (Nonlinear Dynamics Ltd., Newcastle upon Tyne, UK).
Keywords = Neuroblastoma
Keywords = Neuro2A
Keywords = retinoic acid

source_name: poly (A)+ RNAs from Neuro2A cells, labeled with Cyanine-5 (red).


title: J1 ES 0 hr 2, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E201
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201
SCGP Sample ID:				S242
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=201#SAMPLE_209
Short description:			0 hours of an 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days.
Estimated purity:				100%
RNA concentration:			2.0 ug/uL
Num cells for RNA prep:			Undetermined
Sample volume:				15 uL

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array and the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix).

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

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix)

growth_protocol:
Growth medium:				ES Cell Medium - DMEM (high glucose)
Media supplements:			Hyclone FCS, non-essential amino acids, Glutamax, Penicillin/Streptomycin, sodium pyruvate, beta-mercaptoethanol, LIF
Culture conditions:			37 C, 5% CO2


title: s-shaped body - 20s02

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7069


title: renal vesicle - 20v02

description:
>> Amplification protocol <<
Target Amplified manufacturer/kit: Affymetrix (Enzo)/Arcturus
Target Amplified protocol: Arcturus/Affymetrix
Rounds of amplification: 2
URL: http://gudmap.hgu.mrc.ac.uk/gudmap/pages/mic_submission.html?id=GUDMAP:7065


title: J1 ES 0 hr 1, chip MOE430A


title: CPGSC#20, chip MOE430A

status: Public on Sep 01 2005

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S153
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_113
Short description:			0 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			3.8 ug/ul
Num cells for RNA prep:			2X10e6
Sample volume:				30 ul

source_name: V6.5 (P18), Embryonic

growth_protocol:
Growth medium:				ES Cell Medium - DMEM (high glucose)
Media supplements:			Hyclone FCS (heat inactivated), non-essential amino acids, Glutamax, Penicillin/Streptomycin, sodium pyruvate, beta-mercaptoethanol, LIF
Culture conditions:			37 C, 5% CO2

extract_protocol:
RNA prep method:				RNeasy
Cell purification method:			Cultured
Contaminating cell type:			none

tag: Strain:					129SV x C57Bl/6


title: J1 EB 14d 3, chip MOE430A


title: J1 EB 14d 2, chip MOE430A


title: Neuro2A Differentiation RA24h Replicate 7

status: Public on Apr 28 2005

description:
Murine neuroblastoma cell line Neuro2A was cultured in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% FBS at 37°C under 5% CO2 To induce neuronal differentiation, the cells were plated at a density of 3.8 x 10e3 cells/cm2. After 48 h, the medium was replaced with 2% FBS-DMEM containing 20 uM all-trans-retinoic acid , and the incubation was continued to 24 h ,then cells were harvested and RNA was extracted, 4-6 plates per replicate.Total RNAs were isolated from the Neuro2A cells using TRIZOL (Invitrogen) reagent. The poly (A)+ RNAs were isolated from the total RNAs using the uMACS mRNA Isolation Kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) according to the manufacturer's protocol.mRNAs (1 ug) were labeled with Cy5 dye using the BD PowerScript Fluorescent Labeling Kit (BD Biosciences Clontech, Palo Alto, CA) according to the manufacturer's protocol (except for a partial modification of the priming procedure, in which we annealed 0.36 ug random nonamer at 42°C for 90 min). The labeled cDNAs were purified by using a QIAquick PCR Purification Kit (Qiagen Inc., Valencia, CA).  After the cDNAs were mixed with 2 ug mouse Cot-1 DNA and 2 ug poly dA, they were precipitated by ethanol. The precipitant was dissolved in 40 ul hybridization buffer (50% formamide, 5 x SSC, 0.5% SDS), denatured at 100°C for 5 min, and incubated at 42°C for 15 min.Before hybridization, mKIAA oligonucleotide microarrays were treated with blocking buffer (1% BSA, 4 x SSC, 0.5% SDS) at 42°C for 45 min, washed twice with sterile water, and then immediately dried by blown air. Hybridization was carried out at 42°C for 16 h using the Array Booster (Advalytix AG, Brunnthal, Germany). After hybridization, the arrays were washed twice with 2 x SSC/0.1% SDS buffer at 60°C for 10 min and then twice with 0.2 x SSC/0.1% SDS buffer at 60°C for 10 min. After further soaking at RT in 0.05 x SSC buffer, the slides were immediately desiccated by blown air and scanned on the FLA-8000 Fluorescent Image Analyzer (Fujifilm, Tokyo, Japan). The fluorescence intensities were quantified by Phoretix Array software (Nonlinear Dynamics Ltd., Newcastle upon Tyne, UK).
Keywords = Neuroblastoma
Keywords = Neuro2A
Keywords = retinoic acid


title: CPGSC#21, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S153
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_113
Short description:			0 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			3.9 ug/ul
Num cells for RNA prep:			2X10e6
Sample volume:				30 ul


title: CPGSC#22, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S153
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_113
Short description:			0 hours of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.7 ug/ul
Num cells for RNA prep:			2X10e6
Sample volume:				30 ul


title: Neuro2A Differentiation RA24h Replicate 5


title: Neuro2A Differentiation RA24h Replicate 3


title: Neuro2A Differentiation RA12h Replicate 4

description:
Murine neuroblastoma cell line Neuro2A was cultured in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% FBS at 37°C under 5% CO2 To induce neuronal differentiation, the cells were plated at a density of 3.8 x 10e3 cells/cm2. After 48 h, the medium was replaced with 2% FBS-DMEM containing 20 uM all-trans-retinoic acid , and the incubation was continued to 12 h ,then cells were harvested and RNA was extracted, 4-6 plates per replicate.Total RNAs were isolated from the Neuro2A cells using TRIZOL (Invitrogen) reagent. The poly (A)+ RNAs were isolated from the total RNAs using the uMACS mRNA Isolation Kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) according to the manufacturer's protocol.mRNAs (1 ug) were labeled with Cy5 dye using the BD PowerScript Fluorescent Labeling Kit (BD Biosciences Clontech, Palo Alto, CA) according to the manufacturer's protocol (except for a partial modification of the priming procedure, in which we annealed 0.36 ug random nonamer at 42°C for 90 min). The labeled cDNAs were purified by using a QIAquick PCR Purification Kit (Qiagen Inc., Valencia, CA).  After the cDNAs were mixed with 2 ug mouse Cot-1 DNA and 2 ug poly dA, they were precipitated by ethanol. The precipitant was dissolved in 40 ul hybridization buffer (50% formamide, 5 x SSC, 0.5% SDS), denatured at 100°C for 5 min, and incubated at 42°C for 15 min.Before hybridization, mKIAA oligonucleotide microarrays were treated with blocking buffer (1% BSA, 4 x SSC, 0.5% SDS) at 42°C for 45 min, washed twice with sterile water, and then immediately dried by blown air. Hybridization was carried out at 42°C for 16 h using the Array Booster (Advalytix AG, Brunnthal, Germany). After hybridization, the arrays were washed twice with 2 x SSC/0.1% SDS buffer at 60°C for 10 min and then twice with 0.2 x SSC/0.1% SDS buffer at 60°C for 10 min. After further soaking at RT in 0.05 x SSC buffer, the slides were immediately desiccated by blown air and scanned on the FLA-8000 Fluorescent Image Analyzer (Fujifilm, Tokyo, Japan). The fluorescence intensities were quantified by Phoretix Array software (Nonlinear Dynamics Ltd., Newcastle upon Tyne, UK).
Keywords = Neuroblastoma
Keywords = Neuro2A
Keywords = retinoic acid


title: Neuro2A Differentiation RA24h Replicate 2


title: Neuro2A Differentiation RA24h Replicate 6


title: J1 ES 0 hr 3, chip MOE430A


title: Neuro2A Differentiation RA24h Replicate 4


title: Neuro2A Differentiation RA12h Replicate 7


title: Neuro2A Differentiation RA12h Replicate 6


title: Neuro2A Differentiation RA12h Replicate 1


title: Neuro2A Differentiation RA12h Replicate 2


title: CPGSC#49, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S175
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_135
Short description:			14 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			2.0 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				120 ul

growth_protocol:
Growth medium:				ES Cell Medium - DMEM (high glucose)
Media supplements:			Hyclone FCS (heat inactivated), non-essential amino acids, Glutamax, Penicillin/Streptomycin, beta-mercaptoethanol
Culture conditions:			37 C, 5% CO2


title: Neuro2A Differentiation RA6h Replicate 6

description:
Murine neuroblastoma cell line Neuro2A was cultured in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% FBS at 37°C under 5% CO2 To induce neuronal differentiation, the cells were plated at a density of 3.8 x 10e3 cells/cm2. After 48 h, the medium was replaced with 2% FBS-DMEM containing 20 uM all-trans-retinoic acid , and the incubation was continued to 6 h ,then cells were harvested and RNA was extracted, 4-6 plates per replicate.Total RNAs were isolated from the Neuro2A cells using TRIZOL (Invitrogen) reagent. The poly (A)+ RNAs were isolated from the total RNAs using the uMACS mRNA Isolation Kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) according to the manufacturer's protocol.mRNAs (1 ug) were labeled with Cy5 dye using the BD PowerScript Fluorescent Labeling Kit (BD Biosciences Clontech, Palo Alto, CA) according to the manufacturer's protocol (except for a partial modification of the priming procedure, in which we annealed 0.36 ug random nonamer at 42°C for 90 min). The labeled cDNAs were purified by using a QIAquick PCR Purification Kit (Qiagen Inc., Valencia, CA).  After the cDNAs were mixed with 2 ug mouse Cot-1 DNA and 2 ug poly dA, they were precipitated by ethanol. The precipitant was dissolved in 40 ul hybridization buffer (50% formamide, 5 x SSC, 0.5% SDS), denatured at 100°C for 5 min, and incubated at 42°C for 15 min.Before hybridization, mKIAA oligonucleotide microarrays were treated with blocking buffer (1% BSA, 4 x SSC, 0.5% SDS) at 42°C for 45 min, washed twice with sterile water, and then immediately dried by blown air. Hybridization was carried out at 42°C for 16 h using the Array Booster (Advalytix AG, Brunnthal, Germany). After hybridization, the arrays were washed twice with 2 x SSC/0.1% SDS buffer at 60°C for 10 min and then twice with 0.2 x SSC/0.1% SDS buffer at 60°C for 10 min. After further soaking at RT in 0.05 x SSC buffer, the slides were immediately desiccated by blown air and scanned on the FLA-8000 Fluorescent Image Analyzer (Fujifilm, Tokyo, Japan). The fluorescence intensities were quantified by Phoretix Array software (Nonlinear Dynamics Ltd., Newcastle upon Tyne, UK).
Keywords = Neuroblastoma
Keywords = Neuro2A
Keywords = retinoic acid


title: CPGSC#48, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S175
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_135
Short description:			14 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			1.5 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				120 ul


title: Neuro2A Differentiation RA6h Replicate 5


title: CPGSC#47, chip MOE430A

description:
This sample was analyzed as part of the Stem Cell Genomics Project (http://www.scgp.ca:8080/StemBase/). The biological material was submitted to the Ontario Genomics Innovation Centre (http://www.ottawagenomecenter.ca/) by Dr. Michael Rudnicki (mrudnicki@ohri.ca; 501 Smyth Road) for analysis.
Stembase Experiment ID:			E113
Stembase Experiment ID link:		http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113
SCGP Sample ID:				S175
SCGP Sample ID link:			http://www.scgp.ca:8080/StemBase/?path=/browse/experiment&id=113#SAMPLE_135
Short description:			14 days of an 11-point time course study of V6.5 embryonic stem cells and their cognate differentiated embryoid bodies.  All samples investigated in triplicate.
Estimated purity:				100%
RNA concentration:			1.6 ug/ul
Num cells for RNA prep:			Unable to break up embryoid bodies to do a cell count.
Sample volume:				120 ul


title: Neuro2A Differentiation RA6h Replicate 7


title: Neuro2A Differentiation RA12h Replicate 3


title: Neuro2A Differentiation RA12h Replicate 5

description:
Murine neuroblastoma cell line Neuro2A was cultured in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% FBS at 37°C under 5% CO2 To induce neuronal differentiation, the cells were plated at a density of 3.8 x 10e3 cells/cm2. After 48 h, the medium was replaced with 2% FBS-DMEM containing 20 uM all-trans-retinoic acid , and the incubation was continued to 12 h ,then cells were harvested and RNA was extracted, 4-6 plates per replicate.Total RNAs were isolated from the Neuro2A cells using TRIZOL (Invitrogen) reagent. The poly (A)+ RNAs were isolated from the total RNAs using the uMACS mRNA Isolation Kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) according to the manufacturer's protocol.mRNAs (1 ug) were labeled with Cy5 dye using the BD PowerScript Fluorescent Labeling Kit (BD Biosciences Clontech, Palo Alto, CA) according to the manufacturer's protocol (except for a partial modification of the priming procedure, in which we annealed 0.36 ug random nonamer at 42°C for 90 min). The labeled cDNAs were purified by using a QIAquick PCR Purification Kit (Qiagen Inc., Valencia, CA).  After the cDNAs were mixed with 2 ug mouse Cot-1 DNA and 2 ug poly dA, they were precipitated by ethanol. The precipitant was dissolved in 40 ul hybridization buffer (50% formamide, 5 x SSC, 0.5% SDS), denatured at 100°C for 5 min, and incubated at 42°C for 15 min.Before hybridization, mKIAA oligonucleotide microarrays were treated with blocking buffer (1% BSA, 4 x SSC, 0.5% SDS) at 42°C for 45 min, washed twice with sterile water, and then immediately dried by blown air. Hybridization was carried out at 42°C for 16 h using the Array Booster (Advalytix AG, Brunnthal, Germany). After hybridization, the arrays were washed twice with 2 x SSC/0.1% SDS buffer at 60°C for 10 min and then twice with 0.2 x SSC/0.1% SDS buffer at 60°C for 10 min. After further soaking at RT in 0.05 x SSC buffer, the slides were immediately desiccated by blown air and scanned on the FLA-8000 Fluorescent Image Analyzer (Fujifilm, Tokyo, Japan). The fluorescence intensities were quantified by Phoretix Array software (Nonlinear Dynamics Ltd., Newcastle upon Tyne, UK).
Keywords = Neuroblastoma
Keywords = Neuro2A
Keywords = retinoic acid
Lot batch =


title: Neuro2A Differentiation RA24h Replicate 1

description:
Murine neuroblastoma cell line Neuro2A was cultured in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% FBS at 37°C under 5% CO2 To induce neuronal differentiation, the cells were plated at a density of 3.8 x 10e3 cells/cm2. After 48 h, the medium was replaced with 2% FBS-DMEM containing 20 uM all-trans-retinoic acid , and the incubation was continued to 24 h ,then cells were harvested and RNA was extracted, 4-6 plates per replicate.Total RNAs were isolated from the Neuro2A cells using TRIZOL (Invitrogen) reagent. The poly (A)+ RNAs were isolated from the total RNAs using the uMACS mRNA Isolation Kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) according to the manufacturer's protocol.mRNAs (1 ug) were labeled with Cy5 dye using the BD PowerScript Fluorescent Labeling Kit (BD Biosciences Clontech, Palo Alto, CA) according to the manufacturer's protocol (except for a partial modification of the priming procedure, in which we annealed 0.36 ug random nonamer at 42°C for 90 min). The labeled cDNAs were purified by using a QIAquick PCR Purification Kit (Qiagen Inc., Valencia, CA).  After the cDNAs were mixed with 2 ug mouse Cot-1 DNA and 2 ug poly dA, they were precipitated by ethanol. The precipitant was dissolved in 40 ul hybridization buffer (50% formamide, 5 x SSC, 0.5% SDS), denatured at 100°C for 5 min, and incubated at 42°C for 15 min.Before hybridization, mKIAA oligonucleotide microarrays were treated with blocking buffer (1% BSA, 4 x SSC, 0.5% SDS) at 42°C for 45 min, washed twice with sterile water, and then immediately dried by blown air. Hybridization was carried out at 42°C for 16 h using the Array Booster (Advalytix AG, Brunnthal, Germany). After hybridization, the arrays were washed twice with 2 x SSC/0.1% SDS buffer at 60°C for 10 min and then twice with 0.2 x SSC/0.1% SDS buffer at 60°C for 10 min. After further soaking at RT in 0.05 x SSC buffer, the slides were immediately desiccated by blown air and scanned on the FLA-8000 Fluorescent Image Analyzer (Fujifilm, Tokyo, Japan). The fluorescence intensities were quantified by Phoretix Array software (Nonlinear Dynamics Ltd., Newcastle upon Tyne, UK).
Keywords = Neuroblastoma
Keywords = Neuro2A
Keywords = retinoic acid
Lot batch =


title: Neuro2A Differentiation RA6h Replicate 2


title: Neuro2A Differentiation RA6h Replicate 3


title: Neuro2A Differentiation RA6h Replicate 1


title: Neuro2A Differentiation RA3h Replicate 4

description:
Murine neuroblastoma cell line Neuro2A was cultured in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% FBS at 37°C under 5% CO2 To induce neuronal differentiation, the cells were plated at a density of 3.8 x 10e3 cells/cm2. After 48 h, the medium was replaced with 2% FBS-DMEM containing 20 uM all-trans-retinoic acid , and the incubation was continued to 3 h ,then cells were harvested and RNA was extracted, 4-6 plates per replicate.Total RNAs were isolated from the Neuro2A cells using TRIZOL (Invitrogen) reagent. The poly (A)+ RNAs were isolated from the total RNAs using the uMACS mRNA Isolation Kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) according to the manufacturer's protocol.mRNAs (1 ug) were labeled with Cy5 dye using the BD PowerScript Fluorescent Labeling Kit (BD Biosciences Clontech, Palo Alto, CA) according to the manufacturer's protocol (except for a partial modification of the priming procedure, in which we annealed 0.36 ug random nonamer at 42°C for 90 min). The labeled cDNAs were purified by using a QIAquick PCR Purification Kit (Qiagen Inc., Valencia, CA).  After the cDNAs were mixed with 2 ug mouse Cot-1 DNA and 2 ug poly dA, they were precipitated by ethanol. The precipitant was dissolved in 40 ul hybridization buffer (50% formamide, 5 x SSC, 0.5% SDS), denatured at 100°C for 5 min, and incubated at 42°C for 15 min.Before hybridization, mKIAA oligonucleotide microarrays were treated with blocking buffer (1% BSA, 4 x SSC, 0.5% SDS) at 42°C for 45 min, washed twice with sterile water, and then immediately dried by blown air. Hybridization was carried out at 42°C for 16 h using the Array Booster (Advalytix AG, Brunnthal, Germany). After hybridization, the arrays were washed twice with 2 x SSC/0.1% SDS buffer at 60°C for 10 min and then twice with 0.2 x SSC/0.1% SDS buffer at 60°C for 10 min. After further soaking at RT in 0.05 x SSC buffer, the slides were immediately desiccated by blown air and scanned on the FLA-8000 Fluorescent Image Analyzer (Fujifilm, Tokyo, Japan). The fluorescence intensities were quantified by Phoretix Array software (Nonlinear Dynamics Ltd., Newcastle upon Tyne, UK).
Keywords = Neuroblastoma
Keywords = Neuro2A
Keywords = retinoic acid


title: Neuro2A Differentiation RA3h Replicate 5


title: Neuro2A Differentiation RA3h Replicate 2


title: Neuro2A Differentiation RA1h Replicate 4


title: Neuro2A Differentiation RA3h Replicate 3


title: Neuro2A Differentiation RA1h Replicate 2


title: Neuro2A Differentiation RA1h Replicate 1


title: Neuro2A Differentiation 0h Control Replicate 3

description:
Murine neuroblastoma cell line Neuro2A was cultured in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% FBS at 37°C under 5% CO2 To induce neuronal differentiation, the cells were plated at a density of 3.8 x 10e3 cells/cm2. After 48 h, cells were harvested and RNA was extracted at time 0 h as undifferentiated control, 4-6 plates per replicate.Total RNAs were isolated from the Neuro2A cells using TRIZOL (Invitrogen) reagent. The poly (A)+ RNAs were isolated from the total RNAs using the uMACS mRNA Isolation Kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) according to the manufacturer's protocol.mRNAs (1 ug) were labeled with Cy5 dye using the BD PowerScript Fluorescent Labeling Kit (BD Biosciences Clontech, Palo Alto, CA) according to the manufacturer's protocol (except for a partial modification of the priming procedure, in which we annealed 0.36 ug random nonamer at 42°C for 90 min). The labeled cDNAs were purified by using a QIAquick PCR Purification Kit (Qiagen Inc., Valencia, CA).  After the cDNAs were mixed with 2 ug mouse Cot-1 DNA and 2 ug poly dA, they were precipitated by ethanol. The precipitant was dissolved in 40 ul hybridization buffer (50% formamide, 5 x SSC, 0.5% SDS), denatured at 100°C for 5 min, and incubated at 42°C for 15 min.Before hybridization, mKIAA oligonucleotide microarrays were treated with blocking buffer (1% BSA, 4 x SSC, 0.5% SDS) at 42°C for 45 min, washed twice with sterile water, and then immediately dried by blown air. Hybridization was carried out at 42°C for 16 h using the Array Booster (Advalytix AG, Brunnthal, Germany). After hybridization, the arrays were washed twice with 2 x SSC/0.1% SDS buffer at 60°C for 10 min and then twice with 0.2 x SSC/0.1% SDS buffer at 60°C for 10 min. After further soaking at RT in 0.05 x SSC buffer, the slides were immediately desiccated by blown air and scanned on the FLA-8000 Fluorescent Image Analyzer (Fujifilm, Tokyo, Japan). The fluorescence intensities were quantified by Phoretix Array software (Nonlinear Dynamics Ltd., Newcastle upon Tyne, UK).
Keywords = Neuroblastoma
Keywords = Neuro2A
Keywords = retinoic acid


title: Neuro2A Differentiation 0h Control Replicate 5


title: Neuro2A Differentiation 0h Control Replicate 4


title: Neuro2A Differentiation RA6h Replicate 4


title: Neuro2A Differentiation 0h Control Replicate 2

description:
Murine neuroblastoma cell line Neuro2A was cultured in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% FBS at 37°C under 5% CO2 To induce neuronal differentiation, the cells were plated at a density of 3.8 x 10e3 cells/cm2. After 48 h, cells were harvested and RNA was extracted at time 0 h as undifferentiated control, 4-6 plates per replicate.
Total RNAs were isolated from the Neuro2A cells using TRIZOL (Invitrogen) reagent. The poly (A)+ RNAs were isolated from the total RNAs using the uMACS mRNA Isolation Kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) according to the manufacturer's protocol.
mRNAs (1 ug) were labeled with Cy5 dye using the BD PowerScript Fluorescent Labeling Kit (BD Biosciences Clontech, Palo Alto, CA) according to the manufacturer's protocol (except for a partial modification of the priming procedure, in which we annealed 0.36 ug random nonamer at 42°C for 90 min). The labeled cDNAs were purified by using a QIAquick PCR Purification Kit (Qiagen Inc., Valencia, CA).  After the cDNAs were mixed with 2 ug mouse Cot-1 DNA and 2 ug poly dA, they were precipitated by ethanol. The precipitant was dissolved in 40 ul hybridization buffer (50% formamide, 5 x SSC, 0.5% SDS), denatured at 100°C for 5 min, and incubated at 42°C for 15 min.
Before hybridization, mKIAA oligonucleotide microarrays were treated with blocking buffer (1% BSA, 4 x SSC, 0.5% SDS) at 42°C for 45 min, washed twice with sterile water, and then immediately dried by blown air. Hybridization was carried out at 42°C for 16 h using the Array Booster (Advalytix AG, Brunnthal, Germany). After hybridization, the arrays were washed twice with 2 x SSC/0.1% SDS buffer at 60°C for 10 min and then twice with 0.2 x SSC/0.1% SDS buffer at 60°C for 10 min. After further soaking at RT in 0.05 x SSC buffer, the slides were immediately desiccated by blown air and scanned on the FLA-8000 Fluorescent Image Analyzer (Fujifilm, Tokyo, Japan). The fluorescence intensities were quantified by Phoretix Array software (Nonlinear Dynamics Ltd., Newcastle upon Tyne, UK).


title: Neuro2A Differentiation 0h Control Replicate 6

description:
Murine neuroblastoma cell line Neuro2A was cultured in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% FBS at 37°C under 5% CO2 To induce neuronal differentiation, the cells were plated at a density of 3.8 x 10e3 cells/cm2. After 48 h, cells were harvested and RNA was extracted at time 0 h as undifferentiated control, 4-6 plates per replicate.
Total RNAs were isolated from the Neuro2A cells using TRIZOL (Invitrogen) reagent. The poly (A)+ RNAs were isolated from the total RNAs using the uMACS mRNA Isolation Kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) according to the manufacturer's protocol.
mRNAs (1 ug) were labeled with Cy5 dye using the BD PowerScript Fluorescent Labeling Kit (BD Biosciences Clontech, Palo Alto, CA) according to the manufacturer's protocol (except for a partial modification of the priming procedure, in which we annealed 0.36 ug random nonamer at 42°C for 90 min). The labeled cDNAs were purified by using a QIAquick PCR Purification Kit (Qiagen Inc., Valencia, CA).  After the cDNAs were mixed with 2 ug mouse Cot-1 DNA and 2 ug poly dA, they were precipitated by ethanol. The precipitant was dissolved in 40 ul hybridization buffer (50% formamide, 5 x SSC, 0.5% SDS), denatured at 100°C for 5 min, and incubated at 42°C for 15 min.
Before hybridization, mKIAA oligonucleotide microarrays were treated with blocking buffer (1% BSA, 4 x SSC, 0.5% SDS) at 42°C for 45 min, washed twice with sterile water, and then immediately dried by blown air. Hybridization was carried out at 42°C for 16 h using the Array Booster (Advalytix AG, Brunnthal, Germany). After hybridization, the arrays were washed twice with 2 x SSC/0.1% SDS buffer at 60°C for 10 min and then twice with 0.2 x SSC/0.1% SDS buffer at 60°C for 10 min. After further soaking at RT in 0.05 x SSC buffer, the slides were immediately desiccated by blown air and scanned on the FLA-8000 Fluorescent Image Analyzer (Fujifilm, Tokyo, Japan). The fluorescence intensities were quantified by Phoretix Array software (Nonlinear Dynamics Ltd., Newcastle upon Tyne, UK).
Keywords = Neuroblastoma
Keywords = Neuro2A
Keywords = retinoic acid


title: Neuro2A Differentiation RA3h Replicate 1


title: Neuro2A Differentiation RA1h Replicate 5

description:
Murine neuroblastoma cell line Neuro2A was cultured in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% FBS at 37°C under 5% CO2 To induce neuronal differentiation, the cells were plated at a density of 3.8 x 10e3 cells/cm2. After 48 h, the medium was replaced with 2% FBS-DMEM containing 20 uM all-trans-retinoic acid , and the incubation was continued to 1 h ,then cells were harvested and RNA was extracted, 4-6 plates per replicate.Total RNAs were isolated from the Neuro2A cells using TRIZOL (Invitrogen) reagent. The poly (A)+ RNAs were isolated from the total RNAs using the uMACS mRNA Isolation Kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) according to the manufacturer's protocol.mRNAs (1 ug) were labeled with Cy5 dye using the BD PowerScript Fluorescent Labeling Kit (BD Biosciences Clontech, Palo Alto, CA) according to the manufacturer's protocol (except for a partial modification of the priming procedure, in which we annealed 0.36 ug random nonamer at 42°C for 90 min). The labeled cDNAs were purified by using a QIAquick PCR Purification Kit (Qiagen Inc., Valencia, CA).  After the cDNAs were mixed with 2 ug mouse Cot-1 DNA and 2 ug poly dA, they were precipitated by ethanol. The precipitant was dissolved in 40 ul hybridization buffer (50% formamide, 5 x SSC, 0.5% SDS), denatured at 100°C for 5 min, and incubated at 42°C for 15 min.Before hybridization, mKIAA oligonucleotide microarrays were treated with blocking buffer (1% BSA, 4 x SSC, 0.5% SDS) at 42°C for 45 min, washed twice with sterile water, and then immediately dried by blown air. Hybridization was carried out at 42°C for 16 h using the Array Booster (Advalytix AG, Brunnthal, Germany). After hybridization, the arrays were washed twice with 2 x SSC/0.1% SDS buffer at 60°C for 10 min and then twice with 0.2 x SSC/0.1% SDS buffer at 60°C for 10 min. After further soaking at RT in 0.05 x SSC buffer, the slides were immediately desiccated by blown air and scanned on the FLA-8000 Fluorescent Image Analyzer (Fujifilm, Tokyo, Japan). The fluorescence intensities were quantified by Phoretix Array software (Nonlinear Dynamics Ltd., Newcastle upon Tyne, UK).
Keywords = Neuroblastoma
Keywords = Neuro2A
Keywords = retinoic acid


title: Hind_40

description: Gene copy data from breast cancer

source_name: human breast cancer, time: 102, status: 0


title: Neuro2A Differentiation 0h Control Replicate 7


title: Neuro2A Differentiation 0h Control Replicate 1

description:
Murine neuroblastoma cell line Neuro2A was cultured in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% FBS at 37°C under 5% CO2 To induce neuronal differentiation, the cells were plated at a density of 3.8×10e3 cells/cm2. After 48 h, cells were harvested and RNA was extracted at time 0 h as undifferentiated control, 4-6 plates per replicate.
Total RNAs were isolated from the Neuro2A cells using TRIZOL (Invitrogen) reagent. The poly (A)+ RNAs were isolated from the total RNAs using the µMACS mRNA Isolation Kit (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) according to the manufacturer’s protocol.
mRNAs (1 µg) were labeled with Cy5 dye using the BD PowerScript Fluorescent Labeling Kit (BD Biosciences Clontech, Palo Alto, CA) according to the manufacturer’s protocol (except for a partial modification of the priming procedure, in which we annealed 0.36 µg random nonamer at 42°C for 90 min). The labeled cDNAs were purified by using a QIAquick PCR Purification Kit (Qiagen Inc., Valencia, CA).  After the cDNAs were mixed with 2 µg mouse Cot-1 DNA and 2 µg poly dA, they were precipitated by ethanol. The precipitant was dissolved in 40 µl hybridization buffer (50% formamide, 5 × SSC, 0.5% SDS), denatured at 100°C for 5 min, and incubated at 42°C for 15 min.
Before hybridization, mKIAA oligonucleotide microarrays were treated with blocking buffer (1% BSA, 4×SSC, 0.5% SDS) at 42°C for 45 min, washed twice with sterile water, and then immediately dried by blown air. Hybridization was carried out at 42°C for 16 h using the Array Booster (Advalytix AG, Brunnthal, Germany). After hybridization, the arrays were washed twice with 2 × SSC/0.1% SDS buffer at 60°C for 10 min and then twice with 0.2 × SSC/0.1% SDS buffer at 60°C for 10 min. After further soaking at RT in 0.05 × SSC buffer, the slides were immediately desiccated by blown air and scanned on the FLA-8000 Fluorescent Image Analyzer (Fujifilm, Tokyo, Japan). The fluorescence intensities were quantified by Phoretix Array software (Nonlinear Dynamics Ltd., Newcastle upon Tyne, UK).
Keywords = Neuroblastoma
Keywords = Neuro2A
Keywords = retinoic acid.


title: BDC2.5/NOD1

status: Public on Jan 26 2005

city: Cincinnati

first: Jonathan

middle: D

last: Katz

state: OH

address: 3333 Burnet Avenue

department: Division of Endocrinology

institute: Cincinnati Children's Hospital Research Foundation

description:
pancreas from 3 week old BDC2.5/NOD mouse.  RNA was extracted by GITC method. Targets were produced using standard Affymetrix procedures from about 10ug of total RNA.  RNA was isolated twice from 6 animals each and pooled.
Pancreas
Keywords = BDC2.5/NOD, pancreas

source_name: pancreas


title: BDC2.5/NOD