title: 2 - mAdbID:91252

description: mAdb experiment ID: 91252

value: lymph node

value: Submitting diagnosis:DLBCL

value: Follow up years:2.74

value: ECOG performance status:0

value: LDH ratio:0

value: Number of extranodal sites:0


title: 2643 - mAdbID:92502

status: Public on Nov 28 2008

type: RNA

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

country: USA

institute: National Cancer Institute

description: mAdb experiment ID: 92502

hyb_protocol: Affymetrix Hybridization Protocol Other: Following fragmentation, 11 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affy Scanning Protocol Other: Scanning was performed by the Affymetrix 3000 Scanner.

data_processing:
MAS 5.0 Data Processing Protocol
Calculation Method: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
Sample Extraction Protocol
Other: Total RNA was extracted using All Prep RNA/DNA kit (Qiagen, Valencia, CA) according to the manufacturers' protocols.

tag: Gender

value: male

tag: Age

tag: Tissue

tag: Disease state

value: Lymphoma

tag: Individual

tag: Clinical info

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:5.48

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:1.95

value: Number of extranodal sites:1


title: 2006 - mAdbID:91248

description: mAdb experiment ID: 91248

value: Follow up years:1.22

value: LDH ratio:4.2


title: 2162 - mAdbID:91246

description: mAdb experiment ID: 91246

value: female

value: lymph node

value: Follow up status:DEAD

value: Follow up years:0.38

value: LDH ratio:NA

value: Number of extranodal sites:2


title: 41 - mAdbID:90829

description: mAdb experiment ID: 90829

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.51

value: LDH ratio:0.84

value: Number of extranodal sites:0


title: 110 - mAdbID:90896

description: mAdb experiment ID: 90896

value: male

value: Lymphoma

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:ALIVE

value: Follow up years:2.46

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:3

value: LDH ratio:2.22


title: 1192 - mAdbID:90127

description: mAdb experiment ID: 90127

value: female

value: lymph node

value: Follow up status:DEAD

value: Follow up years:0.15

value: ECOG performance status:NA

value: Number of extranodal sites:NA


title: 1298 - mAdbID:89727

description: mAdb experiment ID: 89727

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:4.55

value: ECOG performance status:1

value: LDH ratio:1.14

value: Number of extranodal sites:1


title: 1292 - mAdbID:89749

description: mAdb experiment ID: 89749

value: male

value: Lymphoma

value: Follow up years:0.09

value: ECOG performance status:2

value: LDH ratio:1.01


title: 1197 - mAdbID:89760

description: mAdb experiment ID: 89760

value: female

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:3.12

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:0.61


title: 49 - mAdbID:89591

description: mAdb experiment ID: 89591

value: lymph node

value: Submitting diagnosis:DLBCL

value: Follow up years:2.37

value: LDH ratio:2.07

value: Number of extranodal sites:2


title: 1614 - mAdbID:89731

description: mAdb experiment ID: 89731

value: Follow up status:DEAD

value: Follow up years:4.36

value: ECOG performance status:1

value: LDH ratio:2.57

value: Number of extranodal sites:0


title: 1626 - mAdbID:89726

description: mAdb experiment ID: 89726

value: male

value: Lymphoma

value: Follow up years:1.76

value: LDH ratio:1.43

value: Number of extranodal sites:1


title: 111 - mAdbID:90895

description: mAdb experiment ID: 90895

value: female

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:2.44

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:0.68


title: 107 - mAdbID:89508

description: mAdb experiment ID: 89508

value: lymph node

value: Submitting diagnosis:DLBCL

value: Follow up years:2.94

value: LDH ratio:0.79


title: 1108 - mAdbID:91261

description: mAdb experiment ID: 91261

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:3.30

value: ECOG performance status:0

value: LDH ratio:0.87


title: 1206 - mAdbID:89773

description: mAdb experiment ID: 89773

value: Lymphoma

value: Follow up years:6.50

value: ECOG performance status:1

value: LDH ratio:0.69


title: 98 - mAdbID:89499

description: mAdb experiment ID: 89499

value: male

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:DEAD

value: Follow up years:0.94

value: LDH ratio:1.75

value: Number of extranodal sites:2


title: 1782 - mAdbID:91253

description: mAdb experiment ID: 91253

value: lymph node

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:1.08

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:0.5

value: Number of extranodal sites:NA


title: 103 - mAdbID:89504

description: mAdb experiment ID: 89504

value: female

value: Lymphoma

value: Follow up years:0.03

value: ECOG performance status:2

value: LDH ratio:0.9

value: Number of extranodal sites:1


title: 108 - mAdbID:89509

description: mAdb experiment ID: 89509

value: male

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:2.72

value: ECOG performance status:0

value: LDH ratio:0.76

value: Number of extranodal sites:0


title: 1617 - mAdbID:89735

description: mAdb experiment ID: 89735

value: lymph node

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:0.52

value: ECOG performance status:1

value: LDH ratio:5.25


title: 1289 - mAdbID:89733

description: mAdb experiment ID: 89733

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:DEAD

value: Follow up years:0.03

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:1.95

value: Number of extranodal sites:NA


title: 53 - mAdbID:89393

description: mAdb experiment ID: 89393

value: male

value: Follow up years:3.88

value: ECOG performance status:3

value: LDH ratio:2.88

value: Number of extranodal sites:3


title: 95 - mAdbID:89496

description: mAdb experiment ID: 89496

value: lymph node

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:0.61

value: LDH ratio:1.08


title: 47 - mAdbID:89389

description: mAdb experiment ID: 89389

value: female

value: Lymphoma

value: Follow up years:1.52

value: ECOG performance status:2

value: LDH ratio:1.64

value: Number of extranodal sites:1


title: 109 - mAdbID:89510

description: mAdb experiment ID: 89510

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:DEAD

value: Follow up years:0.15

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:0


title: 99 - mAdbID:89500

description: mAdb experiment ID: 89500

value: male

value: Follow up years:0.40

value: ECOG performance status:1

value: LDH ratio:3.08

value: Number of extranodal sites:2


title: 26 - mAdbID:89388

description: mAdb experiment ID: 89388

value: lymph node

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up status:ALIVE

value: Follow up years:4.01

value: LDH ratio:1.13

value: Number of extranodal sites:0


title: 1628 - mAdbID:89712

description: mAdb experiment ID: 89712

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:3.12

value: LDH ratio:0.47

value: Number of extranodal sites:4


title: 1652 - mAdbID:88534

description: mAdb experiment ID: 88534

value: female

value: Follow up years:1.63

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:NA

value: LDH ratio:1.23

value: Number of extranodal sites:1


title: 21 - mAdbID:89383

description: mAdb experiment ID: 89383

value: male

value: lymph node

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:2.39

value: ECOG performance status:0

value: LDH ratio:0.9


title: 24 - mAdbID:89380

description: mAdb experiment ID: 89380

value: Lymphoma

value: Follow up status:ALIVE

value: Follow up years:5.10

value: ECOG performance status:3

value: LDH ratio:3.67

value: Number of extranodal sites:0


title: 1763 - mAdbID:88509

description: mAdb experiment ID: 88509

value: female

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:5.51

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:1


title: 1200 - mAdbID:88524

description: mAdb experiment ID: 88524

value: lymph node

value: Follow up status:DEAD

value: Follow up years:0.30

value: ECOG performance status:1

value: LDH ratio:30.76

value: Number of extranodal sites:4


title: 1099 - mAdbID:88452

description: mAdb experiment ID: 88452

value: male

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:3.07

value: ECOG performance status:2

value: LDH ratio:1.29


title: 1620 - mAdbID:88488

description: mAdb experiment ID: 88488

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:2.16

value: LDH ratio:0.67

value: Number of extranodal sites:0


title: 1762 - mAdbID:88508

description: mAdb experiment ID: 88508

value: female

value: lymph node

value: Follow up years:5.20

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:0

value: LDH ratio:0.75


title: 1295 - mAdbID:88526

description: mAdb experiment ID: 88526

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:5.16

value: ECOG performance status:1

value: LDH ratio:0.89

value: Number of extranodal sites:NA


title: 97 - mAdbID:88446

description: mAdb experiment ID: 88446

value: male

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:5.06

value: LDH ratio:0.73

value: Number of extranodal sites:1


title: 1756 - mAdbID:88505

description: mAdb experiment ID: 88505

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:3.46

value: LDH ratio:1.24

value: Number of extranodal sites:0


title: 1331 - mAdbID:88529

description: mAdb experiment ID: 88529

value: female

value: lymph node

value: Follow up years:3.29

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:0

value: LDH ratio:0.99


title: 1613 - mAdbID:88482

description: mAdb experiment ID: 88482

value: male

value: Follow up years:5.80

value: ECOG performance status:1

value: LDH ratio:NA

value: Number of extranodal sites:2


title: 1296 - mAdbID:88527

description: mAdb experiment ID: 88527

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:4.78

value: Number of extranodal sites:NA


title: 1089 - mAdbID:88451

description: mAdb experiment ID: 88451

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:5.11

value: LDH ratio:1.16

value: Number of extranodal sites:0


title: 1761 - mAdbID:88507

description: mAdb experiment ID: 88507

value: lymph node

value: Follow up status:DEAD

value: Follow up years:0.23

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:0

value: LDH ratio:3.85

value: Number of extranodal sites:1


title: 61 - mAdbID:88511

description: mAdb experiment ID: 88511

value: male

value: Lymphoma

value: Follow up years:0.89

value: LDH ratio:2


title: 66 - mAdbID:88444

description: mAdb experiment ID: 88444

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:4.03

value: LDH ratio:0.72


title: 2648 - mAdbID:92498

description: mAdb experiment ID: 92498

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:0.24

value: ECOG performance status:2

value: LDH ratio:NA


title: 1742 - mAdbID:88436

description: mAdb experiment ID: 88436

value: lymph node

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:3.27

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:1.12

value: Number of extranodal sites:0


title: 65 - mAdbID:88443

description: mAdb experiment ID: 88443

value: male

value: Lymphoma

value: Follow up years:4.04

value: ECOG performance status:0

value: LDH ratio:0.78


title: 1650 - mAdbID:88499

description: mAdb experiment ID: 88499

value: Submitting diagnosis:DLBCL

value: Follow up status:DEAD

value: Follow up years:0.74

value: Number of extranodal sites:1


title: 1707 - mAdbID:88433

description: mAdb experiment ID: 88433

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:2.80

value: ECOG performance status:1

value: LDH ratio:0.94


title: 1704 - mAdbID:88429

description: mAdb experiment ID: 88429

value: lymph node

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:3.14

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:0.87


title: 1788 - mAdbID:88440

description: mAdb experiment ID: 88440

value: female

value: Lymphoma

value: Follow up years:0.38

value: ECOG performance status:2

value: LDH ratio:1.1

value: Number of extranodal sites:2


title: 1705 - mAdbID:88430

description: mAdb experiment ID: 88430

value: Submitting diagnosis:DLBCL

value: Follow up years:3.93

value: LDH ratio:0.8

value: Number of extranodal sites:5


title: 1703 - mAdbID:88428

description: mAdb experiment ID: 88428

value: male

value: Follow up status:DEAD

value: Follow up years:0.69

value: ECOG performance status:3

value: LDH ratio:2.05

value: Number of extranodal sites:NA


title: 1702 - mAdbID:88427

description: mAdb experiment ID: 88427

value: lymph node

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:1.04

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:0.38

value: Number of extranodal sites:1


title: 1651 - mAdbID:88425

description: mAdb experiment ID: 88425

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:1.66

value: ECOG performance status:0

value: LDH ratio:NA

value: Number of extranodal sites:0


title: 1619 - mAdbID:88422

description: mAdb experiment ID: 88422

value: female

value: Follow up status:DEAD

value: Follow up years:0.24

value: LDH ratio:0.72


title: 1451 - mAdbID:88403

description: mAdb experiment ID: 88403

value: male

value: lymph node

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:1.84

value: ECOG performance status:2

value: LDH ratio:0.6


title: 1241 - mAdbID:88387

description: mAdb experiment ID: 88387

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:1.41

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:1.15

value: Number of extranodal sites:1


title: 1647 - mAdbID:88424

description: mAdb experiment ID: 88424

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up status:ALIVE

value: Follow up years:2.79

value: ECOG performance status:0

value: LDH ratio:NA


title: 1238 - mAdbID:88385

description: mAdb experiment ID: 88385

value: male

value: lymph node

value: Follow up status:DEAD

value: Follow up years:0.15

value: ECOG performance status:3

value: LDH ratio:7.06

value: Number of extranodal sites:2


title: 1335 - mAdbID:88398

description: mAdb experiment ID: 88398

value: female

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:1.38

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:1.36


title: 1336 - mAdbID:88399

description: mAdb experiment ID: 88399

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:2.43

value: LDH ratio:0.7

value: Number of extranodal sites:1


title: 1645 - mAdbID:88423

description: mAdb experiment ID: 88423

value: lymph node

value: Follow up status:ALIVE

value: Follow up years:2.85

value: ECOG performance status:2

value: LDH ratio:1.2


title: 1233 - mAdbID:88381

description: mAdb experiment ID: 88381

value: Follow up years:2.50

value: LDH ratio:0.87

value: Number of extranodal sites:0


title: 1232 - mAdbID:88380

description: mAdb experiment ID: 88380

value: male

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:2.49

value: LDH ratio:1.17


title: 1236 - mAdbID:88384

description: mAdb experiment ID: 88384

value: female

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:2.56

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:2.3


title: 1337 - mAdbID:88400

description: mAdb experiment ID: 88400

value: lymph node

value: Follow up status:DEAD

value: Follow up years:0.01

value: ECOG performance status:4

value: LDH ratio:5.8

value: Number of extranodal sites:1


title: 1553 - mAdbID:88420

description: mAdb experiment ID: 88420

value: Follow up status:ALIVE

value: Follow up years:2.93

value: LDH ratio:2.16


title: 1450 - mAdbID:88402

description: mAdb experiment ID: 88402

value: male

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:1.30

value: ECOG performance status:1

value: LDH ratio:1.43

value: Number of extranodal sites:0


title: 1221 - mAdbID:88379

description: mAdb experiment ID: 88379

value: female

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:3.94

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:0

value: LDH ratio:0.73


title: 1453 - mAdbID:88405

description: mAdb experiment ID: 88405

value: lymph node

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:1.70

value: LDH ratio:0.36


title: 1293 - mAdbID:88395

description: mAdb experiment ID: 88395

value: Follow up status:ALIVE

value: Follow up years:4.80

value: LDH ratio:0.96


title: 1449 - mAdbID:88401

description: mAdb experiment ID: 88401

value: male

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:1.61

value: ECOG performance status:2

value: LDH ratio:7.17

value: Number of extranodal sites:1


title: 1334 - mAdbID:88397

description: mAdb experiment ID: 88397

value: female

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up years:2.87

value: ECOG performance status:1

value: LDH ratio:0.7


title: 1240 - mAdbID:88386

description: mAdb experiment ID: 88386

value: lymph node

value: Follow up years:1.48

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:0.2

value: Number of extranodal sites:0


title: 1219 - mAdbID:88335

description: mAdb experiment ID: 88335

value: male

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:DEAD

value: Follow up years:0.51

value: LDH ratio:1.05


title: 1226 - mAdbID:88342

description: mAdb experiment ID: 88342

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.08

value: ECOG performance status:3

value: LDH ratio:7.35

value: Number of extranodal sites:3


title: 1225 - mAdbID:88341

description: mAdb experiment ID: 88341

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up status:ALIVE

value: Follow up years:2.95

value: ECOG performance status:0

value: LDH ratio:2.17

value: Number of extranodal sites:1


title: 1172 - mAdbID:88285

description: mAdb experiment ID: 88285

value: female

value: lymph node

value: Follow up years:2.81

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:1.34

value: Number of extranodal sites:0


title: 1228 - mAdbID:88344

description: mAdb experiment ID: 88344

value: male

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:2.78

value: LDH ratio:1.53


title: 1173 - mAdbID:88284

description: mAdb experiment ID: 88284

value: Lymphoma

value: Submitting diagnosis:DLBCL

value: Follow up status:DEAD

value: Follow up years:0.86

value: ECOG performance status:2

value: LDH ratio:1.49

value: Number of extranodal sites:3


title: 1766 - mAdbID:88331

description: mAdb experiment ID: 88331

value: lymph node

value: Follow up status:ALIVE

value: Follow up years:1.59

value: ECOG performance status:0

value: LDH ratio:0.86


title: 1101 - mAdbID:88298

description: mAdb experiment ID: 88298

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:5.63

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:1.88

value: Number of extranodal sites:0


title: 1746 - mAdbID:88329

description: mAdb experiment ID: 88329

value: male

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:1.91

value: ECOG performance status:1

value: LDH ratio:1.57


title: 1164 - mAdbID:88291

description: mAdb experiment ID: 88291

value: female

value: Submitting diagnosis:DLBCL

value: Follow up status:DEAD

value: Follow up years:0.19

value: ECOG performance status:2

value: LDH ratio:2.77


title: 1215 - mAdbID:88375

description: mAdb experiment ID: 88375

value: lymph node

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:5.34

value: LDH ratio:1


title: 1167 - mAdbID:88289

description: mAdb experiment ID: 88289

value: Follow up years:1.49

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:1.6

value: Number of extranodal sites:1


title: 115 - mAdbID:87875

description: mAdb experiment ID: 87875

value: Lymphoma

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:1.92

value: ECOG performance status:1

value: LDH ratio:0

value: Number of extranodal sites:0


title: 113 - mAdbID:87873

description: mAdb experiment ID: 87873

value: female

value: Submitting diagnosis:DLBCL

value: Follow up years:2.12

value: ECOG performance status:3

value: LDH ratio:1.47

value: Number of extranodal sites:2


title: 1169 - mAdbID:88287

description: mAdb experiment ID: 88287

value: male

value: lymph node

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:DEAD

value: Follow up years:1.70

value: LDH ratio:1.5

value: Number of extranodal sites:3


title: 104 - mAdbID:87866

description: mAdb experiment ID: 87866

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:3.75

value: Chemotherapy:R-CHOP-Like Regimen

value: Number of extranodal sites:1


title: 1291 - mAdbID:87775

description: mAdb experiment ID: 87775

value: Submitting diagnosis:DLBCL

value: Follow up years:0.03

value: ECOG performance status:NA

value: LDH ratio:NA

value: Number of extranodal sites:NA


title: 106 - mAdbID:87867

description: mAdb experiment ID: 87867

value: male

value: lymph node

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:2.95

value: ECOG performance status:0

value: LDH ratio:0.76


title: 1284 - mAdbID:87771

description: mAdb experiment ID: 87771

value: Lymphoma

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:3.50

value: LDH ratio:0.84


title: 1290 - mAdbID:87774

description: mAdb experiment ID: 87774

value: female

value: Follow up status:ALIVE

value: Follow up years:5.23

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:1


title: 118 - mAdbID:87877

description: mAdb experiment ID: 87877

value: Submitting diagnosis:DLBCL

value: Follow up years:1.63

value: LDH ratio:0.77

value: Number of extranodal sites:1


title: 119 - mAdbID:87878

description: mAdb experiment ID: 87878

value: male

value: lymph node

value: Follow up years:1.60

value: LDH ratio:0.7

value: Number of extranodal sites:0


title: 114 - mAdbID:87874

description: mAdb experiment ID: 87874

value: Lymphoma

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:1.98

value: ECOG performance status:2

value: LDH ratio:0.78


title: 1279 - mAdbID:87766

description: mAdb experiment ID: 87766

value: female

value: Follow up status:ALIVE

value: Follow up years:4.86

value: LDH ratio:1.32


title: 1239 - mAdbID:88272

description: mAdb experiment ID: 88272

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:2.23

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:1.6


title: 1275 - mAdbID:87763

description: mAdb experiment ID: 87763

value: male

value: lymph node

value: Follow up status:DEAD

value: Follow up years:1.88

value: ECOG performance status:1

value: LDH ratio:1.55

value: Number of extranodal sites:1


title: 1271 - mAdbID:87761

description: mAdb experiment ID: 87761

value: Lymphoma

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:4.72


title: 1272 - mAdbID:87762

description: mAdb experiment ID: 87762

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:5.68

value: ECOG performance status:NA

value: LDH ratio:0.88


title: 1255 - mAdbID:87760

description: mAdb experiment ID: 87760

value: female

value: Submitting diagnosis:DLBCL

value: Follow up years:5.17

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:0

value: LDH ratio:1.28


title: 1454 - mAdbID:88260

description: mAdb experiment ID: 88260

value: lymph node

value: Follow up years:0.61

value: ECOG performance status:1

value: LDH ratio:0.76


title: 1251 - mAdbID:87758

description: mAdb experiment ID: 87758

value: Lymphoma

value: Follow up years:2.71

value: LDH ratio:3.32

value: Number of extranodal sites:0


title: 96 - mAdbID:88445

description: mAdb experiment ID: 88445

value: male

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:5.37

value: LDH ratio:0

value: Number of extranodal sites:1


title: 1277 - mAdbID:87765

description: mAdb experiment ID: 87765

value: female

value: Submitting diagnosis:DLBCL

value: Follow up years:5.06

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:0.73


title: 1222 - mAdbID:87753

description: mAdb experiment ID: 87753

value: lymph node

value: Follow up years:3.52

value: ECOG performance status:0

value: LDH ratio:1.17


title: 1185 - mAdbID:87731

description: mAdb experiment ID: 87731

value: Lymphoma

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:3.70

value: LDH ratio:0.9


title: 1186 - mAdbID:87732

description: mAdb experiment ID: 87732

value: male

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:3.42

value: LDH ratio:1.13

value: Number of extranodal sites:0


title: 1184 - mAdbID:87730

description: mAdb experiment ID: 87730

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:4.74

value: LDH ratio:0.74


title: 1189 - mAdbID:87734

description: mAdb experiment ID: 87734

value: lymph node

value: Follow up years:5.12

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:1.19


title: 1181 - mAdbID:87727

description: mAdb experiment ID: 87727

value: female

value: Lymphoma

value: Follow up years:1.71

value: ECOG performance status:1

value: LDH ratio:0.63


title: 1179 - mAdbID:87725

description: mAdb experiment ID: 87725

value: male

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:2.52

value: ECOG performance status:0

value: LDH ratio:0.92

value: Number of extranodal sites:1


title: 1190 - mAdbID:87735

description: mAdb experiment ID: 87735

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:3.65

value: LDH ratio:0.78

value: Number of extranodal sites:0


title: 1211 - mAdbID:87751

description: mAdb experiment ID: 87751

value: female

value: lymph node

value: Follow up years:6.25

value: Chemotherapy:R-CHOP-Like Regimen

value: LDH ratio:0.97


title: 797 - mAdbID:66374

description: mAdb experiment ID: 66374

value: Lymphoma

value: Follow up status:DEAD

value: Follow up years:6.87

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1


title: 749 - mAdbID:66365

description: mAdb experiment ID: 66365

value: Follow up status:ALIVE

value: Follow up years:10.4

value: ECOG performance status:0


title: 792 - mAdbID:66372

description: mAdb experiment ID: 66372

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:5.53


title: 851 - mAdbID:69963

description: mAdb experiment ID: 69963

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:0.05

value: LDH ratio:0.85

value: Number of extranodal sites:0


title: 818 - mAdbID:67459

description: mAdb experiment ID: 67459

value: lymph node

value: Follow up years:0.1

value: ECOG performance status:3

value: LDH ratio:1.86


title: 683 - mAdbID:74474

description: mAdb experiment ID: 74474

value: Lymphoma

value: Follow up years:7.42

value: LDH ratio:0.28


title: 309 - mAdbID:70372

description: mAdb experiment ID: 70372

value: Final microarray diagnosis:ABC DLBCL

value: Follow up status:ALIVE

value: Follow up years:2.8

value: Chemotherapy:CHOP-Like Regimen

value: ECOG performance status:1

value: LDH ratio:0.9


title: 1187 - mAdbID:87733

description: mAdb experiment ID: 87733

value: male

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:5.23

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:0

value: LDH ratio:0.92


title: 758 - mAdbID:66368

description: mAdb experiment ID: 66368

value: lymph node

value: Follow up status:DEAD

value: Follow up years:1.1

value: Number of extranodal sites:0


title: 623 - mAdbID:66196

description: mAdb experiment ID: 66196

value: Lymphoma

value: Follow up years:2.43

value: LDH ratio:0.46


title: 1058 - mAdbID:67511

description: mAdb experiment ID: 67511

value: Follow up years:0.42

value: Chemotherapy:CHOP-Like Regimen

value: LDH ratio:1.61


title: 304 - mAdbID:66099

description: mAdb experiment ID: 66099

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:1.31

value: ECOG performance status:1

value: LDH ratio:1.375


title: 412 - mAdbID:66180

description: mAdb experiment ID: 66180

value: Submitting diagnosis:DLBCL

value: Final microarray diagnosis:GCB DLBCL

value: Follow up status:ALIVE

value: Follow up years:12.12

value: LDH ratio:1.25


title: 306 - mAdbID:73837

description: mAdb experiment ID: 73837

value: lymph node

value: Final microarray diagnosis:Unclassified DLBCL

value: Follow up years:2.69

value: ECOG performance status:2

value: LDH ratio:NA


title: 537 - mAdbID:66145

description: mAdb experiment ID: 66145

value: Lymphoma

value: Follow up status:DEAD

value: Follow up years:4.99

value: Number of extranodal sites:1


title: 305 - mAdbID:66143

description: mAdb experiment ID: 66143

value: Final microarray diagnosis:ABC DLBCL

value: Follow up years:0.82

value: Chemotherapy:CHOP-Like Regimen

value: Number of extranodal sites:0


title: 1002 - mAdbID:66063

description: mAdb experiment ID: 66063

value: Submitting diagnosis:DLBCL

value: Follow up years:0.28

value: ECOG performance status:1

value: LDH ratio:16.68


title: 310 - mAdbID:73838

description: mAdb experiment ID: 73838

value: lymph node

value: Follow up status:ALIVE

value: Follow up years:0.97

value: LDH ratio:1.41


title: Control_year1_rep1_ctrl09-T2

status: Public on Nov 26 2008

city: San Francisco

first: Sergio

last: Baranzini

state: CA

address: 513 Parnassus Ave

department: Neurology

institute: University of California San Francisco

hyb_protocol: hybridization onto Affymetrix® Human Genome U133 Plus2.0 arrays (NIH Neuroscience Microarray Consortium, Phoenix, AZ).

scan_protocol: Affymetrix protocol

data_processing: Normalized in BRBArrayTools using almostRMA, using default affymterix setting chosen by the program. There was no other scaling or trimming.

label: Biotin

source_name: CD4+ Tcells

label_protocol: Affymetrix protocol

growth_protocol: Peripheral blood mononuclear cells (PBMC) were separated in a ficoll gradient and frozen in liquid nitrogen until ready for CD4+ isolation

extract_protocol: RNA was then extracted using RNeasy® Mini kit (Quiagen, Valencia, CA), amplified with MessageAmpTM II aRNA kit 20 (Ambion, Austin, TX)

treatment_protocol: Untouched naïve CD4+ T cells were isolated by negative selection using Dynabeads® magnetic technology (Invitrogen, Carlsbad, CA). CD4+ T cells purity was assessed by FACS analysis (> 95%, data not shown)

tag: naïve CD4+ Tcells


title: U937 cells expressing AML1/ETO - Replica 1

city: Milan

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were  hybridized with each biotin-labeled target.

scan_protocol: Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.

data_processing: The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: U937 myelomoncytic cell line, transfected with HA-tagged AML1/ETO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA  The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.

growth_protocol: U937 cell lines were maintained in RPMI-1640 supplemented with 10% FCS and 2mM glutamine at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each cell line, an RNA pool was obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions.

treatment_protocol: Cell lines were treated for 8h with 100uM ZnSO4 prior to RNA extraction.

tag: U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying monocytic characteristics) transfected with HA-tagged AML1/ETO under the control of the mouse metallothionine promoter treated for 8h with 100µM ZnSO4 to induce transgene expression.


title: Control_year1_rep1_ctrl12-T2


title: U937 cells transfected with empty pSGMtNeo vector - Replica 1

source_name: U937 myelomoncytic cell line, transfected with pSGMtNeo vector

tag: U937 cell line (human cell line established from a diffuse histiocytic lymphoma and displaying monocytic characteristics) transfected with pSGMtNeo vector treated for 8h with 100µM ZnSO4.


title: U937 cells transfected with empty pSGMtNeo vector - Replica 2


title: CIS_year1_rep1_cis14-T4


title: CIS_year1_rep1_cis39-T2


title: Control_year1_rep1_ctrl14-T2


title: U937 cells expressing AML1/ETO - Replica 2


title: Control_year1_rep1_ctrl06-T2


title: Control_year1_rep1_ctrl10-T2


title: Control_year1_rep1_ctrl05-T2


title: Control_year1_rep1_ctrl11-T2


title: Control_year1_rep1_ctrl08-T2


title: CIS_year1_rep1_cis40-T2


title: Control_year1_rep1_ctrl04-T2 a

description: ctrl04-T2 a-HGU133_2


title: 745 - mAdbID:65801

description: mAdb experiment ID: 65801

value: Final microarray diagnosis:GCB DLBCL

value: Follow up years:1.33


title: CIS_year1_rep1_cis34-T2


title: Control_year1_rep1_ctrl03-T2


title: CIS_year1_rep1_cis37-T2


title: CIS_year1_rep1_cis33-T2


title: 1252 - mAdbID:87759

description: mAdb experiment ID: 87759

value: male

value: Lymphoma

value: Follow up status:DEAD

value: Follow up years:0.00

value: Chemotherapy:R-CHOP-Like Regimen

value: ECOG performance status:0

value: LDH ratio:3.72


title: CIS_year1_rep1_cis38-T2


title: CIS_year1_rep1_cis32-T3


title: CIS_year1_rep1_cis29-T3


title: CIS_year1_rep1_cis26-T4


title: CIS_year1_rep1_cis12-T2


title: CIS_year1_rep1_cis23-T2


title: CIS_year1_rep1_cis28-T4


title: CIS_year1_rep1_cis25-T4


title: CIS_year1_rep1_cis22-T4


title: CIS_year1_rep1_cis20-T4


title: CIS_year1_rep1_cis27-T3


title: CIS_year1_rep1_cis08-T4


title: CIS_year1_rep1_cis30-T2


title: CIS_year1_rep1_cis15-T5


title: CIS_year1_rep1_cis06-T4


title: CIS_year1_rep1_cis09-T4


title: CIS_year1_rep1_cis05-T4


title: CIS_year1_rep1_cis21-T4


title: CIS_year1_rep1_cis18-T5


title: CIS_year1_rep1_cis16-T5


title: CIS_year1_rep1_cis24-T5


title: CIS_year1_rep1_cis02-T4


title: CIS_year1_rep1_cis11-T5


title: CIS_year1_rep1_cis07-T5


title: CIS_year1_rep1_cis03-T5


title: CIS_year1_rep1_cis04-T5


title: CIS_year1_rep1_cis01-T5


title: CIS_year1_rep1_cis23-T6


title: Control_baseline_rep1_ctr5


title: Control_baseline_rep1_ctr029


title: Control_baseline_rep1_ctr023


title: Control_baseline_rep1_ctr025


title: Control_baseline_rep1_ctr020


title: Control_baseline_rep1_ctr022


title: Control_baseline_rep1_ctr027


title: Control_baseline_rep1_ctr024


title: Control_baseline_rep1_ctr026


title: Control_baseline_rep1_ctr017


title: Control_baseline_rep1_ctr021


title: Control_baseline_rep1_ctr011


title: Control_baseline_rep1_ctr014


title: Control_baseline_rep1_ctr010(a)


title: Control_baseline_rep1_ctr019


title: Control_baseline_rep1_ctr006


title: Control_baseline_rep1_ctr018


title: Control_baseline_rep1_ctr016(a)


title: Control_baseline_rep1_ctr015


title: Control_baseline_rep1_ctr013


title: Control_baseline_rep1_ctr012


title: Control_baseline_rep1_ctr008


title: Control_baseline_rep1_ctr009


title: Control_baseline_rep1_ctr007


title: Control_baseline_rep2_ctr001b


title: Control_baseline_rep2_ctr002b


title: Control_baseline_rep1_ctr003


title: CIS_baseline_rep1_cis043


title: Control_baseline_rep1_ctr001


title: CIS_baseline_rep1_cis034


title: CIS_baseline_rep1_cis041


title: Control_baseline_rep1_ctr004


title: CIS_baseline_rep1_cis040


title: CIS_baseline_rep1_cis028


title: CIS_baseline_rep1_cis033


title: CIS_baseline_rep1_cis029


title: CIS_baseline_rep1_cis027


title: CIS_baseline_rep1_cis038


title: CIS_baseline_rep1_cis032


title: CIS_baseline_rep1_cis037


title: CIS_baseline_rep1_cis024


title: CIS_baseline_rep1_cis022


title: CIS_baseline_rep1_cis026


title: CIS_baseline_rep1_cis021


title: CIS_baseline_rep1_cis039


title: CIS_baseline_rep1_cis020


title: CIS_baseline_rep1_cis016_2


title: CIS_baseline_rep1_cis030


title: CIS_baseline_rep1_cis018


title: CIS_baseline_rep1_cis025


title: CIS_baseline_rep1_cis017


title: CIS_baseline_rep1_cis014


title: CIS_baseline_rep2_cis013b


title: CIS_baseline_rep1_cis015


title: CIS_baseline_rep2_cis010b


title: CIS_baseline_rep1_cis012


title: CIS_baseline_rep1_cis011


title: CIS_baseline_rep1_cis009


title: CIS_baseline_rep1_cis013


title: CIS_baseline_rep1_cis010


title: CIS_baseline_rep1_cis007


title: CIS_baseline_rep1_cis006


title: Control_baseline_rep1_ctr002


title: CIS_baseline_rep1_cis005


title: neocortex, 5 months mouse#5

city: Boston

first: Philipp

last: Oberdoerffer

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: Gene expression data from mouse neocortex

hyb_protocol: Chips used in this study were the Affymetrix MOE 430 2.0 arrays which have 45, 037 probe sets (Affymetrix, Santa Clara, CA).  cRNA (10 ug) in hybridization cocktail was placed in the chip and hybridized at 45° C for 16 hours with mixing on a rotisserie at 60 rpm. Following hybridization, the hybrization solutions were removed and the gene chips were installed in a fluidics system for washing and staining.

scan_protocol: After staining, the gene chips were read at a resolution of 3 um using a Hewlett Packard GeneArray Scanner (Affymetrix). The averaged images collected from two scanned images were used for the analysis.

data_processing: The GeneChip Operating Software (GCOS) version 1.2 was used to analyze the image data. GCOS determines the presence of mRNA in samples and computes the signals of probe sets using the differences and ratios between PM and MM signals. Signals in each image are normalized to minimize overall variability in hybridization by a global scaling method.

organism: Mus musculus

source_name: neocortex from B6xC3 F1 hybrid mice at 5 months of age

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

growth_protocol: Male B6C3F1 mice were purchased from Harlan-Sprague-Dawley at 6-7 weeks of age. Mice were housed singly in a pathogen-free facility and provided acidifed water ad libitum.

extract_protocol: Total RNA was extracted from frozen tissue using the TRIZOL reagent (Invitrogen, San Diego, CA) and mRNA was purified from the total RNA with oligo-dT-linked oligotex resin (Qiagen, Valencia, CA). Double-stranded DNA was then synthesized from 1 ug of mRNA using the SuperScript Choice System (Invitrogen) with an oligo-dT primer containing a T7 RNA polymerase promoter (Genset, LaJolla, CA), purified with phenol-chloroform-isoamyl alchohol, and precipitated with pellet paint co-precipitant (Novagen, Madison, WI). Purified double-stranded cDNA was used to synthesize biotin-labeled cRNA usind the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY). The biotin-labeled antisense cRNA was then purified with the RNeasy affinity column (Qiagen). After purification, biotin-labeled cRNA was fragmented randomly to sizes ranging from 35 to 200 bases.

treatment_protocol: Control Diet: Mice were fed 24 g/wk of AIN-93M diet which has a total energy content of 16740 kJ/kg.

tag: Strain

value: B6xC3 F1 hybrid

value: 5 months


title: neocortex, 30 months mouse#2

source_name: neocortex from B6xC3 F1 hybrid mice at 30 months of age

value: 30 months


title: neocortex, 5 months mouse#4


title: neocortex, 5 months mouse#1


title: neocortex, 30 months mouse#4


title: neocortex, 5 months mouse#3


title: CIS_baseline_rep1_cis002


title: neocortex, 30 months mouse#3


title: neocortex, 30 months mouse#5


title: CIS_baseline_rep1_cis004


title: CIS_baseline_rep1_cis003


title: neocortex, 5 months mouse#2


title: Control 6

status: Public on Nov 25 2008

city: Pittsburgh

first: Sandra

middle: Anne

last: Founds

state: PA

address: 448 Victoria Building, 3500 Victoria St.

department: School of Nursing

institute: University of Pittsburgh

description: control

hyb_protocol: standard affymetrix

scan_protocol: standard affymetrix

data_processing: MAS 5.0

molecule: polyA RNA

source_name: human placenta first trimester

label_protocol: standard affymetrix

extract_protocol: snap frozen surplus CVS pulverized with polytron

tag: Caucasian, normal karyotypes


title: Control 5

description: control


title: Control 2

description: control


title: Case 4

description: case


title: Control 8

description: control


title: Control 7

description: control


title: CIS_baseline_rep1_cis001


title: neocortex, 30 months mouse#6


title: Case 3

description: case


title: Control 4

description: control


title: Control 3

description: control


title: Control 1

description: control


title: Case 2

description: case


title: Case 1

description: case


title: simulans_bodies_C_2

city: East Lansing

first: Ian

last: Dworkin

state: MI

address: 203 Natural Science Bldg. Michigan State University

department: Zoology

institute: Michigan State University

description: Adult females bodies

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

organism: Drosophila simulans

source_name: CHOICE

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: reared at 25° C on agar-yeast-cornmeal medium with constant humidity in an environmental chamber

extract_protocol: Total RNA from heads or bodies was extracted using TRIzol reagent as per manufacturer instructions. RNA was further purified using a Qiagen RNeasy Mini Kit per the manufacturer’s protocol

value: Adult Female Bodies


title: sechellia_bodies_NC_2

description: Adult females bodies

organism: Drosophila sechellia

source_name: NO CHOICE


title: simulans_bodies_NC_2

description: Adult females bodies


title: simulans_bodies_C_1

description: Adult females bodies


title: sechellia_bodies_C_1

description: Adult females bodies


title: simulans_bodies_NC_1

description: Adult females bodies


title: Muscle_JA16_07

status: Public on Nov 22 2008

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

hyb_protocol: 3.75 micrograms fragmented, biotinylated cDNA was hybridized overnight in 220 ul volume at 45 degrees C in standard Affymetrix eukaryotic hybridization buffer; arrays were washed, stained with phycoerythrin-streptavidin (including anti-phycoerythrin antibody enhancement step) with Affymetrix Fluidics Station 450 as recommended by Affymetrix

scan_protocol: Affymetrix Scanner 3000 was used to generate DAT, CEL, and CHP files as recommended by Affymetrix

data_processing: The MAS5 algorithm was implemented with Affymetrix Gene Chip Operating Software

label_protocol: RNA was reverse transcribed and cDNA was amplified, fragmented, and biotinylated with kits from NuGEN (version 2 Ovation and Version 2 Fragmention & Labeling) as recommended by NuGEN

extract_protocol: Total RNA extracted by Polytron homogenization in Trizol reagent (Invitrogen), followed by RNA cleanup, precipitation, and recovery in water per instructions provided by Invitrogen

treatment_protocol: Mice treated with intraperitoneal injections of JA16 anti-myostatin antibody or saline control on days 1 (0.12 mg/g body weight) and 3 (0.09 mg/g); mice were killed by CO2 inhalation on day5 and gatrocnemius muscle were immediately frozen in liquid nitrogen and stored at -70 degrees C

tag: male C57BL/6

tag: gastrocnemius muscle


title: Muscle_JA16_06


title: sechellia_bodies_C_2

description: Adult females bodies


title: Muscle_JA16_04


title: sechellia_bodies_NC_1

description: Adult females bodies


title: Muscle_JA16_10


title: Muscle_JA16_09


title: Muscle_JA16_03


title: Muscle_JA16_05


title: Muscle_JA16_08


title: Muscle_Saline_06

source_name: Saline


title: Muscle_Saline_10


title: Muscle_JA16_02


title: Muscle_Saline_04


title: Muscle_JA16_01


title: Muscle_Saline_08


title: Muscle_Saline_07


title: Muscle_Saline_09


title: Muscle_Saline_05


title: Muscle_Saline_01


title: Muscle_Saline_02


title: Muscle_Saline_03


title: ctrl-low-2

status: Public on Nov 21 2008

city: Chuo-ku, Kobe

first: Mitsunori

last: Ota

state: Hyogo

address: Minatojima-minamimachi 2-2-3

department: CENTER FOR DEVELOPMENTAL BIOLOGY

country: Japan

institute: RIKEN

description: Control virus-infected NIH3T3 cells harvested at 30% confluency

hyb_protocol: Following fragmentation, cRNA were hybridized to the Affymetrix GeneChip Mouse Genome 430 2.0 Array. Chips were washed and stained with Streptavidin R-phycoerythrin (Invitrogen) in the Fluidics Station 450 (Affymetrix).

scan_protocol: Chips were scanned with the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: After scanning the chips, expression values of probe sets were summarized with the RMA algorithm (Irizarry et al., 2003).

source_name: Control vector expressing cells at low density

label_protocol: Biotinylated cRNAs were prepared according to the Affymetrix standard one-cycle target labeling protocol.

growth_protocol: NIH3T3 cells expressing each constructs were cultured in 35mm dishes and harvested at 37C untill they reach at the indicated cell density.

extract_protocol: Total RNA was extracted with RNeasy kit (Qiagen) followed by further purification.

treatment_protocol: Cells at indicated density were washed with PBS(-) and lysed with the lysis buffer in RNeasy kit (Qiagen) following manufacturer's instructions.


title: ctrl-low-1


title: tead2VP16-over-1

description: Tead2-VP16-expressing NIH3T3 cells harvested at complete confluency

source_name: Tead2-VP16 expressing cells over confluent


title: tead2VP16-conf-2

description: Proliferating Tead2-VP16-expressing NIH3T3 cells harvested at a density slightly exceeding the confluency of normal cells

source_name: Tead2-VP16 expressing cells at high density


title: ctrl-over-2

description: Control virus-infected NIH3T3 cells harvested at complete confluency

source_name: Control vector expressing cells over confluent


title: tead2EnR-low-2

description: Tead2-EnR-expressing NIH3T3 cells harvested at 30% confluency of these cells

source_name: Tead2-EnR expressing cells at low density


title: ctrl-over-1


title: tead2EnR-low-1


title: tead2VP16-over-2


title: yap-conf-1

description: Proliferating Yap-expressing NIH3T3 cells harvested at a density slightly exceeding the confluency of normal cells

source_name: Yap expressing cells at high density


title: yap-conf-2


title: CIS_baseline_rep1_cis008


title: Control (dupl) sample 1a

status: Public on Nov 20 2008

first: Panagiotis

last: Konstantinopoulos

address: 3 Blackfan Circle

department: Hematology/Oncology

institute: Beth Israel Deaconess Medical Center

description: The arrays included duplicates from four normal controls and from two BRCA1 mutation carriers and single arrays from another two BRCA1 mutation carriers

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: The data were analyzed using the gene set comparison tool of BRB-ArrayTools 3.6 (NCI)

source_name: Breast epithelial cells from normal controls

label_protocol: Affymetrix standard protocol

extract_protocol: Total RNA was extracted using the Absolutely RNA Nanoprep kit, Stratagene

tag: Breast epithelial cells


title: Control (dupl) sample 6a


title: Control (dupl) sample 4b


title: Control (dupl) sample 5b


title: BRCA1 carrier (dupl) sample 3b

source_name: Breast epithelial cells from BCRA1 mutation carrier


title: BRCA1 carrier (dupl) sample 2b


title: BRCA1 carrier sample 8


title: BRCA1 carrier (dupl) sample 2a


title: Control (dupl) sample 5a


title: Control (dupl) sample 6b


title: Exp 2971_CLA

status: Public on Nov 19 2008

city: Santa Monica

first: Margaret

last: Flowers

address: 2200 Santa Monica Blvd.

department: Dept of Experimental Therapeutics

institute: John Wayne Cancer Institute

description: Mammary gland, virgin, 8 wk.

hyb_protocol: Affymetrix standard protocols

scan_protocol: Scanning Hardware: Affymetrix 3000 scanner Software: GCOS, manufacturer's recommended settings

data_processing: MAS 5.0 standard processing protocols and settings.

source_name: mouse fed 1% CLA

label_protocol: Affymetrix standard protocols

extract_protocol: Mammary glands were collected according to standard necropsis procedures. Tissue was stored in RNAlater (Sigma, St. Louis, MO) until processing. RNA was obtained using Qiagen RNeasy (Valencia CA) and stored in -80 degrees Celsius.

treatment_protocol: PyV-MT expressing female mice were fed a diet supplemented with 1% conjugated linoleic acid or control chow for 4 weeks. Animals were euthanized at 8 weeks of age and mammary glands were collected for RNA processing.

value: FVB/PyV-Mt

value: 8 weeks

tag: Sex

value: Female

tag: Parity

value: No

value: Mammary gland


title: Control (dupl) sample 1b


title: tead2VP16-conf-1


title: BRCA1 carrier sample 7


title: BRCA1 carrier (dupl) sample 3a


title: Exp 2970_CLA

description: Mammary gland, virgin, 8 wk.


title: Exp 2968_control

description: Mammary gland, virgin, 8 wk.

source_name: mouse fed control chow


title: Control (dupl) sample 4a


title: MLLamp_15.cel

status: Public on Nov 18 2008

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

description: no additional information

hyb_protocol: According to standard Affymetrix protocol.

data_processing: RMA Log base 2

source_name: acute myeloid leukemia

extract_protocol: trizol and RNeasy Mini kit

tag: acute myeloid leukemia

tag: lab code

tag: diagnosis

value: AML M5

tag: age

tag: sex

value: m

tag: tissue

value: BM


title: MLLamp_14.cel

description: no additional information

scan_protocol: According to standard Affymetrix protocol.

value: AML M1

value: f


title: MLLamp_6.cel

description: no additional information

label_protocol: According to standard Affymetrix protocol.

value: AML (secondary after PV)


title: MLLamp_11.cel

description: no additional information

value: tAML M4 (thyroid gland carcinoma)


title: MLLamp_9.cel

description: no additional information

value: tAML (mantle cell lymphoma)

value: PB


title: MLLamp_8.cel

description: no additional information

value: tMDS (melanoma)


title: MLLamp_13.cel

description: no additional information

value: MDS


title: MLLamp_10.cel

description: no additional information

value: AML


title: MLLamp_7.cel

description: no additional information

value: tAML M2 (Hodgkin's NSIIIA)


title: MLLamp_4.cel

description: no additional information


title: MLLamp_12.cel

description: no additional information


title: MLLamp_3.cel

description: no additional information


title: MLLamp_1.cel

description: no additional information

source_name: acute myeloid leukemia samples


title: MLLamp_5.cel

description: no additional information


title: MLLamp_2.cel

description: no additional information


title: yw 1-2 hr 3

status: Public on Nov 17 2008

city: New York

first: Christine

last: Rushlow

address: 100 Washington Sq.E.

department: Biology

institute: NYU

description: wild type, 1 to 2 hr embryo

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: standard Affymetrix procedures

organism: Drosophila melanogaster

source_name: wild type, 1 to 2 hr embryo

label_protocol: cDNA was prepared by GeneChip® HT One-Cycle cDNA Synthesis Kit (Manufactured by Invitrogen for Affymetrix) and labeled by BioArray™ HighYield™ RNA Transcript Labeling Kit (Enzo).

extract_protocol: 1-2 hr embryonic total RNA samples were extracted form duplicate collections of yw and zld-glc embryos by TRIzol (invitrogen).

tag: wild type, 1 to 2 hr embryo


title: yw 1-2 hr 2

description: wild type, 1 to 2 hr embryo


title: MCF-7 cells untreated 6A-SA5 sample 2

city: Chicago

first: Boris

last: Pasche

state: IL

address: 303 E Superior Lurie 6-220

department: Medicine

institute: Northwestern University

description: All protocols were carried out according to the Affymetrix protocols.

hyb_protocol: Affymetrix

scan_protocol: The array was read on the Affymetrix GeneChip Scanner 3000.

data_processing: The microarray data consists of 54,675 probe sets and were normalized using RMA algorithm. Once normalized, genes that were both up- or down-regulated 1.5 fold in *6A cells (SA5) over *9A cells (WB1), and had a p-value of <0.01 using t-test, were uploaded into the Ingenuity Pathway Analysis software (Ingenuity Systems, Redwood City, CA).  The Ingenuity Pathway Analysis software sorts the genes into their appropriate signaling pathways

source_name: MCF-7 cells untreated 6A-SA5 sample 2

label_protocol: Affymetrix

growth_protocol: MCF-7 cells were cultured in RPMI 1640 (Invitrogen Corp., Grand Island, NY) supplemented with 10% Heat Inactivated FBS (Hyclone, Logan, Utah), 2 mM L-glutamine (Invitrogen Corp., Grand Island, NY), non-essential amino acids, 1,000 units/ml penicillin, 10,000 μg/ml streptomycin, 0.006 mg/ml human recombinant insulin (Sigma, St. Louis, MO), and 0.5 mcg/ml amphotericin B (Biologos Inc., Montgomery, AL).

extract_protocol: Qiagen RNA easy kit

treatment_protocol: MCF-7 cells stably transfected with pIRES-TGFBR1*6A-HA-FLAG were plated and grown until 80% confluent. The cells were serum starved overnight then refed with complete media for 18 hr before RNA collection.

tag: MCF-7 cells were stably transfected with pIRES-TGFBR1*6A-HA-FLAG.  Clones were picked up and SA5 refers to the clone name.  The samples were run in triplicate to collect RNA from 3 separate batches of cells and thus named SA5-1, SA5-2, or SA5-3.  “Untreated” refers to the samples that were grown in complete media alone with no exogenously added growth factors.


title: MCF-7 cells untreated 6A-SA5 sample 1

source_name: MCF-7 cells untreated 6A-SA5 sample 1


title: MCF-7 cells untreated 6A-SA5 sample 3

source_name: MCF-7 cells untreated 6A-SA5 sample 3


title: MCF-7 cells untreated WT-WB1 sample 2

data_processing: The microarray data consists of 54,675 probe sets and were normalized using RMA algorithm. Once normalized, genes that were both up- or down-regulated 1.5 fold in *6A cells (SA5) over *9A cells (WB1), and had a p-value of <0.01 using t-test, were uploaded into the Ingenuity Pathway Analysis software (Ingenuity Systems, Redwood City, CA).  The Ingenuity Pathway Analysis software sorts the genes into their appropriate signaling pathways.

source_name: MCF-7 cells untreated WT-WB1 sample 2

treatment_protocol: MCF-7 cells stably transfected with pIRES-TGFBR1-HA-FLAG were plated and grown until 80% confluent. The cells were serum starved overnight then refed with complete media for 18 hr before RNA collection.

tag: MCF-7 cells were stably transfected with pIRES-TGFBR1-HA-FLAG.  Clones were picked up and WB1 refers to the clone name.  The samples were run in triplicate to collect RNA from 3 separate batches of cells and thus named WB1-1, WB1-2, or WB1-3.   “Untreated” refers to the samples that were grown in complete media alone with no exogenously added growth factors.


title: SpFoxp3+no1

status: Public on Nov 16 2008

first: CBDM

last: Lab

department: Microbiology and Immunobiology

hyb_protocol: Biotin-labeled cRNA was fragmented and hybridized to the array in a cocktail containing control oligos at 45°C for 16 hours, rotated at 60rpm, in the Affymetrix GeneChip Hybridization Oven 640.  After hybridization, the arrays were automatically cycled through buffer washes and stained with streptavidin R-phycoerythrin conjugate (Invitrogen) in the Affymetrix GeneChip Fluidics Station 400 (EukGE-WS2v4 protocol).

scan_protocol: After staining and washing, the arrays were scanned in the Affymetrix GeneChip Scanner 3000 using the Affymetrix GCOS (GeneChip Operating Software) to automatically generate .CEL files.

data_processing: RMA

source_name: CD4 Foxp3- T cells activated in vitro with Spleen Dendritic Cells and TGFbeta

label_protocol: BioArray High Yield RNA Transcript Labeling T7 Kit (Enzo Life Sciences)

extract_protocol: RNA isolated with Trizol reagent and amplified twice with the MessageAmp aRNA Kit (Ambion)

tag: Genetic background

tag: Age

tag: Number of mice per chip

value: 3 male

tag: Tissue

value: CD4+Foxp3- T cells and dendritic cells were obtained from spleen

tag: Culture

value: CD4+Foxp3- T cells were culture with Sp-DCs at a 10:1 ratio with anti-CD3 (1ug/ml) + TGFbeta (0.6ng/ml) + IL-2 (5ng/ml on D2 and D4) for 5 days

tag: Post-culture sort

value: Sorted on CD4+ Foxp3/GFP+


title: zld-GCL 1-2 hr 1

description: zld-glc 1-2 hr embryo

source_name: zld germ-line colne, 1 to 2 hr embryo

tag: zld germ-line clone, 1 to 2 hr embryo


title: CD4+MemoryRAno2

source_name: CD44hi Memory T cells that were activated in vitro in the presence of TGFbeta + Retinoic Acid and naive T cells

value: CD44hiCD62L-CD25-CD4+ (Memory) T cells were sorted form spleen and lymph nodes (mesenteric and cervical)

value: Congenically marked (CD45.1 or CD45.2) memory T cells were cultured with CD44negCD62LhiCD25-CD4+ (naive) T cells at a 2:1 ratio with anti-CD3/CD28 beads + IL-2 (20 U/ml) + TGFbeta (10 ng/ml) + Retinoic Acid (100nM) for 48hrs

value: Memory T cells were sorted based on the expression of the congenic marker (CD45.1 or CD45.2)


title: CD4+Memoryno1

source_name: CD44hi Memory T cells that were activated in vitro in the presence of TGFbeta and naive T cells

value: Congenically marked (CD45.1 or CD45.2) memory T cells were cultured with CD44negCD62LhiCD25-CD4+ (naive) T cells at a 2:1 ratio with anti-CD3/CD28 beads + IL-2 (20 U/ml) + TGFbeta (10 ng/ml) for 48hrs


title: CD4+MemoryRAno3


title: MCF-7 cells untreated WT-WB1 sample 3

source_name: MCF-7 cells untreated WT-WB1 sample 3

tag: MCF-7 cells were stably transfected with pIRES-TGFBR1-HA-FLAG.  Clones were picked up and WB1 refers to the clone name.  The samples were run in triplicate to collect RNA from 3 separate batches of cells and thus named WB1-1, WB1-2, or WB1-3.  “Untreated” refers to the samples that were grown in complete media alone with no exogenously added growth factors.


title: CD4+Memoryno3


title: yw 1-2 hr 1

description: wild type, 1 to 2 hr embryo


title: zld-GCL 1-2 hr 3

description: zld-glc 1-2 hr embryo


title: MCF-7 cells untreated WT-WB1 sample 1

source_name: MCF-7 cells untreated WT-WB1 sample 1


title: SpRAFoxp3+no2

source_name: CD4 Foxp3- T cells activated in vitro with Spleen Dendritic Cells and TGFbeta + Retinoic Acid

value: CD4+Foxp3- T cells were culture with Sp-DCs at a 10:1 ratio with anti-CD3 (1ug/ml) + TGFbeta (0.6ng/ml) + RA (100nM) + IL-2 (5ng/ml on D2 and D4) for 5 days


title: CD4+MemoryRAno1


title: zld-GCL 1-2 hr 2

description: zld-glc 1-2 hr embryo

label_protocol: cDNA was prepared by GeneChip® HT One-Cycle cDNA Synthesis Kit (Manufactured by Invitrogen for Affymetrix) and labeled by BioArray™ HighYield™ RNA Transcript Labeling Kit (Enzo)


title: SpFoxp3+no2


title: CD4+Memoryno2


title: SpFoxp3-no1

value: Sorted on CD4+ Foxp3/GFP-


title: SpRAFoxp3+no1


title: LPFoxp3+no2

source_name: CD4 Foxp3- T cells activated in vitro with Lamina Propria Dendritic Cells and TGFbeta

value: CD4+Foxp3- T cells were obtained from spleen and dendritic cells were obtained from lamina propria

value: CD4+Foxp3- T cells were culture with LP-DCs at a 10:1 ratio with anti-CD3 (1ug/ml) + TGFbeta (0.6ng/ml) + IL-2 (5ng/ml on D2 and D4) for 5 days


title: SpRAFoxp3-no2


title: LPFoxp3+no1

source_name: CD4 Foxp3+ T cells activated in vitro with Lamina Propria Dendritic Cells and TGFbeta


title: LPFoxp3-no2


title: Ulna_2

status: Public on Nov 15 2008

city: London

first: Simon

middle: Charles

last: Rawlinson

address: 4 Newark Street

country: United Kingdom

institute: Bart's and The London School of Medicine and Dentistry

description: Samples underwent 1 round of amplification prior to labeling using the Affymetrix GeneChip® One-Cycle cDNA Synthesis Kit.

hyb_protocol: See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Fluidics Station 450.

scan_protocol: Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Scanner 3000 with Workstation.

data_processing: MAS5 algorithm

label: Affymetrix Hyb/Wash/Stain Kit

source_name: Ulnar bone

extract_protocol: Tissue dissected and ground to a paste in liquid nitrogen in pestle and mortar. Immediate immersion/homogenization in QIAzol. Aqueous phase transferred to QIAgen RNeasy (Fibrous tissue) Mini column for RNA prep.

treatment_protocol: Bone samples taken from different skeletal sites

tag: Mouse

tag: Black CD57

tag: Gender

value: Male

tag: Weight

value: Ulnar bone, soft tissue and epipyses removed


title: SpFoxp3-no2


title: LPFoxp3-no1


title: Ulna_1

label_protocol: See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Fluidics Station 450.

value: Ulnar bone, soft tissue and epiphyses removed


title: Mandible_2

source_name: Mandibular bone

value: Mandibular bone, including teeth


title: Calvarial bone_1

source_name: Calvarial bone

value: Calvarial bone, sutures removed


title: Mandible_1


title: Calvarial bone_2


title: mouse_islets_VhlhKO_03

city: Zurich

first: Jens

last: Zehetner

state: Zurich

address: Schafmattstrasse 18

department: Cell Biology

country: Switzerland

institute: ETH Zurich

hyb_protocol: Biotin-labeled cRNA samples (15 µg) were fragmented randomly to 35–200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371, Santa Clara, CA) and were mixed in 300 µl of hybridization buffer containing a hybridization Control cRNA and Control Oligo B2 control (Affymetrix Inc., P/N 900454, Santa Clara, CA), 0.1 mg/ml herring sperm DNA and 0.5 mg/ml acetylated bovine serum albumin in 2-(4-morpholino)-ethane sulfonic acid (MES) buffer, pH 6.7, before hybridization to GeneChip® Mouse Genome 430 2.0 arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 EukGE-WS2v5_450 protocol.

scan_protocol: An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA) was used to measure the fluorescent intensity emitted by the labeled target.

data_processing: Data processing was performed using the Affymetrix GCOS 1.4 software (Affymetrix Inc., Santa Clara, CA). After hybridization and scanning, probe cell intensities were calculated and summarized for the respective probe sets by means of the MAS5 algorithm (Hubbell et al 2002). To compare the expression values of the genes from chip to chip, global scaling was performed, which resulted in the normalization of the trimmed mean of each chip to a target intensity (TGT value) of 500 as detailed in the statistical algorithms description document of Affymetrix (2002). Quality control measures were considered before performing the statistical analysis. These included adequate scaling factors (between 1 and 3 for all samples) and appropriate numbers of present calls calculated by application of a signed-rank call algorithm (Liu et al., 2002). The efficiency of the labeling reaction and the hybridization performance was controlled with the following parameters: Present calls and optimal 3' /5' hybridization ratios (around 1) for the housekeeping genes, for the poly A spike in controls and the prokaryotic control.

source_name: Pancreatic islets, VhlhKO, 03

label_protocol: The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies, Delaware, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. Total RNA samples (30 ng) were reverse-transcribed into double-stranded cDNA with Two-Cycle cDNA Synthesis Kit (Affymetrix Inc., P/N 900494, Santa Clara, CA). The double-stranded cDNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA). The purified double-stranded cDNA were in vitro transcribed in presence of biotin-labeled nucleotides using a IVT Labeling Kit (Affymetrix Inc., P/N 900449, Santa Clara, CA). The biotinylated cRNA was purified using a Sample Cleanup Module (Affymetrix Inc., P/N 900371, Santa Clara, CA) and its quality and quantity was determined using NanoDrop ND 1000 and Bioanalyzer 2100.

extract_protocol: Stratagene MicroRNA kit

tag: disease model

value: Conditional beta cell specific KO mouse model using RIP2-Cre and Vhlh(fl/fl)

tag: citations

value: Herrera PL (2000), Haase VH et al. (2001)

tag: gender

value: male

tag: age

value: 18 weeks

tag: genotype/variation

value: VhlhKO


title: mouse_islets_VhlhKO_02

source_name: Pancreatic islets, VhlhKO, 02

value: female

value: 20 weeks


title: mouse_islets_ctrl_01

source_name: Pancreatic islets, control, 01

value: 26 weeks

value: control


title: mouse_islets_VhlhKO_01

source_name: Pancreatic islets, VhlhKO, 01


title: ovariectomized, oil treatment (control), 76hr, biological rep 1

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

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on Mouse430_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).

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

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

source_name: mammary gland tissues, ovariectomized mice, control, 76hr

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

growth_protocol: Nulliparous Balb/c mice were ovariectomized at six weeks-of-age and rested for two weeks (to purge ovarian hormones) before treatment with sesame oil (vehicle control) or progesterone.

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

treatment_protocol: In the case of progesterone treatment, mice received a daily subcutaneous injection (within the intrascapular region) of 1mg of progesterone dissolved in 100 microliters of sesame oil.  Mice were sacrificed 4, 16, 28, or 76 hours (h) following the first injection.   For controls, an equal number of mice received sesame oil (100 microliters) and were sacrificed at the same time points as the progesterone-treated group.

tag: control


title: ovariectomized, P4 treatment, 76hr, biological rep 2

description: P4 treatment, 76hr, biological rep 2

source_name: mammary gland tissues, ovariectomized mice, progesterone (P4) treatment, 76hr

tag: progesterone (P4) treatment


title: ovariectomized, P4 treatment, 76hr, biological rep 3

description: P4 treatment, 76hr, biological rep 3


title: mouse_islets_ctrl_03

source_name: Pancreatic islets, control, 03


title: ovariectomized, P4 treatment, 76hr, biological rep 1

description: P4 treatment, 76hr, biological rep 1


title: ovariectomized, P4 treatment, 28hr, biological rep 1

description: P4 treatment, 28hr, biological rep 1

source_name: mammary gland tissues, ovariectomized mice, progesterone (P4) treatment, 28hr


title: ovariectomized, P4 treatment, 16hr, biological rep 3

description: P4 treatment, 16hr, biological rep 3

source_name: mammary gland tissues, ovariectomized mice, progesterone (P4) treatment, 16hr


title: ovariectomized, oil treatment (control), 28hr, biological rep 3

source_name: mammary gland tissues, ovariectomized mice, control, 28hr


title: ovariectomized, P4 treatment, 28hr, biological rep 3

description: P4 treatment, 28hr, biological rep 3


title: ovariectomized, oil treatment (control), 28hr, biological rep 1


title: ovariectomized, oil treatment (control), 76hr, biological rep 3


title: ovariectomized, oil treatment (control), 76hr, biological rep 2


title: ovariectomized, P4 treatment, 28hr, biological rep 2

description: P4 treatment, 28hr, biological rep 2


title: ovariectomized, oil treatment (control), 16hr, biological rep 2

source_name: mammary gland tissues, ovariectomized mice, control, 16hr


title: ovariectomized, oil treatment (control), 28hr, biological rep 2


title: mouse_islets_ctrl_02

source_name: Pancreatic islets, control, 02


title: ovariectomized, P4 treatment, 16hr, biological rep 2

description: P4 treatment, 16hr, biological rep 2


title: ovariectomized, P4 treatment, 16hr, biological rep 1

description: P4 treatment, 16hr, biological rep 1


title: ovariectomized, oil treatment (control), 16hr, biological rep 3


title: ovariectomized, P4 treatment, 4hr, biological rep 2

description: P4 treatment, 4hr, biological rep 2

source_name: mammary gland tissues, ovariectomized mice, progesterone (P4) treatment, 4hr


title: ovariectomized, oil treatment (control), 16hr, biological rep 1


title: ovariectomized, oil treatment (control), 4hr, biological rep 2

source_name: mammary gland tissues, ovariectomized mice, control, 4hr


title: Quiescent HMEC C9

city: Durham

first: Zachary

middle: Conrad

last: Hartman

state: NC

address: Research Drive MSRB rm 414

department: Surgery

institute: Duke University

description: Quiescent HMECs were infected for 18hrs.  RNA was then harvested and hybridized to a HU-133+ v2 array.

hyb_protocol: The cRNA was fragmented before hybridization, and we prepared a hybridization cocktail that included the fragmented cRNA, probe array controls, bovine serum albumin and herring sperm DNA. We hybridized the cRNA to the oligonucleotide probes on the probe array for a 16-h incubation at 45 °C. Immediately after the hybridization, the hybridized probe array underwent an automated washing and staining protocol on an Affymetrix fluidics station.

scan_protocol: We scanned the DNA chips with the Affymetrix GeneChip scanner and processed the signals by the GeneChip expression analysis algorithm (v.2; Affymetrix).

data_processing: MAS 5.0 Expression Analysis

source_name: Quiescent Ad-HER2-ki infected HMECs

label_protocol: We generated biotin-labeled cRNA by in vitro transcription from the DNA.

growth_protocol: Used standard HMEC culturing techniques (Clonetics media with growth additives)

extract_protocol: Trizol

treatment_protocol:
Primary HMECs prepared from normal donors undergoing reduction mammoplasties were passaged 2 times and serum starved for 36 hrs.
Infected with a 1st Generation E1-E3- GFP (under CMV promoter) Adenovirus
RNA harvested 18 hours post infection

tag: HMECs

tag: passage 3

tag: serum starved for 36 hrs.

tag: Infected for 18 hrs.


title: ovariectomized, P4 treatment, 4hr, biological rep 3

description: P4 treatment, 4hr, biological rep 3


title: ovariectomized, P4 treatment, 4hr, biological rep 1

description: P4 treatment, 4hr, biological rep 1


title: Quiescent HMEC C10


title: Quiescent HMEC C4


title: Quiescent HMEC A10

source_name: Quiescent Ad-GFP infected HMECs


title: Quiescent HMEC B9

source_name: Quiescent Ad-HER2wt infected HMECs


title: Quiescent HMEC B10


title: Quiescent HMEC B8


title: ovariectomized, oil treatment (control), 4hr, biological rep 1


title: Quiescent HMEC A5


title: ovariectomized, oil treatment (control), 4hr, biological rep 3


title: Quiescent HMEC A4


title: Quiescent HMEC A9


title: Quiescent HMEC A2


title: Quiescent HMEC B4


title: Quiescent HMEC C2


title: Quiescent HMEC B5


title: Quiescent HMEC C3


title: siRNA-96_rep2

status: Public on Nov 14 2008

city: Oxford

first: Helio

last: Pais

address: Jonh Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

description: Cells transfected with siRNA-96

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Expression values were normalized using the Robust Multichip Average (RMA) methodology.

source_name: C3H10T1/2 cell line

label_protocol: Affymetrix protocol

extract_protocol: RNeasy QIAGEN

tag: Mesenchymal derived mouse cell line


title: siRNA-140_rep3

description: Cells transfected with siRNA-140


title: siRNA-96_rep1

description: Cells transfected with siRNA-96


title: antimicroRNA-449_rep2

description: Cells transfected with LNA-antimicroRNA-449


title: siRNA-140_rep1

description: Cells transfected with siRNA-140


title: antimicroRNA-140_rep3

description: Cells transfected with LNA-antimicroRNA-140


title: siRNA-140_rep2

description: Cells transfected with siRNA-140


title: antimicroRNA-449_rep1


title: siRNA-96_rep3

description: Cells transfected with siRNA-96


title: antimicroRNA-140_rep2


title: antimicroRNA-449_rep3


title: antimicroRNA-140_rep1


title: D2-CC-IP2: Drd2 Medium spiny neurons, dissected mouse striatum, chronic cocaine treatment

first: Nathaniel

last: Heintz

address: 1230 York Ave, Box 260

institute: HHMI/Rockefeller University

hyb_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform.

data_processing:
In Genespring GX 7.3.1, data were normalized with the GC-RMA algorithm, and expression values on each chip were normalized to that chip’s 50th percentile.
Using the Limma package from Bioconductor project, data were converted to log2 scale.

label_protocol: Affymetrix two cycle amplification kit, starting with 15 ng of total RNA.

extract_protocol: TRAP affinity purification of ribosomes from BAC transgenic mice (see accompanying manuscript), followed by Trizol-LS extraction, DNAse treatment, and RNeasy-Minelute Cleanup.

treatment_protocol: Acute or chronic treatment with saline or cocaine (see accompanying manuscript for more details).

tag: TRAP RNA

tag: Driver

value: Drd2, Line:CP101, Region:striatum

tag: Collection Day


title: D1-CS-IP2: Drd1a Medium spiny neurons, dissected mouse striatum, chronic saline treatment

scan_protocol: Standard Affymetrix protocol for mouse 430 2.0 platform.

value: Drd1a, Line:CP73, Region:striatum


title: D2-AS-IP2: Drd2 Medium spiny neurons, dissected mouse striatum, acute saline treatment


title: d2_str_ub3: Drd2+ Medium Spiny Neurons, Striatum, Unbound RNA 3

data_processing: GCRMA normalization within biological replicate groups.  Performed with R / Bioconductor.

extract_protocol: TRAP affinity purification of ribosomes from BAC transgenic mice (see accompanying manuscript), followed by Trizol extraction, DNAse treatment, and RNeasy-Minelute Cleanup

tag: cytoplasmic polysomal RNA, unbound

value: drd2, Line:CP101, Region:Striatum


title: D2-CS-IP2: Drd2 Medium spiny neurons, dissected mouse striatum, chronic saline treatment


title: D2-AC-IP2: Drd2 Medium spiny neurons, dissected mouse striatum, acute cocaine treatment


title: D1-CC-IP1: Drd1a Medium spiny neurons, dissected mouse striatum, chronic cocaine treatment


title: D1-CC-IP3: Drd1a Medium spiny neurons, dissected mouse striatum, chronic cocaine treatment


title: D1-CS-IP3: Drd1a Medium spiny neurons, dissected mouse striatum, chronic saline treatment


title: D1-AS-IP3: Drd1a Medium spiny neurons, dissected mouse striatum, acute saline treatment


title: D1-CS-IP1: Drd1a Medium spiny neurons, dissected mouse striatum, chronic saline treatment


title: D2-AS-IP3: Drd2 Medium spiny neurons, dissected mouse striatum, acute saline treatment


title: d1_str_ub3: Drd1+ Medium Spiny Neurons, Striatum, Unbound RNA 3

value: drd1, Line:CP73, Region:Striatum


title: D2-AC-IP1: Drd2 Medium spiny neurons, dissected mouse striatum, acute cocaine treatment


title: D1-CC-IP2: Drd1a Medium spiny neurons, dissected mouse striatum, chronic cocaine treatment


title: D2-AS-IP1: Drd2 Medium spiny neurons, dissected mouse striatum, acute saline treatment


title: D2-AC-IP3: Drd2 Medium spiny neurons, dissected mouse striatum, acute cocaine treatment


title: D2-CC-IP1: Drd2 Medium spiny neurons, dissected mouse striatum, chronic cocaine treatment


title: D2-CS-IP3: Drd2 Medium spiny neurons, dissected mouse striatum, chronic saline treatment


title: D2-CC-IP3: Drd2 Medium spiny neurons, dissected mouse striatum, chronic cocaine treatment


title: D2-CS-IP1: Drd2 Medium spiny neurons, dissected mouse striatum, chronic saline treatment


title: D1-AC-IP1: Drd1a Medium spiny neurons, dissected mouse striatum, acute cocaine treatment


title: D1-AS-IP1: Drd1a Medium spiny neurons, dissected mouse striatum, acute saline treatment


title: WB3: Whole mouse brain lacking striatum.

data_processing:
In Genespring GX 7.3.1, GCRMA normalization was performed within the two biological replicate groups (IP and WB), and expression values on each chip were further normalized to the expression values of several positive control genes and to a constant value of 0.01.
Using the Limma package from Bioconductor project, data were converted to log2 scale.

source_name: Whole mouse brain lacking striatum

extract_protocol: TRAP affinity purification of ribosomes from BAC transgenic mice (IP, see accompanying manuscript) or total homogenized tissue (WB), followed by Trizol-LS extraction, DNAse treatment, and RNeasy-Minelute Cleanup.

tag: Total RNA

tag: Whole mouse brain lacking striatum


title: D1-AC-IP3: Drd1a Medium spiny neurons, dissected mouse striatum, acute cocaine treatment


title: D1-AS-IP2: Drd1a Medium spiny neurons, dissected mouse striatum, acute saline treatment


title: WB1: Whole mouse brain lacking striatum.


title: WB2: Whole mouse brain lacking striatum.


title: D1-AC-IP2: Drd1a Medium spiny neurons, dissected mouse striatum, acute cocaine treatment


title: Purkinje Neuron, Cerebellum, Unbound RNA 2

value: pcp2, Line:DR168, Region:Cerebellum


title: Bergmann Glia, Cerebellum, Unbound RNA 1

value: septin4, Line:DS152, Region:Cerebellum


title: Bergmann Glia, Cerebellum, TRAP RNA 2

source_name: Bergmann Glia, Cerebellum, TRAP RNA 2


title: Purkinje Neuron, Cerebellum, TRAP RNA 6

source_name: Purkinje Neuron, Cerebellum, TRAP RNA 6


title: Bergmann Glia, Cerebellum, Unbound RNA 3


title: Pnoc+ Neurons, Cortex, Unbound RNA 1

source_name: Pnoc+ Neurons, Cortex, Unbound RNA 1

value: pnoc, Line:GM64, Region:Cortex


title: Bergmann Glia, Cerebellum, Unbound RNA 2


title: Mixed Oligodendroglia, Cortex, TRAP RNA 2

value: olig2, Line:JD97, Region:Cortex


title: Purkinje Neuron, Cerebellum, Unbound RNA 3


title: Purkinje Neuron, Cerebellum, TRAP RNA 4

source_name: Purkinje Neuron, Cerebellum, TRAP RNA 4


title: Bergmann Glia, Cerebellum, TRAP RNA 1

source_name: Bergmann Glia, Cerebellum, TRAP RNA 1


title: Purkinje Neuron, Cerebellum, TRAP RNA 1

source_name: Purkinje Neuron, Cerebellum, TRAP RNA 1

value: pcp2, Line:DR166, Region:Cerebellum


title: Pnoc+ Neurons, Cortex, TRAP RNA 3

source_name: Pnoc+ Neurons, Cortex, TRAP RNA 3


title: Purkinje Neuron, Cerebellum, TRAP RNA 3

source_name: Purkinje Neuron, Cerebellum, TRAP RNA 3


title: Purkinje Neuron, Cerebellum, Unbound RNA 1


title: Purkinje Neuron, Cerebellum, TRAP RNA 5

source_name: Purkinje Neuron, Cerebellum, TRAP RNA 5


title: Pnoc+ Neurons, Cortex, TRAP RNA 1

source_name: Pnoc+ Neurons, Cortex, TRAP RNA 1


title: Bergmann Glia, Cerebellum, TRAP RNA 3

source_name: Bergmann Glia, Cerebellum, TRAP RNA 3


title: Pnoc+ Neurons, Cortex, TRAP RNA 2

source_name: Pnoc+ Neurons, Cortex, TRAP RNA 2


title: Mixed Oligodendroglia, Cortex, Unbound RNA 1


title: Mixed Oligodendroglia, Cerebellum, TRAP RNA 2

value: olig2, Line:JD97, Region:Cerebellum


title: Layer 6 Neurons, Cortex, TRAP RNA 3

source_name: Layer 6 Neurons, Cortex, TRAP RNA 3

value: ntsr1, Line:TS16, Region:Cortex


title: Mixed Oligodendroglia, Cerebellum, TRAP RNA 1


title: Mixed Oligodendroglia, Cerebellum, TRAP RNA 3


title: Purkinje Neuron, Cerebellum, TRAP RNA 2

source_name: Purkinje Neuron, Cerebellum, TRAP RNA 2


title: Mixed Oligodendroglia, Cortex, TRAP RNA 1


title: Layer 6 Neurons, Cortex, Unbound RNA 1

source_name: Layer 6 Neurons, Cortex, Unbound RNA 1


title: Granule Neurons, Cerebellum, TRAP RNA 2

source_name: Granule Neurons, Cerebellum, TRAP RNA 2

value: neurod1, Line:JP241, Region:Cerebellum


title: Granule Neurons, Cerebellum, TRAP RNA 3

source_name: Granule Neurons, Cerebellum, TRAP RNA 3


title: Layer 6 Neurons, Cortex, TRAP RNA 1

source_name: Layer 6 Neurons, Cortex, TRAP RNA 1


title: Granule Neurons, Cerebellum, TRAP RNA 1

source_name: Granule Neurons, Cerebellum, TRAP RNA 1


title: Layer 6 Neurons, Cortex, TRAP RNA 2

source_name: Layer 6 Neurons, Cortex, TRAP RNA 2


title: Mixed Oligodendroglia, Cortex, TRAP RNA 3


title: Stellate and Basket Neurons, Cerebellum, TRAP RNA 1

value: lypd6, Line:JP48, Region:Cerebellum


title: Stellate and Basket Neurons, Cerebellum, TRAP RNA 2


title: Unipolar Brush Neurons, Cerebellum, TRAP RNA 3

value: grp, Line:JP25, Region:Cerebellum


title: Unipolar Brush Neurons, Cerebellum, TRAP RNA 1


title: Golgi Neurons, Cerebellum, TRAP RNA 3

source_name: Golgi Neurons, Cerebellum, TRAP RNA 3

value: grm2, Line:JP77, Region:Cerebellum


title: Golgi Neurons, Cerebellum, TRAP RNA 1

source_name: Golgi Neurons, Cerebellum, TRAP RNA 1


title: Layer 5a Neurons, Cortex, TRAP RNA 3

source_name: Layer 5a Neurons, Cortex, TRAP RNA 3

value: etv1, Line:TS88, Region:Cortex


title: Layer 5b Neurons, Cortex, Unbound RNA 1

source_name: Layer 5b Neurons, Cortex, Unbound RNA 1

value: glt25d2, Line:DU9, Region:Cortex


title: Layer 5b Neurons, Cortex, TRAP RNA 1

source_name: Layer 5b Neurons, Cortex, TRAP RNA 1


title: Layer 5b Neurons, Cortex, TRAP RNA 2

source_name: Layer 5b Neurons, Cortex, TRAP RNA 2


title: Layer 5a Neurons, Cortex, Unbound RNA 1

source_name: Layer 5a Neurons, Cortex, Unbound RNA 1


title: Layer 5a Neurons, Cortex, TRAP RNA 2

source_name: Layer 5a Neurons, Cortex, TRAP RNA 2


title: Layer 5a Neurons, Cortex, TRAP RNA 1

source_name: Layer 5a Neurons, Cortex, TRAP RNA 1


title: Drd1+ Medium Spiny Neurons, Striatum, Unbound RNA 1


title: Golgi Neurons, Cerebellum, TRAP RNA 2

source_name: Golgi Neurons, Cerebellum, TRAP RNA 2


title: Unipolar Brush Neurons, Cerebellum, TRAP RNA 2


title: Drd2+ Medium Spiny Neurons, Striatum, Unbound RNA 2


title: Drd2+ Medium Spiny Neurons, Striatum, TRAP RNA 1


title: Drd1+ Medium Spiny Neurons, Striatum, TRAP RNA 1


title: Drd1+ Medium Spiny Neurons, Striatum, TRAP RNA 3


title: Cort+ Neurons, Cortex, TRAP RNA 3

source_name: Cort+ Neurons, Cortex, TRAP RNA 3

value: cort, Line:GM130, Region:Cortex


title: Drd2+ Medium Spiny Neurons, Striatum, TRAP RNA 3


title: Layer 5b Neurons, Cortex, TRAP RNA 3

source_name: Layer 5b Neurons, Cortex, TRAP RNA 3


title: Drd2+ Medium Spiny Neurons, Striatum, Unbound RNA 1


title: Drd1+ Medium Spiny Neurons, Striatum, Unbound RNA 2


title: Drd2+ Medium Spiny Neurons, Striatum, TRAP RNA 2


title: Mature Oligodendrocytes, Cortex, Unbound RNA 1

value: cmtm5, Line:JD307, Region:Cortex


title: Drd1+ Medium Spiny Neurons, Striatum, TRAP RNA 2


title: Mature Oligodendrocytes, Cortex, TRAP RNA 3


title: Mature Oligodendrocytes, Cortex, TRAP RNA 1


title: Cort+ Neurons, Cortex, TRAP RNA 2

source_name: Cort+ Neurons, Cortex, TRAP RNA 2


title: Mature Oligodendrocytes, Cortex, TRAP RNA 2


title: Cort+ Neurons, Cortex, TRAP RNA 1

source_name: Cort+ Neurons, Cortex, TRAP RNA 1


title: Stellate and Basket Neurons, Cerebellum, TRAP RNA 3


title: Mature Oligodendrocytes, Cerebellum, TRAP RNA 2

value: cmtm5, Line:JD307, Region:Cerebellum


title: Mature Oligodendrocytes, Cerebellum, TRAP RNA 1


title: Mature Oligodendrocytes, Cerebellum, Unbound RNA 3


title: Cholinergic Neurons, Corpus Striatum, Unbound RNA 2

value: chat, Line:DW167, Region:Corpus Striatum


title: Mature Oligodendrocytes, Cerebellum, TRAP RNA 3


title: Cholinergic Neurons, Corpus Striatum, Unbound RNA 1


title: Cholinergic Neurons, Corpus Striatum, TRAP RNA 2


title: Cholinergic Neurons, Corpus Striatum, TRAP RNA 1


title: Cholinergic Neurons, Spinal Cord, Unbound RNA 2

value: chat, Line:DW167, Region:Spinal Cord


title: Cholinergic Neurons, Spinal Cord, Unbound RNA 1


title: Cholinergic Neurons, Corpus Striatum, TRAP RNA 3


title: Cholinergic Neurons, Basal Forebrain, Unbound RNA 2

value: chat, Line:DW167, Region:Basal Forebrain


title: Cholinergic Neurons, Spinal Cord, TRAP RNA 2


title: Cholinergic Neurons, Basal Forebrain, Unbound RNA 1


title: Cholinergic Neurons, Basal Forebrain, TRAP RNA 2


title: Cholinergic Neurons, Basal Forebrain, Unbound RNA 3


title: Cholinergic Neurons, Spinal Cord, Unbound RNA 3


title: Cholinergic Neurons, Spinal Cord, TRAP RNA 1


title: Motor Neurons, Brainstem, Unbound RNA 2

source_name: Motor Neurons, Brainstem, Unbound RNA 2

value: chat, Line:DW167, Region:Brainstem


title: Cholinergic Neurons, Spinal Cord, TRAP RNA 3


title: Motor Neurons, Brainstem, TRAP RNA 2

source_name: Motor Neurons, Brainstem, TRAP RNA 2


title: Cck+ Neurons, Cortex, TRAP RNA 3

source_name: Cck+ Neurons, Cortex, TRAP RNA 3

value: cck, Line:GM391, Region:Cortex


title: Astrocytes, Cortex, Unbound RNA 2

source_name: Astrocytes, Cortex, Unbound RNA 2

value: aldh1l1, Line:JD133, Region:Cortex


title: Motor Neurons, Brainstem, Unbound RNA 3

source_name: Motor Neurons, Brainstem, Unbound RNA 3


title: Cck+ Neurons, Cortex, TRAP RNA 2

source_name: Cck+ Neurons, Cortex, TRAP RNA 2


title: Motor Neurons, Brainstem, TRAP RNA 1

source_name: Motor Neurons, Brainstem, TRAP RNA 1


title: Motor Neurons, Brainstem, Unbound RNA 1

source_name: Motor Neurons, Brainstem, Unbound RNA 1


title: Cholinergic Neurons, Basal Forebrain, TRAP RNA 3


title: Astrocytes, Cortex, TRAP RNA 4

source_name: Astrocytes, Cortex, TRAP RNA 4


title: Astrocytes, Cortex, TRAP RNA 3

source_name: Astrocytes, Cortex, TRAP RNA 3


title: Cholinergic Neurons, Basal Forebrain, TRAP RNA 1


title: Astrocytes, Cortex, TRAP RNA 2

source_name: Astrocytes, Cortex, TRAP RNA 2

value: aldh1l1, Line:JD130, Region:Cortex


title: Cck+ Neurons, Cortex, TRAP RNA 1

source_name: Cck+ Neurons, Cortex, TRAP RNA 1


title: Cck+ Neurons, Cortex, Unbound RNA 1

source_name: Cck+ Neurons, Cortex, Unbound RNA 1


title: Motor Neurons, Brainstem, TRAP RNA 3

source_name: Motor Neurons, Brainstem, TRAP RNA 3


title: Astrocytes, Cortex, Unbound RNA 1

source_name: Astrocytes, Cortex, Unbound RNA 1


title: Astrocytes, Cortex, TRAP RNA 1

source_name: Astrocytes, Cortex, TRAP RNA 1


title: Astrocytes, Cerebellum, TRAP RNA 1

source_name: Astrocytes, Cerebellum, TRAP RNA 1

value: aldh1l1, Line:JD130, Region:Cerebellum


title: Astrocytes, Cerebellum, TRAP RNA 3

source_name: Astrocytes, Cerebellum, TRAP RNA 3


title: Astrocytes, Cerebellum, TRAP RNA 2

source_name: Astrocytes, Cerebellum, TRAP RNA 2


title: Muscle control k70

city: Stirling

first: Iain

last: Gallagher

address: Room 4B133 Cottrell Building, University of Stirling, Airthrey Road

department: Faculty of Health Sciences and Sport

institute: University of Stirling

hyb_protocol: As Affymetrix

scan_protocol: As Affymetrix

data_processing: Data presented in the paper was quality controlled using the Microarray Suite software (MAS 5.0). All array data were normalized through implementations of the MAS5 algorithm, to a global scaling intensity of 100. Probesets declared absent by MAS5 across all chips were removed from further analysis.

source_name: vastus lateralis, control subject

label_protocol: Total RNA was labelled, converted to cRNA and fragmented as recommended by Affymetrix.

extract_protocol: Total RNA was isolated from muscle samples using TRIzol (Invitrogen, Stockholm, Sweden) and quantified using a Nano-drop spectrophotometer.

treatment_protocol: Muscle biopsies were obtained from the lateral portion of the vastus lateralis muscle, 10-20 cm above the knee. The biopsies were obtained using a Bergström biopsy needle after local anaesthesia in the ICU patients and just after sedation in the control patients.

tag: Gender:male, Age:76yrs


title: Muscle control k69

tag: Gender:male, Age:60yrs


title: Muscle septic k63

source_name: vastus lateralis, septic patient

tag: Gender:female, Age:71yrs


title: Muscle control k65

tag: Gender:male, Age:70yrs


title: Muscle septic k54

tag: Gender:female, Age:56yrs


title: Muscle control k67


title: Muscle septic k61

tag: Gender:male, Age:77yrs


title: Muscle septic k59

tag: Gender:male, Age:74yrs


title: Muscle septic k62

tag: Gender:male, Age:48yrs


title: Muscle control k71

tag: Gender:male, Age:71yrs


title: Muscle control k66


title: Muscle septic k50

tag: Gender:male, Age:46yrs


title: Muscle septic k57


title: Muscle control k72


title: Muscle control k68

tag: Gender:female, Age:72yrs


title: Muscle septic k56

tag: Gender:female, Age:69yrs


title: Muscle septic k64

tag: Gender:female, Age:25yrs


title: Muscle septic k55


title: Muscle septic k53


title: Muscle septic k60

tag: Gender:female, Age:67yrs


title: Muscle septic k49


title: melanoma mice model tumor tissue 3

status: Public on Nov 11 2008

city: Los Angeles

first: David

last: Wong

address: 73-017 CHS, 10833 Le Conte Ave

department: Dental Research Institute School of Dentistry

institute: University of California at Los Angeles

description: Affymetrix protocol

data_processing: Dchip

source_name: melanoma mice model tumor tissue 3

extract_protocol: RNeasy Mini kit

treatment_protocol: inject with B16/F1 melanoma cells

tag: C57BL/C mice, inject with B16/F1 melanoma cells


title: non small cell lung cancer model saliva in tumor mice 1

description: Affymetrix protocol

source_name: non small cell lung cancer model saliva from tumor mice 1

treatment_protocol: inject with KLN-205 cancer cells

tag: DBA mice, inject with KLN-205 cancer cells


title: non small cell lung cancer model saliva in control mice 3

description: Affymetrix protocol

source_name: non small cell lung cancer model saliva from control mice 3

treatment_protocol: inject with PBS

tag: DBA mice, inject with PBS


title: non small cell lung cancer model saliva in tumor mice 2

description: Affymetrix protocol

source_name: non small cell lung cancer model saliva from tumor mice 2


title: non small cell lung cancer model saliva in control mice 1

description: Affymetrix protocol

source_name: non small cell lung cancer model saliva from control mice 1


title: non small cell lung cancer model saliva in tumor mice 3

description: Affymetrix protocol

source_name: non small cell lung cancer model saliva from tumor mice 3


title: NKp80+

status: Public on Nov 12 2008

city: Tübingen

first: Sabrina

last: Kuttruff

address: Auf der Morgenstelle 15

department: of Immunology

country: Germany

institute: University of Tübingen

description: Expression array of NKp80+ CD8+ CCR7- alpha beta T cells

scan_protocol: Affymetrix- GeneChip® Scanner 3000

data_processing: Data were processed and normalized using the GCOS software

source_name: CD8+ CCR7- NKp80+ T cells pooled from 6 healthy donors

extract_protocol:
Qiagen- RNeasy Mini Kit
http://www1.qiagen.com/literature/handbooks/literature.aspx?id=1000291

treatment_protocol: PBMC were isolated via Ficoll density centrifugation. Peripheral blood cells from six individuals were pooled and enriched for CD8+ T cells via MACS depletion of CD4+ and CD14+ cells. Cells then were stained for the surface molecules TCR alpha beta, CD3, CD8, CCR7 and NKp80. Cell sorting into TCR alpha beta+, CD3+, CD8+, CCR7-, NKp80+/- fractions was performed on a FACS Aria Cell Sorter (BD). Sorted cells were sorted by -80°C before RNA extraction.

tag: 6 healthy blood donors

tag: gender

value: 3 female, 3 male

tag: Age

tag: Tissue

value: CD8+ CCR7- NKp80+ T cells isolated via FACS sorting


title: melanoma mice model tumor tissue

description: Affymetrix protocol

source_name: melanoma mice model tumor tissue


title: melanoma mice model serum in control mice 3

description: Affymetrix protocol

source_name: melanoma mice model serum from control mice 3

tag: C57BL/C mice, inject with PBS


title: melanoma mice model gland tissue in tumor mice 3

description: Affymetrix protocol

source_name: melanoma mice model gland tissue from tumor mice 3


title: melanoma mice model tumor tissue 2

description: Affymetrix protocol

source_name: melanoma mice model tumor tissue 2


title: melanoma mice model serum in tumor mice 3

description: Affymetrix protocol

source_name: melanoma mice model serum from tumor mice 3


title: melanoma mice model gland tissue in tumor mice 2

description: Affymetrix protocol

source_name: melanoma mice model gland tissue from tumor mice 2


title: melanoma mice model serum in control mice 2

description: Affymetrix protocol

source_name: melanoma mice model serum from control mice 2


title: melanoma mice model gland tissue in control mice 3

description: Affymetrix protocol

source_name: melanoma mice model gland tissue from control mice 3


title: melanoma mice model saliva in tumor mice 2

description: Affymetrix protocol

source_name: melanoma mice model saliva from tumor mice 2

tag: C57BL/C mice , inject with B16/F1 melanoma cells


title: melanoma mice model serum in tumor mice 2

description: Affymetrix protocol

source_name: melanoma mice model serum from tumor mice 2


title: melanoma mice model serum in control mice 1

description: Affymetrix protocol

source_name: melanoma mice model serum from control mice 1


title: NKp80-

description: Expression array of NKp80- CD8+ CCR7- alpha beta T cells

source_name: CD8+ CCR7- NKp80- T cells pooled from 6 healthy donors

value: CD8+ CCR7- NKp80- T cells isolated via FACS sorting


title: melanoma mice model saliva in tumor mice 1

description: Affymetrix protocol

source_name: melanoma mice model saliva from tumor mice


title: melanoma mice model gland tissue in control mice 2

description: Affymetrix protocol

source_name: melanoma mice model gland tissue from control mice 2


title: melanoma mice model gland tissue in tumor mice 1

description: Affymetrix protocol

source_name: melanoma mice model gland tissue from tumor mice 1


title: melanoma mice model saliva in tumor mice 3

description: Affymetrix protocol

source_name: melanoma mice model saliva from tumor mice 3


title: melanoma mice model saliva control 2

description: Affymetrix protocol

source_name: melanoma mice model saliva from control mice 2

tag: C57BL/C mice control, inject with PBS


title: melanoma mice model serum in tumor mice 1

description: Affymetrix protocol

source_name: melanoma mice model serum from tumor mice 1


title: melanoma mice model gland tissue in control mice 1

description: Affymetrix protocol

source_name: melanoma mice model gland tissue from control mice 1


title: melanoma mice model saliva control 3

description: Affymetrix protocol

source_name: melanoma mice model saliva from control mice 3


title: non small cell lung cancer model saliva in control mice 2

description: Affymetrix protocol

source_name: non small cell lung cancer model saliva from control mice 2