title: TE-10

description: Gene expression data from the CCLE


title: TE-14

status: Public on Mar 20 2012

type: RNA

city: Cambridge

first: Nicolas

last: Stransky

state: MA

address: 7 Cambridge center

department: Cancer Program

country: USA

institute: Broad Institute

description: Gene expression data from the CCLE

hyb_protocol: Fragmentation of the biotin-labeled cRNA prepared the sample for hybridization on the GeneChip Human U133 2.0 (PN 900467). The washing and staining was performed on the GeneChip Fluidics station using standard Affymetrix protocols outlined in the Expression Analysis Technical Manual, 2001, Affymetrix.

scan_protocol: The GeneChip® Scanner 3000 was used for scanning the arrays.

data_processing: The data were analyzed with 2.14.0, using the packages affyio_1.22.0 and affy_1.32.0, and RMA as normalization method. rma() was used with default options (normalize=TRUE, background=TRUE) and with the package hgu133plus2hsentrezgcdf_15.0.0 from Brainarray for the CDF file.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: RIKEN

label_protocol: The Affymetrix One-Cycle Target labeling assay was used to synthesize hybridization target using 1 mg of total RNA. Labeled cRNA hybridization target was produced using a 3-day, semi-automated workflow

growth_protocol: Cells lines were cultured following growth recommendations from the cell line source vendors. Cells were incubated at 37 ºC at 5% CO2 until 70% confluency was reached.  Pellets were harvested 48 hours post media change, flash frozen, and stored at -80 ºC until nucleic acid extraction.

extract_protocol: RNA was isolated from frozen cell pellets, containing an average cell count of 4.5 million cells, via Trizol (Invitrogen) extraction following the manufacturers instructions. Samples were quantified using both the Nanodrop 8000 spectrophotometer (ThermoScientific) and via Agilent 2100 Bioanalyzer.

tag: primary site

value: oesophagus

tag: histology

value: carcinoma

tag: histology subtype1


title: TE-4

description: Gene expression data from the CCLE


title: TE 617.T

description: Gene expression data from the CCLE

source_name: ATCC

value: rhabdomyosarcoma


title: T84

description: Gene expression data from the CCLE

value: adenocarcinoma


title: T98G

description: Gene expression data from the CCLE

value: glioma


title: T-47D

description: Gene expression data from the CCLE

value: breast


title: TC-71

description: Gene expression data from the CCLE

source_name: DSMZ

value: bone


title: TCC-PAN2

description: Gene expression data from the CCLE

source_name: HSRRB

value: pancreas


title: T24

description: Gene expression data from the CCLE


title: T1-73

description: Gene expression data from the CCLE

value: osteosarcoma


title: SW948

description: Gene expression data from the CCLE


title: SW620

description: Gene expression data from the CCLE


title: SW837

description: Gene expression data from the CCLE


title: SW 780

description: Gene expression data from the CCLE


title: T3M-4

description: Gene expression data from the CCLE


title: BEAS-2B_Cr-transformed_Clone_rep_6

status: Public on Mar 22 2012

city: Tuxedo

first: Hailey

middle: A.

last: Clancy

state: NY

address: 57 Old Forge Road

department: Environmental Medicine

institute: New York University

description:
Cr-6
reanalysis of GSM591438

hyb_protocol: cRNA generated by the labeling procedure was hybridized for 16 hr to the Affymetrix array according to the manufacturer's manual. Genechips were processed using protocol FS450_0007 for Genechip® fluidics station 450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files; data from cel files were batch normalized in R using the COMBAT package.   The probe-level analysis of the batch-normalized data was done by the RMA-16 algorithm using GeneSpring GX11.5 program.

label: biotin

source_name: 0.50uM K2CrO4_60 days_metal removed_clone isolated from agar (4 wks)_grown in monolayer (3 wks)

label_protocol: The cDNA probes were synthesized using the WT Expression Kit for Affymetrix Whole Transcript Expression Arrays (Ambion), fragmented, and labeled using Affymetrix Whole Transcript Terminal Labeling Kit (Affymetrix).

growth_protocol: cell were grown under standard laboratory conditions in DMEM supplemented with 10% FBS and 1% PenStrep; a single cell suspension of 5,000 cells per 9.6 square cm was seeded in soft agar at a concentration of 0.35%

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s protocol and purified using RNeasy Plus Micro Kit (Qiagen).

treatment_protocol: Cells were treated with an aqueous filter-sterlized solution of metals at the concentrations and days indicated prior to seeding in soft agar; metal was removed before seeding in soft agar and for the remainder of the experiment.

tag: cell line background

tag: background cell type

value: immortalized human bronchial epithelial cell

tag: cell type

value: clone isolated from agar (4 wks) and grown in monolayer (3 wks)

tag: exposed to

value: 0.50uM K2CrO4 for 60 days


title: SW579

description: Gene expression data from the CCLE

value: thyroid


title: SW48

description: Gene expression data from the CCLE


title: SW 1573

description: Gene expression data from the CCLE

value: lung


title: SW-1710

description: Gene expression data from the CCLE


title: SW 1783

description: Gene expression data from the CCLE


title: SW 1353

description: Gene expression data from the CCLE

value: chondrosarcoma


title: SW1463

description: Gene expression data from the CCLE


title: SW 1990

description: Gene expression data from the CCLE


title: SW403

description: Gene expression data from the CCLE


title: SUIT-2

description: Gene expression data from the CCLE


title: SW1417

description: Gene expression data from the CCLE


title: SW 900

description: Gene expression data from the CCLE


title: SW 1271

description: Gene expression data from the CCLE


title: SW1116

description: Gene expression data from the CCLE


title: SW 1088

description: Gene expression data from the CCLE


title: Sq-1

description: Gene expression data from the CCLE


title: SU.86.86

description: Gene expression data from the CCLE


title: SNU-C5

description: Gene expression data from the CCLE

source_name: KCLB


title: SW480

description: Gene expression data from the CCLE


title: SNU-C4

description: Gene expression data from the CCLE


title: SNU-C2A

description: Gene expression data from the CCLE


title: SNU-C1

description: Gene expression data from the CCLE


title: SNU-878

description: Gene expression data from the CCLE

value: liver


title: SNU-626

description: Gene expression data from the CCLE


title: SNU-840

description: Gene expression data from the CCLE

value: ovary


title: SNU-620

description: Gene expression data from the CCLE

value: stomach


title: SNU-761

description: Gene expression data from the CCLE

value: carcinoma


title: SNU-478

description: Gene expression data from the CCLE


title: SNU-475

description: Gene expression data from the CCLE


title: SNU-407

description: Gene expression data from the CCLE


title: SNU-283

description: Gene expression data from the CCLE


title: SNU-738

description: Gene expression data from the CCLE

value: oligodendroglioma


title: SNU-520

description: Gene expression data from the CCLE


title: SNU-899

description: Gene expression data from the CCLE


title: SNU-410

description: Gene expression data from the CCLE


title: SNU-245

description: Gene expression data from the CCLE


title: SNU-503

description: Gene expression data from the CCLE


title: SNU-46

description: Gene expression data from the CCLE


title: SNU-466

description: Gene expression data from the CCLE


title: SNU-423

description: Gene expression data from the CCLE


title: SNU-61

description: Gene expression data from the CCLE


title: SNU-5

description: Gene expression data from the CCLE


title: SNU-213

description: Gene expression data from the CCLE


title: SNU-398

description: Gene expression data from the CCLE


title: SNU-449

description: Gene expression data from the CCLE


title: SNU-216

description: Gene expression data from the CCLE


title: SNU-201

description: Gene expression data from the CCLE


title: SNU-387

description: Gene expression data from the CCLE


title: SNU-182

description: Gene expression data from the CCLE


title: SNU-308

description: Gene expression data from the CCLE


title: SNU-175

description: Gene expression data from the CCLE


title: SNU-1214

description: Gene expression data from the CCLE


title: SNU-1

description: Gene expression data from the CCLE


title: SNU-119

description: Gene expression data from the CCLE

value: adenocarcinoma


title: SNU-1196

description: Gene expression data from the CCLE


title: SNU-1105

description: Gene expression data from the CCLE

value: glioma


title: SNU-16

description: Gene expression data from the CCLE


title: SNU-1272

description: Gene expression data from the CCLE

value: kidney


title: SNU-1040

description: Gene expression data from the CCLE


title: SNU-1077

description: Gene expression data from the CCLE

value: endometrium


title: SK-N-MC

description: Gene expression data from the CCLE

value: bone


title: SNU-1079

description: Gene expression data from the CCLE


title: SK-N-SH

description: Gene expression data from the CCLE

value: neuroblastoma


title: SNU-1076

description: Gene expression data from the CCLE


title: SK-OV-3

description: Gene expression data from the CCLE


title: SK-N-FI

description: Gene expression data from the CCLE


title: SK-N-BE(2)

description: Gene expression data from the CCLE


title: SNG-M

description: Gene expression data from the CCLE


title: SK-MEL-30

description: Gene expression data from the CCLE

value: skin


title: SK-MEL-31

description: Gene expression data from the CCLE


title: SK-N-AS

description: Gene expression data from the CCLE


title: SK-MEL-3

description: Gene expression data from the CCLE


title: SK-MEL-2

description: Gene expression data from the CCLE


title: SK-HEP-1

description: Gene expression data from the CCLE


title: SK-N-DZ

description: Gene expression data from the CCLE


title: SK-MEL-5

description: Gene expression data from the CCLE


title: SNB-19

description: Gene expression data from the CCLE


title: SK-LMS-1

description: Gene expression data from the CCLE

value: sarcoma


title: SK-UT-1

description: Gene expression data from the CCLE

value: leiomyosarcoma


title: SK-MEL-28

description: Gene expression data from the CCLE


title: SK-ES-1

description: Gene expression data from the CCLE


title: SK-LU-1

description: Gene expression data from the CCLE


title: SK-MEL-24

description: Gene expression data from the CCLE


title: SK-MES-1

description: Gene expression data from the CCLE


title: SK-MEL-1

description: Gene expression data from the CCLE


title: SK-BR-3

description: Gene expression data from the CCLE

value: breast


title: SK-CO-1

description: Gene expression data from the CCLE


title: SH-10-TC

description: Gene expression data from the CCLE


title: SJRH30

description: Gene expression data from the CCLE

value: rhabdomyosarcoma


title: SCLC-21H

description: Gene expression data from the CCLE

value: lung


title: SJSA-1

description: Gene expression data from the CCLE

value: osteosarcoma


title: SIMA

description: Gene expression data from the CCLE


title: SH-SY5Y

description: Gene expression data from the CCLE


title: SF126

description: Gene expression data from the CCLE

value: astrocytoma


title: SH-4

description: Gene expression data from the CCLE


title: SCC-25

description: Gene expression data from the CCLE


title: SCC-4

description: Gene expression data from the CCLE


title: SCaBER

description: Gene expression data from the CCLE


title: SHP-77

description: Gene expression data from the CCLE


title: SBC-5

description: Gene expression data from the CCLE


title: RKO

description: Gene expression data from the CCLE


title: RT112/84

description: Gene expression data from the CCLE

source_name: ECACC


title: RT-112

description: Gene expression data from the CCLE


title: RT4

description: Gene expression data from the CCLE


title: SF-295

description: Gene expression data from the CCLE

source_name: NCI/DCTD


title: S-117

description: Gene expression data from the CCLE


title: RMUG-S

description: Gene expression data from the CCLE

value: ovary


title: RMG-I

description: Gene expression data from the CCLE

value: carcinoma


title: RKN

description: Gene expression data from the CCLE


title: SCC-9

description: Gene expression data from the CCLE


title: RH-41

description: Gene expression data from the CCLE

value: alveolar


title: RL95-2

description: Gene expression data from the CCLE


title: RERF-LC-MS

description: Gene expression data from the CCLE


title: RERF-LC-KJ

description: Gene expression data from the CCLE


title: RCM-1

description: Gene expression data from the CCLE

value: adenocarcinoma


title: RERF-LC-Sq1

description: Gene expression data from the CCLE


title: RVH-421

description: Gene expression data from the CCLE


title: RERF-LC-Ad2

description: Gene expression data from the CCLE


title: RD

description: Gene expression data from the CCLE

value: embryonal


title: RD-ES

description: Gene expression data from the CCLE


title: RCC10RGB

description: Gene expression data from the CCLE

value: kidney


title: RERF-LC-Ad1

description: Gene expression data from the CCLE


title: QGP-1

description: Gene expression data from the CCLE

value: pancreas


title: PL45

description: Gene expression data from the CCLE


title: PK-45H

description: Gene expression data from the CCLE


title: PK-59

description: Gene expression data from the CCLE


title: PK-1

description: Gene expression data from the CCLE


title: PE/CA-PJ34 (clone C12)

description: Gene expression data from the CCLE


title: PLC/PRF/5

description: Gene expression data from the CCLE

value: liver


title: PE/CA-PJ15

description: Gene expression data from the CCLE


title: PSN1

description: Gene expression data from the CCLE


title: RERF-GC-1B

description: Gene expression data from the CCLE

value: stomach


title: PE/CA-PJ49

description: Gene expression data from the CCLE


title: PE/CA-PJ41 (clone D2)

description: Gene expression data from the CCLE


title: PC-3

description: Gene expression data from the CCLE

value: prostate


title: PA-TU-8988T

description: Gene expression data from the CCLE


title: PA-TU-8988S

description: Gene expression data from the CCLE


title: PA-TU-8902

description: Gene expression data from the CCLE


title: PANC-1

description: Gene expression data from the CCLE


title: Panc 08.13

description: Gene expression data from the CCLE


title: Panc 10.05

description: Gene expression data from the CCLE


title: PC-14

description: Gene expression data from the CCLE


title: Panc 02.13

description: Gene expression data from the CCLE


title: Panc 03.27

description: Gene expression data from the CCLE


title: Panc 05.04

description: Gene expression data from the CCLE


title: Panc 04.03

description: Gene expression data from the CCLE


title: Panc 02.03

description: Gene expression data from the CCLE


title: OVSAHO

description: Gene expression data from the CCLE


title: OVTOKO

description: Gene expression data from the CCLE


title: OVMANA

description: Gene expression data from the CCLE


title: OV56

description: Gene expression data from the CCLE


title: OVK18

description: Gene expression data from the CCLE


title: OVKATE

description: Gene expression data from the CCLE


title: OVCAR-8

description: Gene expression data from the CCLE


title: OVCAR-4

description: Gene expression data from the CCLE


title: OV7

description: Gene expression data from the CCLE


title: ONS-76

description: Gene expression data from the CCLE


title: OE33

description: Gene expression data from the CCLE

value: oesophagus

value: other

value: metaplasia


title: OUMS-23

description: Gene expression data from the CCLE


title: OUMS-27

description: Gene expression data from the CCLE

value: bone

value: chondrosarcoma


title: OE19

description: Gene expression data from the CCLE


title: OAW42

description: Gene expression data from the CCLE


title: OC 316

description: Gene expression data from the CCLE

source_name: ICLC


title: OC 314

description: Gene expression data from the CCLE


title: SCC-15

description: Gene expression data from the CCLE


title: OCUM-1

description: Gene expression data from the CCLE


title: NUGC-4

description: Gene expression data from the CCLE


title: NIH:OVCAR-3

description: Gene expression data from the CCLE


title: OV-90

description: Gene expression data from the CCLE


title: NUGC-2

description: Gene expression data from the CCLE


title: NH-6

description: Gene expression data from the CCLE

value: neuroblastoma


title: NMC-G1

description: Gene expression data from the CCLE

value: glioma


title: NCI-H841

description: Gene expression data from the CCLE

value: lung


title: NCI-H810

description: Gene expression data from the CCLE

value: carcinoma


title: NCI-H838

description: Gene expression data from the CCLE


title: NCI-H854

description: Gene expression data from the CCLE


title: NCI-H82

description: Gene expression data from the CCLE


title: NCI-H727

description: Gene expression data from the CCLE


title: NCI-N87

description: Gene expression data from the CCLE


title: NCI-H650

description: Gene expression data from the CCLE


title: NCI-H716

description: Gene expression data from the CCLE


title: NUGC-3

description: Gene expression data from the CCLE


title: NCI-H660

description: Gene expression data from the CCLE


title: NCI-H889

description: Gene expression data from the CCLE


title: NCI-H69

description: Gene expression data from the CCLE


title: NCI-H647

description: Gene expression data from the CCLE


title: NCI-H747

description: Gene expression data from the CCLE


title: NCI-H522

description: Gene expression data from the CCLE


title: NCI-H526

description: Gene expression data from the CCLE


title: NCI-H524

description: Gene expression data from the CCLE


title: NCI-H520

description: Gene expression data from the CCLE


title: NCI-H441

description: Gene expression data from the CCLE


title: NCI-H460

description: Gene expression data from the CCLE


title: NCI-H508

description: Gene expression data from the CCLE


title: NCI-H596

description: Gene expression data from the CCLE


title: NCI-H510

description: Gene expression data from the CCLE


title: NCI-H358

description: Gene expression data from the CCLE


title: NCI-H446

description: Gene expression data from the CCLE


title: NCI-H28

description: Gene expression data from the CCLE

value: pleura

value: mesothelioma


title: NCI-H322

description: Gene expression data from the CCLE

value: adenocarcinoma


title: NCI-H2444

description: Gene expression data from the CCLE


title: NCI-H2342

description: Gene expression data from the CCLE


title: NCI-H2452

description: Gene expression data from the CCLE


title: NCI-H2405

description: Gene expression data from the CCLE


title: NCI-H226

description: Gene expression data from the CCLE


title: NCI-H2347

description: Gene expression data from the CCLE


title: NCI-H2286

description: Gene expression data from the CCLE


title: NCI-H2228

description: Gene expression data from the CCLE


title: NCI-H23

description: Gene expression data from the CCLE


title: NCI-H2196

description: Gene expression data from the CCLE


title: NCI-H2291

description: Gene expression data from the CCLE


title: NCI-H2170

description: Gene expression data from the CCLE


title: NCI-H2172

description: Gene expression data from the CCLE


title: NCI-H2171

description: Gene expression data from the CCLE


title: NCI-H2227

description: Gene expression data from the CCLE


title: NCI-H2141

description: Gene expression data from the CCLE


title: RERF-LC-AI

description: Gene expression data from the CCLE


title: NCI-H211

description: Gene expression data from the CCLE


title: NCI-H2122

description: Gene expression data from the CCLE


title: NCI-H2106

description: Gene expression data from the CCLE


title: NCI-H2110

description: Gene expression data from the CCLE


title: NCI-H2087

description: Gene expression data from the CCLE


title: NCI-H2030

description: Gene expression data from the CCLE


title: NCI-H2085

description: Gene expression data from the CCLE


title: RPMI-7951

description: Gene expression data from the CCLE

value: skin


title: NCI-H2029

description: Gene expression data from the CCLE


title: NCI-H2081

description: Gene expression data from the CCLE


title: NCI-H2066

description: Gene expression data from the CCLE


title: NCI-H2023

description: Gene expression data from the CCLE


title: NCI-H2126

description: Gene expression data from the CCLE


title: NCI-H196

description: Gene expression data from the CCLE


title: NCI-H1975

description: Gene expression data from the CCLE


title: NCI-H1944

description: Gene expression data from the CCLE


title: NCI-H1869

description: Gene expression data from the CCLE


title: NCI-H2052

description: Gene expression data from the CCLE


title: NCI-H1734

description: Gene expression data from the CCLE


title: NCI-H1755

description: Gene expression data from the CCLE


title: NCI-H1792

description: Gene expression data from the CCLE


title: NCI-H1793

description: Gene expression data from the CCLE


title: NCI-H1703

description: Gene expression data from the CCLE


title: NCI-H1694

description: Gene expression data from the CCLE


title: NCI-H1693

description: Gene expression data from the CCLE


title: NCI-H1836

description: Gene expression data from the CCLE


title: NCI-H1781

description: Gene expression data from the CCLE


title: NCI-H2009

description: Gene expression data from the CCLE


title: NCI-H1963

description: Gene expression data from the CCLE


title: NCI-H1651

description: Gene expression data from the CCLE


title: NCI-H1650

description: Gene expression data from the CCLE


title: NCI-H1666

description: Gene expression data from the CCLE


title: NCI-H1568

description: Gene expression data from the CCLE


title: NCI-H1573

description: Gene expression data from the CCLE


title: NCI-H1648

description: Gene expression data from the CCLE


title: NCI-H1618

description: Gene expression data from the CCLE


title: NCI-H1581

description: Gene expression data from the CCLE


title: NCI-H1563

description: Gene expression data from the CCLE


title: NCI-H1838

description: Gene expression data from the CCLE


title: NCI-H1435

description: Gene expression data from the CCLE


title: NCI-H146

description: Gene expression data from the CCLE


title: NCI-H1437

description: Gene expression data from the CCLE


title: NCI-H1623

description: Gene expression data from the CCLE


title: NCI-H1385

description: Gene expression data from the CCLE


title: NCI-H1341

description: Gene expression data from the CCLE


title: NCI-H1355

description: Gene expression data from the CCLE


title: NCI-H1373

description: Gene expression data from the CCLE


title: NCI-H1155

description: Gene expression data from the CCLE


title: NCI-H1339

description: Gene expression data from the CCLE


title: NCI-H1395

description: Gene expression data from the CCLE


title: NCI-H1299

description: Gene expression data from the CCLE


title: MSTO-211H

description: Gene expression data from the CCLE


title: MOR/CPR

description: Gene expression data from the CCLE


title: NB-1

description: Gene expression data from the CCLE


title: NCI-H1184

description: Gene expression data from the CCLE


title: NCI-H1105

description: Gene expression data from the CCLE


title: ML-1

description: Gene expression data from the CCLE

value: thyroid


title: MKN7

description: Gene expression data from the CCLE


title: NCI-H661

description: Gene expression data from the CCLE


title: MPP 89

description: Gene expression data from the CCLE


title: MHH-ES-1

description: Gene expression data from the CCLE


title: NCI-H1092

description: Gene expression data from the CCLE


title: MIA PaCa-2

description: Gene expression data from the CCLE

value: pancreas


title: MKN1

description: Gene expression data from the CCLE

value: stomach


title: MFE-296

description: Gene expression data from the CCLE

value: endometrium


title: NCI-H1048

description: Gene expression data from the CCLE


title: MHH-NB-11

description: Gene expression data from the CCLE


title: MFE-319

description: Gene expression data from the CCLE


title: MEL-HO

description: Gene expression data from the CCLE


title: MEL-JUSO

description: Gene expression data from the CCLE


title: MG-63

description: Gene expression data from the CCLE

value: osteosarcoma


title: MDST8

description: Gene expression data from the CCLE


title: MKN-45

description: Gene expression data from the CCLE


title: MFE-280

description: Gene expression data from the CCLE


title: MeWo

description: Gene expression data from the CCLE


title: MDA-MB-468

description: Gene expression data from the CCLE

value: breast


title: MDA PCa 2b

description: Gene expression data from the CCLE

value: prostate


title: MKN74

description: Gene expression data from the CCLE


title: MDA-MB-453

description: Gene expression data from the CCLE


title: MDA-MB-415

description: Gene expression data from the CCLE


title: MDA-MB-361

description: Gene expression data from the CCLE


title: MDA-MB-436

description: Gene expression data from the CCLE


title: MDA-MB-157

description: Gene expression data from the CCLE


title: MDA-MB-175-VII

description: Gene expression data from the CCLE


title: MDA-MB-231

description: Gene expression data from the CCLE


title: MDA-MB-435S

description: Gene expression data from the CCLE


title: MDA-MB-134-VI

description: Gene expression data from the CCLE


title: MCF7

description: Gene expression data from the CCLE


title: Malme-3M

description: Gene expression data from the CCLE


title: MCAS

description: Gene expression data from the CCLE

value: ovary


title: LS513

description: Gene expression data from the CCLE


title: LS411N

description: Gene expression data from the CCLE


title: LU65

description: Gene expression data from the CCLE


title: LXF-289

description: Gene expression data from the CCLE


title: M059K

description: Gene expression data from the CCLE


title: LNCaP clone FGC

description: Gene expression data from the CCLE


title: LU99

description: Gene expression data from the CCLE


title: LOU-NH91

description: Gene expression data from the CCLE


title: LN-229

description: Gene expression data from the CCLE


title: LS123

description: Gene expression data from the CCLE


title: LS1034

description: Gene expression data from the CCLE


title: LS 180

description: Gene expression data from the CCLE


title: LN-18

description: Gene expression data from the CCLE


title: LC-1/sq-SF

description: Gene expression data from the CCLE


title: LoVo

description: Gene expression data from the CCLE


title: LK-2

description: Gene expression data from the CCLE


title: LUDLU-1

description: Gene expression data from the CCLE


title: LOX IMVI

description: Gene expression data from the CCLE


title: LCLC-103H

description: Gene expression data from the CCLE


title: LCLC-97TM1

description: Gene expression data from the CCLE


title: KYSE-520

description: Gene expression data from the CCLE

value: oesophagus


title: KYSE-70

description: Gene expression data from the CCLE


title: KYSE-450

description: Gene expression data from the CCLE


title: LMSU

description: Gene expression data from the CCLE


title: L3.3

description: Gene expression data from the CCLE

source_name: Academic Lab


title: KYSE-510

description: Gene expression data from the CCLE


title: Li-7

description: Gene expression data from the CCLE

value: liver


title: KYSE-410

description: Gene expression data from the CCLE


title: KYSE-30

description: Gene expression data from the CCLE


title: KYSE-270

description: Gene expression data from the CCLE


title: KU-19-19

description: Gene expression data from the CCLE


title: KP-N-YN

description: Gene expression data from the CCLE

value: neuroblastoma


title: KS-1

description: Gene expression data from the CCLE

value: glioma


title: KYSE-180

description: Gene expression data from the CCLE

value: carcinoma


title: KPL-1

description: Gene expression data from the CCLE


title: KYSE-140

description: Gene expression data from the CCLE


title: KP-N-RT-BM-1

description: Gene expression data from the CCLE


title: KP-N-SI9s

description: Gene expression data from the CCLE


title: KP-2

description: Gene expression data from the CCLE


title: KNS-60

description: Gene expression data from the CCLE


title: KNS-81

description: Gene expression data from the CCLE


title: KP4

description: Gene expression data from the CCLE


title: KP-3

description: Gene expression data from the CCLE


title: KMRC-20

description: Gene expression data from the CCLE

value: kidney


title: KMRC-3

description: Gene expression data from the CCLE


title: KMBC-2

description: Gene expression data from the CCLE


title: KLE

description: Gene expression data from the CCLE


title: KNS-62

description: Gene expression data from the CCLE

value: lung


title: KM12

description: Gene expression data from the CCLE

value: adenocarcinoma


title: KMRC-2

description: Gene expression data from the CCLE


title: KMRC-1

description: Gene expression data from the CCLE


title: KELLY

description: Gene expression data from the CCLE


title: KCI-MOH1

description: Gene expression data from the CCLE


title: KG-1-C

description: Gene expression data from the CCLE


title: KNS-42

description: Gene expression data from the CCLE


title: JMSU-1

description: Gene expression data from the CCLE


title: K029AX

description: Gene expression data from the CCLE

value: skin


title: KALS-1

description: Gene expression data from the CCLE


title: JL-1

description: Gene expression data from the CCLE

value: pleura

value: mesothelioma


title: JIMT-1

description: Gene expression data from the CCLE


title: NCI-H1436

description: Gene expression data from the CCLE


title: JHUEM-3

description: Gene expression data from the CCLE


title: KE-39

description: Gene expression data from the CCLE

value: stomach


title: JHUEM-1

description: Gene expression data from the CCLE

value: endometrium


title: JHOS-4

description: Gene expression data from the CCLE


title: JHOM-2B

description: Gene expression data from the CCLE


title: KATO III

description: Gene expression data from the CCLE


title: JHOS-2

description: Gene expression data from the CCLE


title: JHH-6

description: Gene expression data from the CCLE


title: JHH-2

description: Gene expression data from the CCLE


title: JHH-7

description: Gene expression data from the CCLE


title: JHOM-1

description: Gene expression data from the CCLE


title: IST-MES2

description: Gene expression data from the CCLE


title: IST-MES1

description: Gene expression data from the CCLE


title: JHH-5

description: Gene expression data from the CCLE


title: JHH-1

description: Gene expression data from the CCLE


title: JHUEM-2

description: Gene expression data from the CCLE


title: J82

description: Gene expression data from the CCLE


title: IPC-298

description: Gene expression data from the CCLE


title: IMR-32

description: Gene expression data from the CCLE


title: IM95

description: Gene expression data from the CCLE


title: JHOC-5

description: Gene expression data from the CCLE


title: IGROV1

description: Gene expression data from the CCLE


title: IA-LM

description: Gene expression data from the CCLE


title: IGR-37

description: Gene expression data from the CCLE


title: IGR-39

description: Gene expression data from the CCLE


title: Ishikawa (Heraklio) 02 ER-

description: Gene expression data from the CCLE


title: JHH-4

description: Gene expression data from the CCLE


title: HUP-T4

description: Gene expression data from the CCLE

value: pancreas


title: HuH28

description: Gene expression data from the CCLE


title: huH-1

description: Gene expression data from the CCLE


title: HuH-7

description: Gene expression data from the CCLE


title: HuG1-N

description: Gene expression data from the CCLE


title: HuCCT1

description: Gene expression data from the CCLE


title: HUP-T3

description: Gene expression data from the CCLE


title: HT55

description: Gene expression data from the CCLE


title: HT-29

description: Gene expression data from the CCLE


title: HSC-3

description: Gene expression data from the CCLE


title: HT-144

description: Gene expression data from the CCLE


title: HT-1080

description: Gene expression data from the CCLE

value: fibrosarcoma


title: IGR-1

description: Gene expression data from the CCLE


title: HuH-6

description: Gene expression data from the CCLE

value: other

value: hepatoblastoma


title: HT-1197

description: Gene expression data from the CCLE


title: HT115

description: Gene expression data from the CCLE


title: Hs 944.T

description: Gene expression data from the CCLE


title: HSC-4

description: Gene expression data from the CCLE


title: Hs 936.T

description: Gene expression data from the CCLE


title: Hs 895.T

description: Gene expression data from the CCLE


title: Hs 934.T

description: Gene expression data from the CCLE


title: Hs 939.T

description: Gene expression data from the CCLE


title: Hs 940.T

description: Gene expression data from the CCLE


title: Hs 870.T

description: Gene expression data from the CCLE

value: bone

value: osteosarcoma


title: HT-1376

description: Gene expression data from the CCLE


title: HSC-2

description: Gene expression data from the CCLE


title: Hs 822.T

description: Gene expression data from the CCLE


title: Hs 746T

description: Gene expression data from the CCLE


title: Hs 821.T

description: Gene expression data from the CCLE


title: Hs 863.T

description: Gene expression data from the CCLE


title: Hs 819.T

description: Gene expression data from the CCLE

value: chondrosarcoma


title: Hs 742.T

description: Gene expression data from the CCLE

value: breast


title: Hs 852.T

description: Gene expression data from the CCLE


title: Hs 840.T

description: Gene expression data from the CCLE

value: papilloma


title: Hs 739.T

description: Gene expression data from the CCLE

value: carcinoma


title: Hs 698.T

description: Gene expression data from the CCLE


title: Hs 729

description: Gene expression data from the CCLE

value: rhabdomyosarcoma


title: Hs 839.T

description: Gene expression data from the CCLE


title: Hs 737.T

description: Gene expression data from the CCLE


title: Hs 706.T

description: Gene expression data from the CCLE


title: Hs 683

description: Gene expression data from the CCLE

value: glioma


title: Hs 888.T

description: Gene expression data from the CCLE


title: Hs 766T

description: Gene expression data from the CCLE


title: Hs 675.T

description: Gene expression data from the CCLE


title: Hs 695T

description: Gene expression data from the CCLE

value: skin


title: Hs 618.T

description: Gene expression data from the CCLE

value: lung

value: adenocarcinoma


title: Hs 600.T

description: Gene expression data from the CCLE


title: Hs 343.T

description: Gene expression data from the CCLE


title: KYSE-150

description: Gene expression data from the CCLE

value: oesophagus


title: Hs 578T

description: Gene expression data from the CCLE


title: Hs 281.T

description: Gene expression data from the CCLE


title: Hs 606.T

description: Gene expression data from the CCLE


title: Hs 229.T

description: Gene expression data from the CCLE


title: Hs 294T

description: Gene expression data from the CCLE


title: Hs 172.T

description: Gene expression data from the CCLE


title: HPAC

description: Gene expression data from the CCLE


title: Hs 688(A).T

description: Gene expression data from the CCLE


title: Hs 274.T

description: Gene expression data from the CCLE


title: HLE

description: Gene expression data from the CCLE

value: liver


title: HEC-6

description: Gene expression data from the CCLE

value: endometrium


title: HLF-a

description: Gene expression data from the CCLE


title: Hey-A8

description: Gene expression data from the CCLE

value: ovary


title: HPAF-II

description: Gene expression data from the CCLE

value: pancreas


title: HEC-108

description: Gene expression data from the CCLE


title: HEC-251

description: Gene expression data from the CCLE


title: HDQ-P1

description: Gene expression data from the CCLE


title: HMCB

description: Gene expression data from the CCLE


title: HGC-27

description: Gene expression data from the CCLE

value: stomach


title: HLF

description: Gene expression data from the CCLE


title: HEC-59

description: Gene expression data from the CCLE


title: HCC827

description: Gene expression data from the CCLE


title: HCC-44

description: Gene expression data from the CCLE


title: HCC-95

description: Gene expression data from the CCLE


title: HCC38

description: Gene expression data from the CCLE


title: HEC-1-B

description: Gene expression data from the CCLE


title: HEC-50B

description: Gene expression data from the CCLE


title: HEC-265

description: Gene expression data from the CCLE


title: Hep G2

description: Gene expression data from the CCLE


title: HCC4006

description: Gene expression data from the CCLE


title: HEC-1-A

description: Gene expression data from the CCLE


title: HCT 116

description: Gene expression data from the CCLE


title: HCT-15

description: Gene expression data from the CCLE


title: Hep 3B2.1-7

description: Gene expression data from the CCLE


title: HCC-78

description: Gene expression data from the CCLE


title: HCC70

description: Gene expression data from the CCLE


title: HOS

description: Gene expression data from the CCLE

value: bone


title: HEC-151

description: Gene expression data from the CCLE


title: HCC-56

description: Gene expression data from the CCLE


title: HCC-366

description: Gene expression data from the CCLE


title: HCC1954

description: Gene expression data from the CCLE


title: HCC2157

description: Gene expression data from the CCLE


title: HCC-2279

description: Gene expression data from the CCLE


title: HCC202

description: Gene expression data from the CCLE


title: HCC-33

description: Gene expression data from the CCLE


title: HCC1599

description: Gene expression data from the CCLE


title: HCC-15

description: Gene expression data from the CCLE


title: HCC1806

description: Gene expression data from the CCLE


title: HCC2935

description: Gene expression data from the CCLE


title: HCC1419

description: Gene expression data from the CCLE


title: HCC1937

description: Gene expression data from the CCLE


title: HCC-1195

description: Gene expression data from the CCLE


title: HCC1569

description: Gene expression data from the CCLE


title: HCC1395

description: Gene expression data from the CCLE


title: HCC1187

description: Gene expression data from the CCLE


title: GMS-10

description: Gene expression data from the CCLE


title: HCC1500

description: Gene expression data from the CCLE


title: GP2d

description: Gene expression data from the CCLE


title: H4

description: Gene expression data from the CCLE


title: GOS-3

description: Gene expression data from the CCLE

value: astrocytoma


title: GSU

description: Gene expression data from the CCLE


title: GSS

description: Gene expression data from the CCLE


title: GI-1

description: Gene expression data from the CCLE

value: gliosarcoma


title: GCT

description: Gene expression data from the CCLE


title: HCC1143

description: Gene expression data from the CCLE

value: breast


title: G-292, clone A141B1

description: Gene expression data from the CCLE

value: osteosarcoma


title: HCC2218

description: Gene expression data from the CCLE

value: carcinoma


title: HARA

description: Gene expression data from the CCLE


title: GAMG

description: Gene expression data from the CCLE


title: FaDu

description: Gene expression data from the CCLE


title: FU-OV-1

description: Gene expression data from the CCLE


title: FTC-133

description: Gene expression data from the CCLE

value: thyroid


title: FU97

description: Gene expression data from the CCLE


title: GCIY

description: Gene expression data from the CCLE


title: G-361

description: Gene expression data from the CCLE


title: ESS-1

description: Gene expression data from the CCLE


title: EN

description: Gene expression data from the CCLE


title: EPLC-272H

description: Gene expression data from the CCLE


title: ECC12

description: Gene expression data from the CCLE


title: EBC-1

description: Gene expression data from the CCLE


title: ES-2

description: Gene expression data from the CCLE


title: EFE-184

description: Gene expression data from the CCLE


title: EC-GI-10

description: Gene expression data from the CCLE


title: EFO-21

description: Gene expression data from the CCLE


title: EFM-192A

description: Gene expression data from the CCLE


title: DV-90

description: Gene expression data from the CCLE


title: EFO-27

description: Gene expression data from the CCLE


title: EFM-19

description: Gene expression data from the CCLE


title: DMS 53

description: Gene expression data from the CCLE


title: DMS 454

description: Gene expression data from the CCLE


title: DMS 273

description: Gene expression data from the CCLE


title: ECC10

description: Gene expression data from the CCLE


title: DU4475

description: Gene expression data from the CCLE


title: DMS 114

description: Gene expression data from the CCLE


title: DMS 153

description: Gene expression data from the CCLE


title: DBTRG-05MG

description: Gene expression data from the CCLE

value: glioma


title: DU 145

description: Gene expression data from the CCLE

value: prostate


title: DAN-G

description: Gene expression data from the CCLE


title: Daoy

description: Gene expression data from the CCLE


title: Detroit 562

description: Gene expression data from the CCLE


title: DLD-1

description: Gene expression data from the CCLE


title: DMS 79

description: Gene expression data from the CCLE

value: lung


title: DK-MG

description: Gene expression data from the CCLE


title: D283 Med

description: Gene expression data from the CCLE


title: CPC-N

description: Gene expression data from the CCLE


title: COV504

description: Gene expression data from the CCLE


title: COV644

description: Gene expression data from the CCLE


title: COR-L47

description: Gene expression data from the CCLE


title: D341 Med

description: Gene expression data from the CCLE


title: COR-L88

description: Gene expression data from the CCLE


title: COV318

description: Gene expression data from the CCLE


title: COV434

description: Gene expression data from the CCLE


title: CW-2

description: Gene expression data from the CCLE


title: COR-L311

description: Gene expression data from the CCLE


title: COLO 829

description: Gene expression data from the CCLE

value: skin


title: COR-L24

description: Gene expression data from the CCLE


title: COR-L105

description: Gene expression data from the CCLE

value: adenocarcinoma


title: COLO-818

description: Gene expression data from the CCLE


title: COLO-800

description: Gene expression data from the CCLE


title: COLO-783

description: Gene expression data from the CCLE


title: COLO 741

description: Gene expression data from the CCLE


title: COLO-699

description: Gene expression data from the CCLE


title: COR-L95

description: Gene expression data from the CCLE


title: COLO-849

description: Gene expression data from the CCLE


title: COLO-678

description: Gene expression data from the CCLE


title: COV362

description: Gene expression data from the CCLE


title: COLO 792

description: Gene expression data from the CCLE


title: COLO-679

description: Gene expression data from the CCLE


title: COLO 205

description: Gene expression data from the CCLE


title: COLO 668

description: Gene expression data from the CCLE


title: COLO-704

description: Gene expression data from the CCLE


title: COR-L23

description: Gene expression data from the CCLE


title: COLO-680N

description: Gene expression data from the CCLE

value: oesophagus


title: COLO-320

description: Gene expression data from the CCLE


title: CL-34

description: Gene expression data from the CCLE


title: CL-40

description: Gene expression data from the CCLE


title: CL-11

description: Gene expression data from the CCLE


title: ChaGo-K-1

description: Gene expression data from the CCLE


title: CFPAC-1

description: Gene expression data from the CCLE


title: CHP-212

description: Gene expression data from the CCLE

value: neuroblastoma


title: CAS-1

description: Gene expression data from the CCLE


title: CHP-126

description: Gene expression data from the CCLE


title: CJM

description: Gene expression data from the CCLE


title: CGTH-W-1

description: Gene expression data from the CCLE


title: CHL-1

description: Gene expression data from the CCLE


title: CL-14

description: Gene expression data from the CCLE


title: CCF-STTG1

description: Gene expression data from the CCLE


title: CCK-81

description: Gene expression data from the CCLE


title: Calu-3

description: Gene expression data from the CCLE


title: Calu-6

description: Gene expression data from the CCLE


title: Capan-1

description: Gene expression data from the CCLE


title: Caov-4

description: Gene expression data from the CCLE

value: ovary


title: CAMA-1

description: Gene expression data from the CCLE


title: CAL-54

description: Gene expression data from the CCLE

value: kidney


title: Capan-2

description: Gene expression data from the CCLE

value: pancreas


title: CAL-85-1

description: Gene expression data from the CCLE


title: Caov-3

description: Gene expression data from the CCLE


title: CAL-78

description: Gene expression data from the CCLE

value: bone

value: chondrosarcoma

value: dedifferentiated


title: CAL 27

description: Gene expression data from the CCLE


title: Calu-1

description: Gene expression data from the CCLE


title: CAL-148

description: Gene expression data from the CCLE

value: breast


title: CAL-12T

description: Gene expression data from the CCLE


title: CAL-51

description: Gene expression data from the CCLE


title: CAL-29

description: Gene expression data from the CCLE


title: CAL-120

description: Gene expression data from the CCLE


title: CAL-62

description: Gene expression data from the CCLE


title: CADO-ES1

description: Gene expression data from the CCLE


title: C32

description: Gene expression data from the CCLE


title: BT-549

description: Gene expression data from the CCLE


title: C2BBe1

description: Gene expression data from the CCLE


title: Caki-2

description: Gene expression data from the CCLE


title: Caki-1

description: Gene expression data from the CCLE


title: BT-483

description: Gene expression data from the CCLE


title: BxPC-3

description: Gene expression data from the CCLE


title: BT-20

description: Gene expression data from the CCLE


title: BT-474

description: Gene expression data from the CCLE


title: BICR 6

description: Gene expression data from the CCLE


title: BICR 56

description: Gene expression data from the CCLE


title: C3A

description: Gene expression data from the CCLE

value: liver


title: B-CPAP

description: Gene expression data from the CCLE

value: carcinoma


title: BICR 31

description: Gene expression data from the CCLE


title: BICR 18

description: Gene expression data from the CCLE


title: AZ-521

description: Gene expression data from the CCLE

value: stomach


title: BC-3C

description: Gene expression data from the CCLE


title: AM-38

description: Gene expression data from the CCLE

value: glioma


title: BEN

description: Gene expression data from the CCLE


title: Becker

description: Gene expression data from the CCLE


title: BFTC-905

description: Gene expression data from the CCLE


title: BICR 16

description: Gene expression data from the CCLE


title: AsPC-1

description: Gene expression data from the CCLE


title: BFTC-909

description: Gene expression data from the CCLE


title: Alexander cells

description: Gene expression data from the CCLE


title: BICR 22

description: Gene expression data from the CCLE


title: BHT-101

description: Gene expression data from the CCLE

value: thyroid


title: AU565

description: Gene expression data from the CCLE


title: ABC-1

description: Gene expression data from the CCLE

value: lung


title: ACC-MESO-1

description: Gene expression data from the CCLE

value: pleura

value: mesothelioma


title: A-673

description: Gene expression data from the CCLE


title: A-498

description: Gene expression data from the CCLE


title: A-375

description: Gene expression data from the CCLE

value: skin


title: AGS

description: Gene expression data from the CCLE

value: adenocarcinoma


title: ACHN

description: Gene expression data from the CCLE


title: A172

description: Gene expression data from the CCLE


title: A-704

description: Gene expression data from the CCLE


title: 8305C

description: Gene expression data from the CCLE


title: A2780

description: Gene expression data from the CCLE

value: ovary


title: 769-P

description: Gene expression data from the CCLE

value: kidney


title: 8505C

description: Gene expression data from the CCLE


title: 647-V

description: Gene expression data from the CCLE


title: 8-MG-BA

description: Gene expression data from the CCLE


title: A101D

description: Gene expression data from the CCLE


title: 22Rv1

description: Gene expression data from the CCLE

value: prostate


title: A549

description: Gene expression data from the CCLE


title: 143B

description: Gene expression data from the CCLE

value: bone

value: osteosarcoma


title: 5637

description: Gene expression data from the CCLE


title: 786-O

description: Gene expression data from the CCLE


title: 23132/87

description: Gene expression data from the CCLE


title: 639-V

description: Gene expression data from the CCLE


title: 42-MG-BA

description: Gene expression data from the CCLE


title: 1321N1

description: Gene expression data from the CCLE

value: astrocytoma


title: CD4 memory T cells_72_hour_Young-3

status: Public on Mar 14 2012

city: Stanford

first: Mingcan

last: Yu

state: CA

address: CCSR Bldg. Rm. 2215, 269 Campus Drive West

department: Medicine: Immunology and Rheumatology

institute: Stanford University School of Medicine

description: Gene expression data from CD4 memory T cells at 72 hours after stimulation

hyb_protocol: 10 ug cRNA were hybridized for 16 hr at 45 degree and 60 rpm to Human U133A1 Arrays in a hybridization oven 640 (Affymetrix). GeneChips were washed and stained using the Affymetrix Fluidics450 station.

scan_protocol: GeneChips were scanned using a seventh-generation GeneChip Scanner 3000 (Affymetrix).

data_processing: The CEL/CHP files were analyzed using Affymetrix default analysis settings and the Rosetta Resolver System.

source_name: CD4 memory T cells_72_hour_Young

label_protocol: Biotinylated cRNA was obtained using the BioArray HighYield RNA Transcript Labeling Kit (Enzo).

extract_protocol: Total RNA was purified using the Rneasy Mini Kit (Qiagen).

treatment_protocol: T cells were stimulated with myeloid dendritic cells and TSST

value: CD4 memory T cells

tag: age

value: 20-35 years


title: CD4 memory T cells_72_hour_Old-5

source_name: CD4 memory T cells_72_hour_Old

value: 70-75 years


title: CD4 memory T cells_40_hour_Young-5

description: Gene expression data from CD4 memory T cells at 40 hours after stimulation

source_name: CD4 memory T cells_40_hour_Young


title: CD4 memory T cells_40_hour_Old-5

source_name: CD4 memory T cells_40_hour_Old


title: CD4 memory T cells_0_hour_Young-5

description: Gene expression data from CD4 memory T cells before stimulation

source_name: CD4 memory T cells_0_hour_Young


title: CD4 memory T cells_16_hour_Young-3

description: Gene expression data from CD4 memory T cells at 16 hours after stimulation

source_name: CD4 memory T cells_16_hour_Young


title: CD4 memory T cells_40_hour_Young-3


title: CD4 memory T cells_16_hour_Old-5

source_name: CD4 memory T cells_16_hour_Old


title: CD4 memory T cells_0_hour_Old-5

source_name: CD4 memory T cells_0_hour_Old


title: CD4 memory T cells_16_hour_Young-5


title: CD4 memory T cells_16_hour_Old-3


title: CD4 memory T cells_0_hour_Young-3


title: CD4 memory T cells_72_hour_Young-5


title: CD4 memory T cells_72_hour_Old-3


title: CD4 memory T cells_40_hour_Old-3


title: CD4 memory T cells_72_hour_Old-2


title: CD4 memory T cells_16_hour_Young-2


title: CD4 memory T cells_40_hour_Young-1


title: CD4 memory T cells_0_hour_Young-2


title: CD4 memory T cells_16_hour_Old-2


title: CD4 memory T cells_0_hour_Old-3


title: CD4 memory T cells_40_hour_Young-2


title: CD4 memory T cells_72_hour_Young-2


title: CD4 memory T cells_72_hour_Young-1


title: CD4 memory T cells_72_hour_Old-1


title: CD4 memory T cells_0_hour_Old-2


title: CD4 memory T cells_40_hour_Old-2


title: CD4 memory T cells_16_hour_Young-1


title: CD4 memory T cells_0_hour_Young-1


title: CD4 memory T cells_16_hour_Old-1


title: CD4 memory T cells_40_hour_Old-1


title: CD4 memory T cells_0_hour_Old-1


title: HUVEC 658 VPA

city: Gothenburg

first: Per-Arne

last: Svensson

department: Department of molecular and clinical medicine

country: Sweden

institute: institute of medicine

hyb_protocol: Cene chip Human Gene 1.0 ST array were processed according to Affymetrix GeneChip Expression wash, stain and scan manual.

scan_protocol: Scanned in GeneChip Scanner 3000 7G

data_processing: Raw data was normalized using RMA  in the Affymetrix software Expression console

source_name: umbilical vein

label_protocol: 200 ng of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the Ambion WT Expression kit and Affymetrix GeneChip WT terminal labeling and hybridization used manual.

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were cultured in EGM-2 complete medium and all experiments were performed in passages 1 or 2.

extract_protocol: Total RNA was prepared using RNeasy Mini RNA kit (Qiagen, Hilden, Germany) and genomic DNA was removed using RNase-free DNase I set (Qiagen).

treatment_protocol: Confluent HUVECs were cultured in the absence or presence of 4mM VPA for 24h.

value: HUVEC

tag: treatment

value: VPA


title: HUVEC 642 VPA


title: HUVEC 627 VPA


title: HUVEC 625 Cont

value: control


title: HUVEC 634 VPA


title: HUVEC 658 Cont


title: HUVEC 627 Cont


title: HUVEC 642 Cont


title: HUVEC 634 Cont


title: AN3 CA

description: Gene expression data from the CCLE

source_name: ATCC

value: endometrium

value: carcinoma


title: HUVEC 625 VPA


title: PMN-IL10-4-061807

status: Public on Feb 16 2012

city: Manhasset

first: Dennis

last: Davidson

state: New York

address: 350 Community Dr

department: Pediatrics

institute: The Feinstein Institute for Medical Research

description: Gene Expression data from the Umbilical Cord Blood Polymorphonuclear cells treated with 10^ -8 M Interleukin-10 for 1 hr followed by 10ng/ml Lipopolysaccharide stimulation for 4 hrs

hyb_protocol: Fragmented cRNA (n=5) were hybridized to Affymetrix Human U133 plus 2.0 microarray chips in hybridization oven for 18hr at 45˚C, processed by Gene Chip 450 fluidics station.

scan_protocol: Chips were scanned by Gene Chip 3000 scanner

data_processing: Raw data (n=5 patients) was uploaded onto GeneSifter (internet-based microarray data analysis software), log transformed and normalized using GC-RMA (v 1.1)

source_name: Umbilical Cord blood Polymorphonucler cells; LPS+IL-10

label_protocol: Total RNA was amplified and labled using Ambion MessageAmp II-Biotin enhanced kit. Total RNA and cRNA purity and integrity were monitored by 260/280 and 260/230 ratios respectively, using a Bioanalyzer .

growth_protocol: PMNs and MONOs were resuspended in RPMI 1640+10%FCS at 5x106 cells/mL.

extract_protocol: Total RNA was isolated using Qiagen RNeasy spin columns.

treatment_protocol: Cells were pre-incubated with PBS (vehicle control) or equimolar concentrations (10-8 M) of IL-10 or DEX for 1 h, then stimulated with LPS (10 ng/mL) for 4 h. Cells were harvested and suspended in RNAlater to preserve RNA.

tag: tissue

value: Human umbilical cord blood

value: Polymorphonuclear cells


title: Mono-LPS-4-061807

description: Gene Expression data from the Umbilical Cord Blood Monocytes treated with PBS vehicle for 1 hr followed by 10ng/ml Lipopolysaccharide  stimulation for 4 hrs

source_name: Umbilical Cord blood Monocytes; LPS

value: Monocytes


title: PMN-IL10-2-2093


title: PMN-LPS-1-2084

description: Gene Expression data from the Umbilical Cord Blood Polymorphonuclear cells treated with PBS vehicle for 1 hr followed by 10ng/ml Lipopolysaccharide stimulation for 4 hrs

source_name: Umbilical Cord blood Polymorphonucler cells; LPS


title: Mono-IL10-5-081707

description: Gene Expression data from the Umbilical Cord Blood Monocytes treated with 10^ -8 M Interleukin-10 for 1 hr followed by 10ng/ml Lipopolysaccharide  stimulation for 4 hrs

source_name: Umbilical Cord blood Monocytes; LPS+IL-10


title: PMN-LPS-2-2092


title: PMN-IL10-1-2085


title: PMN-IL10-3-2101


title: PMN-LPS-5-081707


title: PMN-LPS-3-2100


title: Mono-LPS-5-081707


title: Mono-LPS-3-2104


title: Mono-LPS-2-2096


title: PMN-LPS-4-061807


title: Mono-IL10-3-2105


title: Mono-LPS-1-2088


title: Mono-IL10-4-061807


title: PMN-IL10-5-081707


title: Mono-IL10-1-2089


title: cdc28-4, 37 degrees, t=210, replicate 2

status: Public on Feb 03 2012

city: Durham

first: Laura

middle: Anne

last: Simmons Kovacs

state: NC

department: Biology

institute: Duke University

description: 210 minutes after synchronization, no CDK activity

hyb_protocol: Hybridization was preformed at the Duke Institute for Genome Sciences and Policy DNA Microarray Core Facility (www.genome.duke.edu/cores/microarray)

scan_protocol: Scanning was preformed at the Duke Institute for Genome Sciences and Policy DNA Microarray Core Facility (www.genome.duke.edu/cores/microarray)

data_processing: CEL files from samples 1-48 were normalized and summarized alongside previously published arrays (GSE8799) according to the dChip method as implemented in the affy package of BioConductor using standard parameters.

organism: Saccharomyces cerevisiae

label_protocol: Samples 1-33 were labeled using the Affymetrix GeneChip One Cycle Labeling procedure.  Samples 34-48 were labeled using the Ambion MessageAmp Premier kit.

growth_protocol: Cells were grown at 25°C in YEPD to a final concentration of 3-5x107 cells/mL.  Small daughter cells were collected by centrofugal elutriation.  The synchronized population was resuspended in YEPD prewarmed to 37°C at time=0.  Samples were taken at each time indicated.

extract_protocol: Total RNA was extracted using a standard hot acid phenol protocol and cleaned with a Qiagen RNeasy MinElute Cleanup Kit.

tag: genotype

tag: time

value: 210 minutes after synchronization

tag: cdk activity

value: no


title: cdc28-4, 37 degrees, t=250, replicate 2

description: 250 minutes after synchronization, no CDK activity

value: 250 minutes after synchronization


title: cdc28-4, 37 degrees, t=310, replicate 2

description: 310 minutes after synchronization, no CDK activity

value: 310 minutes after synchronization


title: cdc28-4, 37 degrees, t=190, replicate 2

description: 190 minutes after synchronization, no CDK activity

value: 190 minutes after synchronization


title: cdc28-4, 37 degrees, t=230, replicate 2

description: 230 minutes after synchronization, no CDK activity

value: 230 minutes after synchronization


title: cdc28-4, 37 degrees, t=290, replicate 2

description: 290 minutes after synchronization, no CDK activity

value: 290 minutes after synchronization


title: cdc28-4, 37 degrees, t=270, replicate 2

description: 270 minutes after synchronization, no CDK activity

value: 270 minutes after synchronization


title: cdc28-4, 37 degrees, t=350, replicate 2

description: 350 minutes after synchronization, no CDK activity

value: 350 minutes after synchronization


title: cdc28-4, 37 degrees, t=330, replicate 2

description: 330 minutes after synchronization, no CDK activity

value: 330 minutes after synchronization


title: cdc28-4, 37 degrees, t=170, replicate 2

description: 170 minutes after synchronization, no CDK activity

value: 170 minutes after synchronization


title: cdc28-4, 37 degrees, t=130, replicate 2

description: 130 minutes after synchronization, no CDK activity

value: 130 minutes after synchronization


title: cdc28-4, 37 degrees, t=110, replicate 2

description: 110 minutes after synchronization, no CDK activity

value: 110 minutes after synchronization


title: cdc28-4, 37 degrees, t=90, replicate 2

description: 90 minutes after synchronization, no CDK activity

source_name: cdc28-4, 37 degrees, t=90

value: 90 minutes after synchronization


title: cdc28-4, 37 degrees, t=50, replicate 2

description: 50 minutes after synchronization, no CDK activity

source_name: cdc28-4, 37 degrees, t=50

value: 50 minutes after synchronization


title: cdc28-4, 37 degrees, t=70, replicate 2

description: 70 minutes after synchronization, no CDK activity

source_name: cdc28-4, 37 degrees, t=70

value: 70 minutes after synchronization


title: cdc28-4, 37 degrees, t=10, replicate 2

description: 10 minutes after synchronization, no CDK activity

source_name: cdc28-4, 37 degrees, t=10

value: 10 minutes after synchronization


title: cdc28-4, 37 degrees, t=270, replicate 1


title: Mono-IL10-2-2097

description: Gene Expression data from the Umbilical Cord Blood Monocytes treated with 10^ -8 M Interleukin-10 for 1 hr followed by 10ng/ml Lipopolysaccharide  stimulation for 4 hrs

value: Human umbilical cord blood

value: Monocytes


title: cdc28-4, 37 degrees, t=150, replicate 2

description: 150 minutes after synchronization, no CDK activity

value: 150 minutes after synchronization

value: no


title: cdc28-4, 37 degrees, t=210, replicate 1

description: 210 minutes after synchronization, no CDK activity

value: 210 minutes after synchronization


title: cdc28-4, 37 degrees, t=230, replicate 1

value: 230 minutes after synchronization


title: cdc28-4, 37 degrees, t=290, replicate 1

value: 290 minutes after synchronization


title: cdc28-4, 37 degrees, t=250, replicate 1

description: 250 minutes after synchronization, no CDK activity

value: 250 minutes after synchronization


title: cdc28-4, 37 degrees, t=130, replicate 1


title: cdc28-4, 37 degrees, t=150, replicate 1


title: cdc28-4, 37 degrees, t=30, replicate 2

description: 30 minutes after synchronization, no CDK activity

source_name: cdc28-4, 37 degrees, t=30

value: 30 minutes after synchronization


title: cdc28-4, 37 degrees, t=110, replicate 1


title: cdc28-4, 37 degrees, t=30, replicate 1


title: cdc28-4, 37 degrees, t=50, replicate 1


title: cdc28-4, 37 degrees, t=70, replicate 1


title: cdc28-4, 37 degrees, t=10, replicate 1


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 119

status: Public on Jan 24 2012

city: San Francisco

first: Linda

last: Giudice

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

description: 119 LUSY119

hyb_protocol: Individual samples were hybridized to Human Gene 1.0 ST arrays (Affymetrix) containing 19,492 genes.

scan_protocol: Data were scanned according to the protocol described in the WT sense target-labeling assay manual from Affymetrix (version 4; product code FS450_0007).

data_processing: The intensity values of different probe sets (genes) in the GeneChip Operating Software (Affymetrix) were imported into GeneSpring GX version 10.0 software (Agilent Technologies, Santa Clara, CA) and processed using the robust multiarray analysis (RMA) algorithm for background adjustment, normalization, and log2 transformation of perfect-match values. The data at each time point were normalized to the corresponding sample at t = 0 h. Then, the normalization was conducted within each time-group: data from E2P4-treated samples were normalized to those from E2-treated samples, which were normalized to the vehicle control, with the resulting data thus reflecting the specific temporal response to P4. We performed three major comparisons of the response to P4: within the nonendometriosis group, within the endometriosis group, and between hESFendo and hESFnonendo. The resulting gene lists generated included only genes showing >1.5-fold change in expression and a P value of <0.05 by using a two-way ANOVA parametric test and Benjamini-Hochberg multiple testing correction for false discovery rate.

source_name: hESF, no endometriosis, 14 days of E2

label_protocol: For each sample, 100 ng of total RNA was reverse-transcribed to cDNA by using 500 ng of T7-(N6) primer and SuperScript II. A second strand of DNA was generated using DNA polymerase, followed by overnight in vitro transcription to generate cRNA. After samples were processed through cRNA clean-up spin columns (Affymetrix), 10 μg of cRNA was reverse-transcribed using random primers and SuperScript II. Mixtures were digested with RNase H, and cDNA was purified by cDNA clean-up spin columns (Affymetrix). Finally, 5.5 μg of sense cDNA was fragmented and labeled using a GeneChip WT-terminal labeling kit. The quality of the cDNA and the fragmented cDNA was assessed with an Agilent Bioanalyzer.

growth_protocol: Endometrial tissue was digested with collagenase, and hESFs were isolated and plated with Dulbecco's Modified Eagle medium (DMEM)/molecular cell developmental biology 105 (MCDB-105) medium with 10% charcoal-stripped fetal bovine serum (FBS), insulin (5 mg/ml), gentamicin, penicillin, and streptomycin. All cells used were at Passage 2. Subsequently, hESFs were plated in 6-cm plastic dishes, and after they reached confluency, medium was changed to a low-serum medium (LSM; i.e., DMEM/MCDB-105 medium containing ascorbic acid, transferrin, and gentamicin with 2% FBS) for 24 h prior to treatment.

extract_protocol: Total RNA was isolated from individual plates and purified using an RNeasy mini-kit (Qiagen, Valencia, CA) following the manufacturer's protocol. Samples were stored in RNase-free H2O, purity was analyzed by the A260:A280 nm ratio, and RNA quality and integrity were assessed by using a Bioanalyzer 2100 unit (Agilent Technologies, Santa Clara, CA). All samples had high-quality RNA (RNA integrity number [RIN] = 9.7–10).

treatment_protocol: Duplicate cultures of hESF in LSM were treated with E2P4 (10 nM E2 + 1 μM P4), with 10 nM E2 alone (E2), or with vehicle (vehicle control), and cells and CM were collected at time (t) of 0 h, 6 h (early response), 48 h (intermediate response), and 14 days (late response). CM was changed every 2 days.

tag: individual identifier

tag: gender

value: female

tag: disease

value: no endometriosis

value: endometrium

value: human endometrial stromal fibroblasts (hESF)

tag: in vitro treatment

value: estradiol (E2)

tag: treatment duration

value: 14 days


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 118

description: 118 LUSY118

source_name: hESF, no endometriosis, 14 days of vehicle control

value: vehicle control


title: cdc28-4, 37 degrees, t=190, replicate 1

description: 190 minutes after synchronization, no CDK activity

value: 190 minutes after synchronization


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 116

description: 116 LUSY116

source_name: hESF, no endometriosis, 48 hours of E2

value: 48 hours


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 112

description: 112 LUSY112a

source_name: hESF, endometriosis, 14 days of E2P4

value: endometriosis

value: estradiol + progesterone (E2P4)


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 117

description: 117 LUSY117

source_name: hESF, no endometriosis, 48 hours of E2P4


title: cdc28-4, 37 degrees, t=90, replicate 1

value: 90 minutes after synchronization

value: no


title: cdc28-4, 37 degrees, t=170, replicate 1

value: 170 minutes after synchronization


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 115

description: 115 LUSY115

source_name: hESF, no endometriosis, 48 hours of vehicle control


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 120

description: 120 LUSY120

source_name: hESF, no endometriosis, 14 days of E2P4


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 110

description: 110 LUSY110

source_name: hESF, endometriosis, 14 days of vehicle control


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 111

description: 111 LUSY111

source_name: hESF, endometriosis, 14 days of E2


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 114

description: 114 LUSY114

source_name: hESF, no endometriosis, 6 hours of E2P4

value: 6 hours


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 113

description: 113 LUSY113

source_name: hESF, no endometriosis, 6 hours of E2


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 104

description: 104 LUSY104

source_name: hESF, endometriosis, 6 hours of vehicle control


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 107

description: 107 LUSY107

source_name: hESF, endometriosis, 48 hours of vehicle control


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 101

description: 101 LUSY101


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 109

description: 109 LUSY109

source_name: hESF, endometriosis, 48 hours of E2P4


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 105

description: 105 LUSY105

source_name: hESF, endometriosis, 6 hours of E2


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 103

description: 103 LUSY103

source_name: hESF, endometriosis, at t=0


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 108

description: 108 LUSY108

source_name: hESF, endometriosis, 48 hours of E2


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 100

description: 100 LUSY100


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 106

description: 106 LUSY106

source_name: hESF, endometriosis, 6 hours of E2P4


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 98

description: 98 LUSY98


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 96

description: 96 LUSY96


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 102

description: 102 LUSY102


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 99

description: 99 LUSY99


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 97

description: 97 LUSY97


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 95

description: 95 LUSY95


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 94

description: 94 LUSY94


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 93

description: 93 LUSY93a


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 85

description: 85 LUSY85


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 83

description: 83 LUSY83


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 92

description: 92 LUSY92


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 70

description: 70 LUSY70


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 67

description: 67 LUSY67


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 71

description: 71 LUSY71

source_name: hESF, no endometriosis, at t=0


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 87

description: 87 LUSY87


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 91

description: 91 LUSY91


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 65

description: 65 LUSY65


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 86

description: 86 LUSY86


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 63

description: 63 LUSY63


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 89

description: 89 LUSY89


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 84

description: 84 LUSY84


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 53

description: 53 LUSY53


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 90

description: 90 LUSY90


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 68

description: 68 LUSY68


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 64

description: 64 LUSY64


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 62

description: 62 LUSY62


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 88

description: 88 LUSY88


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 66

description: 66 LUSY66


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 69

description: 69 LUSY69


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 56

description: 56 LUSY56


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 55

description: 55 LUSY55

source_name: hESF, no endometriosis, 14 days of E2


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 61

description: 61 LUSY61


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 52

description: 52 LUSY52

source_name: hESF, no endometriosis, 48 hours of E2


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 54

description: 54 LUSY54

source_name: hESF, no endometriosis, 14 days of vehicle control


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 51

description: 51 LUSY51

source_name: hESF, no endometriosis, 48 hours of vehicle control


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 72

description: 72 LUSY72

source_name: hESF, no endometriosis, 6 hours of vehicle control


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 49

description: 49 LUSY49


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 47

description: 47 LUSY47a


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 50

description: 50 LUSY50


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 46

description: 46 LUSY46


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 44

description: 44 LUSY44


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 45

description: 45 LUSY45

source_name: hESF, no endometriosis, 48 hours of E2P4


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 43

description: 43 LUSY43


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 48

description: 48 LUSY48

source_name: hESF, no endometriosis, 14 days of E2P4


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 39

description: 39 LUSY39a


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 42

description: 42 LUSY42

source_name: hESF, no endometriosis, 6 hours of E2P4


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 41

description: 41 LUSY41

source_name: hESF, no endometriosis, 6 hours of E2


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 32

description: 32 LUSY32


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 40

description: 40 LUSY40


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 29

description: 29 LUSY29


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 23

description: 23 LUSY23


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 27

description: 27 LUSY27


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 24

description: 24 LUSY24


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 22

description: 22 LUSY22


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 26

description: 26 LUSY26


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 28

description: 28 LUSY28


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 25

description: 25 LUSY25


title: NK cells rep4 mRNA (HUG)

status: Public on Jan 23 2012

city: Nutley

first: Donavan

last: Cheng

state: NJ

address: 340 Kingsland Ave

department: Translational Research Sciences

institute: Hoffmann-LaRoche

description: Isolated at University Hospital of Geneva (HUG)

hyb_protocol: Fragmented and labeled aRNA was hybridized to the Affymetrix U133 Plus 2.0 chips according to manufacturer’s instructions. Wash and stain protocol FS450_0004.

scan_protocol: GeneChips were scanned using the GC 30007G scanner.

data_processing: Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure. Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release. As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis. A total 18,391 out of 54,675 probesets passed the QC and curation processes.

source_name: NK cells

label_protocol: Total RNA (100ng) was transcribed and labeled into amplified RNA (aRNA) using the 3’IVT express kit (Affymetrix Inc., Santa Clara, CA) according to manufacturer’s instruction on a GCAS (Gene Chip Array Station).

extract_protocol: Total RNA, including small non-coding RNAs, was extracted using the mirVana RNA isolation kit (Ambion, Inc, Austin, TX, USA) according to manufacturer’s protocol. RNA was quantified using a ND-1000 spectrophotometer (Nanodrop Technology®, Cambridge, UK) and RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA). The 260/280 ratio were between 1.7 and 2.1 and the RINs (RNA Integrity Numbers) greater than 6 for all samples.

value: NK cells


title: NK cells rep5 mRNA (HUG)


title: Neutrophils rep1 mRNA (HUG)

source_name: Neutrophils

value: Neutrophils


title: NK cells rep3 mRNA (HUG)


title: Neutrophils rep5 mRNA (HUG)


title: NK cells rep2 mRNA (HUG)


title: Neutrophils rep3 mRNA (HUG)


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 21

description: 21 LUSY21

value: female


title: Neutrophils rep4 mRNA (HUG)


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 31

description: 31 LUSY31

value: no endometriosis


title: Neutrophils rep2 mRNA (HUG)


title: Eosinophils rep2 mRNA (HUG)

source_name: Eosinophils

value: Eosinophils


title: Endometrial tissue-isolated human endometrial stromal fibroblast (hESF) 30

description: 30 LUSY30

value: endometrium

value: human endometrial stromal fibroblasts (hESF)


title: Eosinophils rep3 mRNA (HUG)


title: Eosinophils rep1 mRNA (HUG)


title: NK cells rep1 mRNA (HUG)


title: CD8+ T cells rep4 mRNA (HUG)

source_name: CD8+ T cells

value: CD8+ T cells


title: CD8+ T cells rep5 mRNA (HUG)


title: CD4+ T cells rep5 mRNA (HUG)

source_name: CD4+ T cells

value: CD4+ T cells


title: CD8+ T cells rep3 mRNA (HUG)


title: CD8+ T cells rep1 mRNA (HUG)


title: CD4+ T cells rep4 mRNA (HUG)


title: CD4+ T cells rep1 mRNA (HUG)


title: Monocytes rep4 mRNA (HUG)

source_name: CD14+ monocytes

value: CD14+ monocytes


title: Monocytes rep5 mRNA (HUG)


title: CD8+ T cells rep2 mRNA (HUG)


title: Monocytes rep2 mRNA (HUG)


title: Monocytes rep3 mRNA (HUG)


title: B cells rep2 mRNA (HUG)

source_name: CD19+ B cells

value: CD19+ B cells


title: B cells rep1 mRNA (HUG)


title: Monocytes rep1 mRNA (HUG)


title: B cells rep4 mRNA (HUG)


title: Neutrophils rep3 mRNA (Roche)

description: Isolated using the EasySep® Human Neutrophil Enrichment Kit (Stem Cell Technologies, Grenoble, France)

data_processing: Data was normalized in R/Bioconductor using the robust multi-array average (RMA) expression measure.  Probesets were annotated using the latest annotation available in Bioconductor and curated using an internal Roche probe inspector tool, which updates gene annotation per probeset based on the latest human genome draft release.  As an additional quality measure, probesets were also curated using the tool for sequence specificity; probesets mapping to non-unique locations in the genome were flagged and ignored in subsequent analysis.  A total of 20,367 out of 54,675 probesets passed the QC and curation processes, corresponding to 11,629 unique genes.

source_name: Neutrophils from healthy donor pool 7


title: mDC rep5 mRNA (Roche)

description: CD123+ plasmacytoid dendritic cells (pDCs), CD11c+ myeloid dendritic cells (mDCs) and CD14+ monocytes were isolated using the EasySep®  Human pDCs Enrichment Kit, a custom EasySep®  Human mDCs Enrichment Kit (containing antibodies directed against CD3, CD19, CD14, CD16, CD19, CD25, CD34, CD56, CD66b, GlyA, CD85g, CD45RA, CD123 and dextran) and the Human CD14 positive Selection Kit (all from Stemcell Biotechnologies) respectively according to manufacturer’s instructions.

source_name: mDCs from healthy donor pool 18

value: mDCs


title: pDC rep5 mRNA (Roche)

source_name: pDCs from healthy donor pool 18

value: pDCs


title: mDC rep4 mRNA (Roche)

source_name: mDCs from healthy donor pool 17


title: B cells rep5 mRNA (HUG)


title: pDC rep4 mRNA (Roche)

source_name: pDCs from healthy donor pool 17


title: pDC rep2 mRNA (Roche)

source_name: pDCs from healthy donor pool 14


title: pDC rep1 mRNA (Roche)

source_name: pDCs from healthy donor pool 13


title: Neutrophils rep1 mRNA (Roche)

source_name: Neutrophils from healthy donor pool 3


title: pDC rep3 mRNA (Roche)

source_name: pDCs from healthy donor pool 16


title: mDC rep1 mRNA (Roche)

source_name: mDCs from healthy donor pool 14


title: mDC rep3 mRNA (Roche)

source_name: mDCs from healthy donor pool 16


title: mDC rep2 mRNA (Roche)

source_name: mDCs from healthy donor pool 15


title: Neutrophils rep2 mRNA (Roche)

source_name: Neutrophils from healthy donor pool 4


title: CD4+ T cells rep2 mRNA (HUG)


title: Eosinophils rep4 mRNA (Roche)

description: Isolated using EasySep® Human Eosinophil Enrichment Kit (Stem Cell Technologies)

source_name: Eosinophils from healthy donor pool 8


title: Eosinophils rep3 mRNA (Roche)

source_name: Eosinophils from healthy donor pool 7


title: B cells rep3 mRNA (HUG)


title: CD8+ T cells rep3 mRNA (Roche)

description: CD14+ monocytes, CD8+ T cells, CD56+ NK cells and CD19 B cells were isolated using the Human CD14 positive Selection Kit, Human CD8+ T cells Enrichment Kit, EasySep® Human CD56+ NK cells Enrichment Kit, EasySep® Human CD19+ B cells Enrichment Kit (all from Stem Cell Technologies) respectively according to manufacturer’s instructions.

source_name: CD8+ T cells from healthy donor pool 12


title: CD8+ T cells rep2 mRNA (Roche)

source_name: CD8+ T cells from healthy donor pool 11


title: Eosinophils rep1 mRNA (Roche)

source_name: Eosinophils from healthy donor pool 3


title: CD8+ T cells rep5 mRNA (Roche)

source_name: CD8+ T cells from healthy donor pool 4


title: CD8+ T cells rep4 mRNA (Roche)

source_name: CD8+ T cells from healthy donor pool 3


title: Eosinophils rep2 mRNA (Roche)

source_name: Eosinophils from healthy donor pool 4


title: NK cells rep4 mRNA (Roche)

source_name: NK cells from healthy donor pool 7


title: NK cells rep5 mRNA (Roche)

source_name: NK cells from healthy donor pool 9


title: NK cells rep3 mRNA (Roche)

source_name: NK cells from healthy donor pool 6


title: NK cells rep2 mRNA (Roche)

source_name: NK cells from healthy donor pool 12


title: B cells rep5 mRNA (Roche)

source_name: CD19+ B cells from healthy donor pool 9

value: B cells


title: CD8+ T cells rep1 mRNA (Roche)

source_name: CD8+ T cells from healthy donor pool 10


title: Monocytes rep7 mRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 2

value: Monocytes


title: B cells rep4 mRNA (Roche)

source_name: CD19+ B cells from healthy donor pool 8


title: Monocytes rep9 mRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 7


title: B cells rep3 mRNA (Roche)

source_name: CD19+ B cells from healthy donor pool 7


title: B cells rep1 mRNA (Roche)

source_name: CD19+ B cells from healthy donor pool 11


title: Monocytes rep10 mRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 8


title: Monocytes rep8 mRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 6


title: Flag_P1

status: Public on Jan 15 2012

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: GeneChip Hybridization Control Kit and GeneChip Hybridization, Wash, Stain Kit (Affymetrix) were used to hybidize Human Gene 1.0ST arrays.

scan_protocol: Standard Affymetrix Scan protocol was followed.

data_processing: The data were analyzed with Partek Genomics Suite version 6.4 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Flag plasmid, passage #1

label_protocol: Biotinylated ss-cDNA were prepared with GeneChip WT cDNA synthesis and Amplification Kit, GeneChip WT terminal Labeling Kit and GeneChip Sample Cleanup Module (Affymetrix).

growth_protocol: HeLa cells (ATCC, CCL-2)  were grown at 37degres in 10%FBS DMEM. They were passaged every 2 days. P1, P2, P3, P4 in the sample names refer to the cell passage number.

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

treatment_protocol: HeLa cells were seeded one day before transfection with pCMV-Flag-Evi1 plasmid or pCMV-Flag plasmid. The cells were used for RNA extraction 24hr after transfection.

tag: cell line

value: HeLa cells


title: Monocytes rep2 mRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 13


title: Monocytes rep3 mRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 15


title: Monocytes rep4 mRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 16


title: Monocytes rep5 mRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 17


title: Monocytes rep6 mRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 18


title: Flag_P3

source_name: Flag plasmid, passage #3


title: B cells rep2 mRNA (Roche)

source_name: CD19+ B cells from healthy donor pool 6


title: Flag-Evi1_P1

source_name: Flag-Evi1 plasmid, passage #1


title: Flag-Evi1_P4

source_name: Flag-Evi1 plasmid, passage #4


title: Flag_P4

source_name: Flag plasmid, passage #4


title: Flag-Evi1_P2

source_name: Flag-Evi1 plasmid, passage #2


title: Flag-Evi1_P3

source_name: Flag-Evi1 plasmid, passage #3


title: Flag_P2

source_name: Flag plasmid, passage #2


title: Monocytes rep1 mRNA (Roche)

source_name: CD14+ monocytes from healthy donor pool 1


title: NK cells rep1 mRNA (Roche)

source_name: NK cells from healthy donor pool 10


title: Skov3 Evi1 siRNA P11

source_name: Evi1 siRNA, passage #11

growth_protocol: SKOV-3 cells (ATCC, HTB-77) were grown at 37degres in 10%FBS RPMI. They were passaged every 3-4 days. P8, P9, P10, P11 in the sample names refer to the cell passage number.

treatment_protocol: SKOV-3 cells were seeded one day before transfection with pCMV-Flag-Evi1 plasmid, pCMV-Flag plasmid, Evi1 siRNA (Evi1 ON-TARGETplus siRNA#8 plus #10) or control siRNA (ON-TARGETplus Non-targeting Pool, Dharmacon)

value: SKOV-3 cells

tag: cell passage

tag: transfectant

value: Evi1 siRNA


title: Skov3 Ctl siRNA P11

source_name: Control siRNA, passage #11

value: Control siRNA


title: Skov3 Flag P11

source_name: Flag plasmid, passage #11

value: Flag plasmid


title: Skov3 Evi1 siRNA P10

source_name: Evi1 siRNA, passage #10


title: Skov3 Ctl siRNA P10

source_name: Control siRNA, passage #10


title: Skov3 Flag-Evi1 P9

source_name: Flag-Evi1 plasmid, passage #9

value: Flag-Evi1 plasmid


title: Skov3 Flag-Evi1 P8

source_name: Flag-Evi1 plasmid, passage #8


title: Skov3 Flag P9

source_name: Flag plasmid, passage #9


title: Skov3 Flag P10

source_name: Flag plasmid, passage #10


title: Skov3 Ctl siRNA P9

source_name: Control siRNA, passage #9


title: Skov3 Flag-Evi1 P10

source_name: Flag-Evi1 plasmid, passage #10


title: Skov3 Flag P8

source_name: Flag plasmid, passage #8


title: 100µM-Zol-treated_LotII_24h_rep1

status: Public on Jan 01 2012

city: Paris

first: Nadejda

last: Vintonenko

address: 1 Avenue Claude Vellefaux

country: France

institute: Inserm

description: Lot II

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. Transfer 80μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Raw data were processed with the apt-probeset-summarize program from the Affymetrix Power Tools (v1.10.2) for background correction and normalization. RMA algorithm with full quantile normalization  was applied using the array design library files V1 release 4 and normalised values expressed on a log base 2 scale. Transcripts and genes were annotated with the Affymetrix release 29 annotation file based on the human genome version 18 assembly.  Data analysis was performed with the R Bioconductor LIMMA package. Only genes with FDR<0.05 and fold change≥1.5 in paired comparison between treatment and their corresponding controls were considered as differentially regulated.

source_name: MDA-MB-231, 24h, Lot II

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: MDA-MB-231 cell line were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1% sodium pyruvate and 1% penicillin sodium and 1% streptomycin antibiotics (10% FCS-DMEM) at 37°C in a humidified atmosphere containing 5% carbon dioxide.

extract_protocol: Total RNA was isolated using RNeasy mini kit (Qiagen) by direct lyses on the 10cm culture dish with 600 μl RLT Buffer following manufacture’s instructions. cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix) starting from 300 ng of total RNAs.

treatment_protocol: Fluvastatin, or Zoledronate, or their solvent for mock-treated cells were added to the standard 10% FCS-DMEM to final concentration of 2 µM for Fluvastatine ( 12h and 24hincubation times), 30 µM for Zoledronate (12h, 24h, or 48h incubation times); or 100 µM for Zoledronate (24h incubation).  Mock-treated (control) cells were obtained in parallel for each time point. Four independent replicates were used for each condition.

tag: cell line origin

value: breast cancer

tag: agent

value: Zoledronate

tag: dose


title: Skov3 Evi1 siRNA P9

source_name: Evi1 siRNA, passage #9


title: Control_LotII_24h_rep1

description: Lot II

value: Control


title: Skov3 Ctl siRNA P8

source_name: Control siRNA, passage #8


title: Control_LotII_24h_rep4

description: Lot II


title: 100µM-Zol-treated_LotII_24h_rep3

description: Lot II


title: Control_LotII_24h_rep2

description: Lot II


title: 100µM-Zol-treated_LotII_24h_rep2

description: Lot II


title: 100µM-Zol-treated_LotII_24h_rep4

description: Lot II


title: 30µM-Zol-treated_LotII_48h_rep3

description: Lot II

source_name: MDA-MB-231, 48h, Lot II


title: Control_LotII_24h_rep3

description: Lot II


title: 2µM-Fluva-treated_LotI_24h_rep3

description: Lot I

source_name: MDA-MB-231, 24h, Lot I

value: Fluvastatin


title: 30µM-Zol-treated_LotII_48h_rep1

description: Lot II


title: Control_LotII_48h_rep4

description: Lot II


title: 30µM-Zol-treated_LotII_48h_rep2

description: Lot II


title: Control_LotII_48h_rep2

description: Lot II


title: 2µM-Fluva-treated_LotI_24h_rep4

description: Lot I


title: Control_LotII_48h_rep1

description: Lot II


title: 30µM-Zol-treated_LotI_24h_rep3

description: Lot I


title: 30µM-Zol-treated_LotI_24h_rep4

description: Lot I


title: 30µM-Zol-treated_LotI_24h_rep1

description: Lot I


title: 30µM-Zol-treated_LotI_24h_rep2

description: Lot I


title: Control_LotI_24h_rep3

description: Lot I


title: Skov3 Flag-Evi1 P11

source_name: Flag-Evi1 plasmid, passage #11


title: Control_LotI_24h_rep2

description: Lot I


title: 2µM-Fluva-treated_LotI_24h_rep1

description: Lot I


title: Control_LotII_48h_rep3

description: Lot II


title: Skov3 Evi1 siRNA P8

source_name: Evi1 siRNA, passage #8


title: 2µM-Fluva-treated_LotI_12h_rep4

description: Lot I

source_name: MDA-MB-231, 12h, Lot I


title: Control_LotI_24h_rep4

description: Lot I


title: Control_LotI_24h_rep1

description: Lot I


title: 2µM-Fluva-treated_LotI_24h_rep2

description: Lot I


title: 2µM-Fluva-treated_LotI_12h_rep2

description: Lot I


title: 2µM-Fluva-treated_LotI_12h_rep1

description: Lot I


title: 30µM-Zol-treated_LotII_48h_rep4

description: Lot II


title: 2µM-Fluva-treated_LotI_12h_rep3

description: Lot I


title: Control_LotI_12h_rep4

description: Lot I


title: Control_LotI_12h_rep3

description: Lot I


title: Control_LotI_12h_rep1

description: Lot I


title: Control_LotI_12h_rep2

description: Lot I


title: 30µM-Zol-treated_LotI_12h_rep3

description: Lot I


title: 30µM-Zol-treated_LotI_12h_rep4

description: Lot I


title: 30µM-Zol-treated_LotI_12h_rep2

description: Lot I


title: 30µM-Zol-treated_LotI_12h_rep1

description: Lot I


title: CD1cpos2

status: Public on Dec 17 2011

city: München

first: Olivia

last: Prazeres da Costa

state: Bavaria

address: Trogerstr. 30

department: Medical Microbiology, Immunology and Hygiene

country: Germany

institute: Technische Universität München

description: gene expression data from freshly isolated blood dendritic cells

hyb_protocol: Affymetrix Hybridization protocol

scan_protocol: Affymetrix Scanner 3000 7G

data_processing: RMA normalization

source_name: blood dendritic cells

label_protocol: One Cycle Target Labeling Kit

growth_protocol: Cells were lysed in TriReagent (Sigma) directly after isolation

extract_protocol: TriReagent (Sigma) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Samples remained untreated

tag: cell subtype

value: blood dendritic cells


title: Mel3

status: Public on Dec 13 2011

city: Memphis

first: Jena

middle: J

last: Steinle

state: TN

address: 930 Madison Ave, Suite 768

department: Ophthalmology

institute: University of Tennessee Health Science Center

description: cell culture extract

hyb_protocol: Following fragmentation, 15 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed in Expression Console using Affymetrix default analysis settings for RMA quantile normalization.

source_name: melphalan-treated REC, 24 hour, 4ug/ml

label_protocol: Biotinylated cDNA were prepared from 200 ng total RNA according to the standard whole transcript labeling protocol for Affymetrix ST arrays (Ambion WT Expression Kit Manual, 2010, Ambion; GeneChip Whole Transcript Sense Target Labeling Kit  Manual, 2007, Affymetrix).

growth_protocol: Human retinal endothelial cells were grown in M131 medium until 90% confluence.

extract_protocol: Extraction of total RNA was performed using RNA Stat-60, according to the manufacturer's instructions. RNA purity was checked by OD260/280 readings, and RNA integrity was checked using Agilent Bioanalyzer capillary electrophoresis profiles.

treatment_protocol: 4 dishes remained untreated. 4 dishes treated with 4ug/ml melphalan for 24 hours.  All cells collected into Trizol.

tag: cell type

value: retinal endothelial cells

tag: treatment

value: melphalan


title: CD16pos2

tag: tissue


title: CD16pos1


title: CD1cpos3


title: Mel2

description: cell culture extract


title: MNT3

description: cell culture extract

source_name: non-treated REC, 24 hr


title: MNT4

description: cell culture extract


title: Mel4

description: cell culture extract


title: CD16neg1


title: CD16pos3


title: CD16neg2


title: CD16neg3


title: MNT2

description: cell culture extract


title: MNT1

description: cell culture extract


title: CD1cpos1


title: Mel1

description: cell culture extract


title: Carbo3

description: cell culture extract

source_name: carboplatin-treated REC, 24 hr, 1mM

treatment_protocol: 4 dishes remained untreated. 4 dishes treated with 1mM carboplatin for 24 hours.  All cells collected into Trizol.

value: carboplatin


title: Carbo4

description: cell culture extract


title: Carbo2

description: cell culture extract


title: Carbo1

description: cell culture extract


title: CNT4

description: cell culture extract