title: LM223

description:
LM001_525_AGE_1_LM223_10_08_08
Inclusion number in the clinical trial : 168


title: LM235

status: Public on Oct 25 2012

type: RNA

city: Houston

first: Pierre

last: Saintigny

address: 1515 Holcombe

department: Thoracic / Head and Neck Medical Oncology

country: USA

institute: The University of Texas M.D. Anderson Cancer Center

description:
LM001_525_AGE_1_LM235_10_20_08
Inclusion number in the clinical trial : 189

hyb_protocol: Hybridization mixtures were prepared according to Affymetrix procedures to accommodate 5 μg of cDNA targets from NuGEN amplification. Human Gene 1.ST platform were hybridized, revealed and washed according to the Affymetrix protocol.

scan_protocol: Gene chips were scanned using a 7 G scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix).

data_processing: Raw data of microarrays were processed using quantile normalization and RMA algorithm (RMAExpress); expression values were log2 transformed

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: BATTLE_trial_core biopsy_chemorefractory non-small cell lung cancer

label_protocol: RNA amplifications were performed using the WT-Amplification™ Pico (NuGEN) kit. For all experiments, the manufacturers' protocols were strictly followed. WT-Ovation™ Pico products (NuGEN) are labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). Each labeled cRNA targets are synthesized according to manufacturer's protocols. The quantity and quality of the amplified cRNA or cDNA were assessed by a ND-1000 spectrophotometer (Nanodrop Technologies), and Agilent Bioanalyzer (Agilent Technologies), respectively.

growth_protocol: Core biopsies from patients included in the Biomarker-integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE)

extract_protocol: RNA was extracted and purified from OCT-embedded tissue using the RNeasy Mini Kit (Qiagen) including on-column DNase (Qiagen) digestion as described by the manufacturer's protocol.

treatment_protocol: Samples were OCT-embedded and frozen before RNA extraction

tag: egfr mutation

value: Mutant

tag: egfr activating mutation

value: Yes

tag: egfr mutation exon

value: Exon 19/Exon 20

tag: egfr mutation pattern

tag: kras mutation

value: WT

tag: egfr index


title: LM222

description:
LM001_525_AGE_1_LM222_10_08_08
Inclusion number in the clinical trial : 167

tag: concomitant t790m


title: Ovarian cancer tissue from Taiwan LD048

type: genomic

city: Singapore

first: Liang

last: Goh

address: College Road

country: Singapore

institute: Duke-NUS graduate medical school

description:
Epithelial ovarian cancers
primary_data_description:  Log relative ratio calclulated by Affymetric Genotyping Console

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Affymetrix standard procedure

data_processing: CEL files and CHP files are processed and normalized with Hapmap CHB using the Affymetric Genotyping Console.

label: Biotin

molecule: genomic DNA

source_name: Ovarian Cancer tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Tumor genomic DNAs were extracted by using phenol-chloroform extraction method. Tumor RNAs were extracted by using Qiazol followed by column clean-up using miRNeasy kit (Qiagen).

tag: histotype

value: Serous


title: LM217

description:
LM001_525_AGE_1_LM217_10_08_08
Inclusion number in the clinical trial : 159


title: LM220

description:
LM001_525_AGE_1_LM220_10_08_08
Inclusion number in the clinical trial : 163


title: LM221

description:
LM001_525_AGE_1_LM221_10_08_08
Inclusion number in the clinical trial : 166


title: LM224

description:
LM001_525_AGE_1_LM224_10_08_08
Inclusion number in the clinical trial : 170

tag: treatment

value: erlotinib

tag: randomization date

tag: date of progression

tag: progression-free survival status

tag: progression-free survival time (months)


title: Ovarian cancer tissue from Taiwan LB761

value: Clear Cell


title: T824

city: Sheffield

first: Ian

middle: Wallace

last: Brock

state: South Yorkshire

address: Beachhill Road

department: Cancer Studies

country: United Kingdom

institute: University of Sheffield Medical School

hyb_protocol: Appropriate equal amounts of Cy5-labeled sample and Cy3-labeled reference DNA were mixed to a 39ul final volume. 71ul Hybridization Master Mix (1mg/ml Cot-1 DNA 5ul, Agilent 10X blocking agent 11ul, and Agilent 2X HiRPM Hybridization buffer 55ul) was added and incubated at 95C for 3 min followed by 37C for 30min. 100ul of the hybridization sample mixture was applied onto the microarray gasket well and was covered by a microarray slide. The slide was incubated in a 65C rotator rack for 24 hours. After hybridization, slide was washed sequentially.

scan_protocol: Scanned on Agilent Technologies Scanner G2505C US83603551. Images were quantified using Agilent Feature Extraction Software (v10.7.3.1).

data_processing: Agilent Feature Extraction Software (v10.7.3.1) was used for background subtraction and Lowess normalization.

source_name: Peripheral blood

label_protocol: 500ng sample and normal genomic DNA were fragmented by restriction digestion with Alu I/Rsa I (65degrees C for 20mins) and then were labeled with Cy5 and Cy3, respectively, at 85C for 30 min. Labeled DNA were purified using Microcon 30kDa spin columns. Degree of labeling was determined by measuring the absorbance at A260nm(DNA), A550nm(Cy3), and A650nm(Cy5) using a NanoDrop.

extract_protocol: Normal blood DNA was extracted with the QIAGEN Flexigene Kit (Cat No.: 51206).

tag: tissue

value: peripheral blood

source_name: Colorectal tumor tissue

extract_protocol: Tumor DNA was extracted from fresh frozen material using the QIAGEN Blood & Cell Culture DNA Maxi Kit (Cat. No.: 13362).

value: colorectal tumor


title: Ovarian cancer tissue from Taiwan LB333


title: 828T


title: T741


title: LM216

description:
LM001_525_AGE_1_LM216_10_08_08
Inclusion number in the clinical trial : 158


title: T223


title: T795


title: LM143

description:
Human Gene 1.0 ST_525_LM_143_1_07_15_08
Inclusion number in the clinical trial : 156


title: LM142

description:
Human Gene 1.0 ST_525_LM_142_1_07_15_08
Inclusion number in the clinical trial : 154

value: Unknown

value: Exon 21


title: Ovarian cancer tissue from Taiwan LB364


title: Ovarian cancer tissue from Taiwan LB310


title: 1350T


title: 1120T


title: LM140

description:
Human Gene 1.0 ST_525_LM_140_1_07_15_08
Inclusion number in the clinical trial : 151

value: Exon 20


title: 863T


title: 158T


title: LM141

description:
Human Gene 1.0 ST_525_LM_141_1_07_15_08
Inclusion number in the clinical trial : 152


title: Ovarian cancer tissue from Taiwan LB044


title: LM138

description:
Human Gene 1.0 ST_525_LM_138_06_24_08
Inclusion number in the clinical trial : 149


title: 632T


title: Ovarian cancer tissue from Taiwan LA590


title: Ovarian cancer tissue from Taiwan LA731


title: Ovarian cancer tissue from Taiwan LA554


title: Ovarian cancer tissue from Taiwan LD100


title: LM137

description:
Human Gene 1.0 ST_525_LM_137_06_24_08
Inclusion number in the clinical trial : 148


title: 150T


title: Ovarian cancer tissue from Taiwan LA543


title: T122


title: Ovarian cancer tissue from Taiwan LA269


title: Ovarian cancer tissue from Taiwan LB004


title: 153T


title: T23


title: LM135

description:
Human Gene 1.0 ST_525_LM_135_06_24_08
Inclusion number in the clinical trial : 146


title: T85


title: T16


title: Ovarian cancer tissue from Taiwan LA805


title: Ovarian cancer tissue from Taiwan LA527


title: Ovarian cancer tissue from Taiwan L609

value: Mucinous


title: Ovarian cancer tissue from Taiwan LA473


title: LM133

description:
Human Gene 1.0 ST_525_LM_133_06_24_08
Inclusion number in the clinical trial : 144


title: LM134

description:
Human Gene 1.0 ST_525_LM_134_06_24_08
Inclusion number in the clinical trial : 145


title: T208


title: T167


title: T248


title: T135


title: T86


title: Ovarian cancer tissue from Taiwan LA073


title: T212


title: Ovarian cancer tissue from Taiwan L953


title: LM130

description:
Human Gene 1.0 ST_525_LM_130_06_17_08
Inclusion number in the clinical trial : 139


title: Ovarian cancer tissue from Taiwan LB165


title: T110


title: LM127

description:
Human Gene 1.0 ST_525_LM_127_06_17_08
Inclusion number in the clinical trial : 110


title: T109


title: Ovarian cancer tissue from Taiwan L553

description:
Epithelial ovarian cancers
primary_data_description:  Log relative ratio calclulated by Affymetric Genotyping Console


title: LM136

description:
Human Gene 1.0 ST_525_LM_136_06_24_08
Inclusion number in the clinical trial : 147

value: Exon 19/Exon 21

value: loss-16 TC/L858R


title: LM125

description:
Human Gene 1.0 ST_525_LM_125_06_17_08
Inclusion number in the clinical trial : 127


title: T203


title: LM122

description:
Human Gene 1.0 ST_525_LM_122_06_17_08
Inclusion number in the clinical trial : 122


title: T202


title: T138


title: LM121

description:
Human Gene 1.0 ST_525_LM_121_06_17_08
Inclusion number in the clinical trial : 121


title: Ovarian cancer tissue from Taiwan LD116


title: T107


title: T88


title: T249


title: LM120

description:
Human Gene 1.0 ST_525_LM_120_06_17_08
Inclusion number in the clinical trial : 118


title: Ovarian cancer tissue from Japan JPKO-64

description:
Epithelial ovarian cancers
primary_data_description:Log relative ratio calclulated by Affymetric Genotyping Console

data_processing: CEL files and CHP files are processed and normalized with Hapmap JPT using the Affymetric Genotyping Console.

extract_protocol: Tumor genomic DNAs were extracted by using phenol-chloroform extraction method.

value: mucinous-borderline


title: Ovarian cancer tissue from Taiwan L822


title: T244


title: T104


title: T221


title: Ovarian cancer tissue from Japan JPKO-88


title: T206


title: Ovarian cancer tissue from Japan JPKO-44


title: LM117

description:
Human Gene 1.0 ST_525_LM_117_05_13_08
Inclusion number in the clinical trial : 136


title: T97


title: LM116

description:
Human Gene 1.0 ST_525_LM_116_05_13_08
Inclusion number in the clinical trial : 133


title: LM486

description:
LM001_525_AGE_1_LM486_04_01_10
Inclusion number in the clinical trial : 340

label_protocol: RNA amplifications were performed using the WT-Amplification™ Pico (NuGEN) kit.  WT-Ovation™ Pico products (NuGEN) are labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). Each labeled cRNA targets are synthesized according to manufacturer's protocols. The quantity and quality of the amplified cRNA or cDNA were assessed by a ND-1000 spectrophotometer (Nanodrop Technologies), and Agilent Bioanalyzer (Agilent Technologies), respectively.

tag: histology-iw revised

value: Squamous Cell Carcinoma

tag: egfr-iw type

value: No

tag: kras-iw mutation  (yes/no)

tag: gender

value: Male

tag: race

value: White

value: IIB

value: Former

tag: biopsy site (grouped)

value: sorafenib

tag: markergroup

tag: 8-week disease control (1=yes, 0=no)

tag: pfsc (1=progressed; 0=not progressed)

tag: pfsm (month)


title: Ovarian cancer tissue from Japan JPKO-33

tag: histotype


title: T142


title: Ovarian cancer tissue from Japan JPKO-34


title: T53


title: T98


title: LM484

description:
LM001_525_AGE_1_LM484_04_01_10
Inclusion number in the clinical trial : 337

tag: egfr mutation

value: WT

tag: kras mutation

tag: egfr index

value: IV

value: 8:Deep lymph nodes

tag: treatment


title: T271

value: peripheral blood

value: colorectal tumor


title: T201


title: LM483

description:
LM001_525_AGE_1_LM483_04_01_10
Inclusion number in the clinical trial : 336

value: Adenocarcinoma

value: Asian


title: Ovarian cancer tissue from Japan JPKO-13

value: mucinous


title: Ovarian cancer tissue from Japan JPKO-62


title: T45


title: Ovarian cancer tissue from Taiwan LB271

value: Serous


title: HCT116 IDH2 R172K/+ (45G3 clone) Cells, biological replicate 2

city: Cambridge

first: Joshua

middle: M

last: Korn

state: MA

address: 250 Mass Ave

institute: Novartis

hyb_protocol: Affymetrix GeneChip eukaryotic hybridization protocol (Affymetrix Inc.)

scan_protocol: GeneChip Scanner 3000 (Affymetrix Inc.)

data_processing: Micorarray Analysis Suite version 5.0 (MAS 5.0) background correction, scaled to 150

source_name: HCT116 IDH2 R172K/+ clone 45G3, cells grown for 6 days

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 (NuGen Lts)

growth_protocol: Cells grown for 6 days in 5% CO2 at 37ºC

extract_protocol: Qiagen Rneasy Kit, manufacturer's protocol

tag: cell line

tag: clone

tag: idh mutational status at the mrna level


title: HCT116 IDH2 R172K/+ (45G3 clone) Cells, biological replicate 1


title: LM473

description:
LM001_525_AGE_1_LM473_03_31_10
Inclusion number in the clinical trial : 318

tag: histology-iw revised

tag: egfr-iw type

value: Never


title: LM471

description:
LM001_525_AGE_1_LM471_03_31_10
Inclusion number in the clinical trial : 314

value: NSCLC

tag: kras-iw mutation  (yes/no)

tag: gender


title: HCT116 IDH2 R172K/+ (47C2 clone) Cells, biological replicate 1

source_name: HCT116 IDH2 R172K/+ clone 47C2, cells grown for 6 days


title: T80

tag: tissue


title: HCT116 IDH2 R172K/+ (47C2 clone) Cells, biological replicate 2


title: T90


title: LM475

description:
LM001_525_AGE_1_LM475_03_31_10
Inclusion number in the clinical trial : 321

value: No

value: Female

tag: race

tag: biopsy site (grouped)

tag: markergroup


title: Ovarian cancer tissue from Taiwan L513


title: HCT116 IDH2 R140Q/+ (17H5 clone) Cells, biological replicate 1

source_name: HCT116 IDH2 R140Q/+ clone 17H5, cells grown for 6 days


title: HCT116 IDH2 R140Q/+ (8G12 clone) Cells, biological replicate 2

source_name: HCT116 IDH2 R140Q/+ clone 8G12, cells grown for 6 days


title: LM455

description:
LM001_525_AGE_1_LM455_08_05_09
Inclusion number in the clinical trial : 292

value: White

tag: 8-week disease control (1=yes, 0=no)

tag: pfsc (1=progressed; 0=not progressed)

tag: pfsm (month)


title: T184


title: Ovarian cancer tissue from Japan JPKO-31

tag: histotype

value: endometroid


title: LM453

description:
LM001_525_AGE_1_LM453_08_19_09
Inclusion number in the clinical trial : 290

tag: egfr mutation

tag: kras mutation

tag: egfr index


title: Ovarian cancer tissue from Japan JPKO-9


title: HCT116 IDH2 R140Q/+ (8G12 clone) Cells, biological replicate 1

tag: cell line

tag: clone


title: HCT116 IDH2 R140Q/+ (17H5 clone) Cells, biological replicate 2

tag: idh mutational status at the mrna level


title: HCT116 IDH1 R132C/+ (16F8 clone, non-expressing of mutant allele) Cells, biological replicate 2

source_name: HCT116 IDH1 R132C/+ non-expressing clone 16F8 (note that this clone does not express the mutant IDH1 at the mRNA level) cells grown for 6 days

value: wild-type


title: Ovarian cancer tissue from Japan JPKO-27


title: LM451

description:
LM001_525_AGE_1_LM451_08_19_09
Inclusion number in the clinical trial : 288

tag: histology-iw revised

tag: egfr-iw type

value: Male

value: IIB

value: Former

tag: treatment

value: sorafenib


title: Ovarian cancer tissue from Japan JPKO-63


title: T83

tag: tissue

value: peripheral blood


title: LM449

description:
LM001_525_AGE_1_LM449_08_19_09
Inclusion number in the clinical trial : 286

value: WT

tag: kras-iw mutation  (yes/no)

tag: gender

tag: race

value: IV


title: HCT116 IDH1 R132C/+ (3A4 clone) Cells, biological replicate 2

source_name: HCT116 IDH1 R132C/+ clone 3A4, cells grown for 6 days


title: T46

value: colorectal tumor


title: HCT116 IDH1 R132C/+ (16F8 clone, non-expressing of mutant allele) Cells, biological replicate 1


title: HCT116 IDH1 R132H/+ (2H1 clone) Cells, biological replicate 2

source_name: HCT116 IDH1 R132H/+ clone 2H1, cells grown for 6 days


title: HCT116 IDH1 R132H/+ (2H1 clone) Cells, biological replicate 1


title: LM446

description:
LM001_525_AGE_1_LM446_08_19_09
Inclusion number in the clinical trial : 281

tag: biopsy site (grouped)

tag: markergroup

tag: 8-week disease control (1=yes, 0=no)


title: HCT116 IDH1 R132H/+ (2C11 clone) Cells, biological replicate 2

source_name: HCT116 IDH1 R132H/+ clone 2C11, cells grown for 6 days


title: HCT116 Parental Cells, biological replicate 2

source_name: HCT116 Parental clone, cells grown for 6 days

value: parental


title: HCT116 IDH1 R132H/+ (2C11 clone) Cells, biological replicate 1


title: HCT116 IDH1 R132C/+ (3A4 clone) Cells, biological replicate 1


title: HCT116 Parental Cells, biological replicate 1


title: UM-SCC-81B at T24

city: Ann Arbor

first: yugang

last: wang

state: MI

address: 1011 N Universtiy Dr., room 5205

department: BMS

institute: University of Michigan

description:
UM-SCC-81B-GD24
Gene expression data from UM-SCC-81B cells cultured under low glucose (0.1 mM) for 24 hours.

hyb_protocol: The biotin-labeled RNA was fragmented and 10μg of it was hybridized to Human Genome U133 Plus 2.0 Arrays (Affymetrix) at 45°C for 16 hours. Labeled bacterial RNAs of known concentration were spiked in the hybridization to generate an internal standard and to allow normalization between chips. Chips were washed, and stained with streptavidin R-phycoerythrin (Molecular Probes, Eugene, OR USA).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000, which can acquire high-resolution scanning at 1.56 μm pixel resolution.

data_processing: After scanning the chips, the data ware analyzed by using Affymetrix GeneChip-related software such as GCOS, Data Mining Tool and Affymetrix web database 'NetAffx'.

source_name: Head & Neck tumor UM-SCC-81B cells, 24 hr GD treatment

label_protocol: 5μg of total RNA was amplified and biotin-labeled according to the GeneChip Expression Analysis Technical Manual. Briefly, RNA was converted to double-stranded complementary DNA (cDNA) using SuperScript II RT (Invitrogen, Carlsbad, CA USA) with a T7-(dT)24 primer (Affymetrix, Inc., Santa Clara, CA, USA). Then, the cDNA was used in an in vitro transcription reaction in the presence of biotin-modified ribonucleotides (Enzo, Farmingdale, NY USA) to produce large amounts of single-stranded RNA.

growth_protocol: UM-SCC-81B cells were maintained in Dulbecco's Modified Eagle Medium high glucose (DMEM, Invitrogen, Carlsbad, CA) with 10% (vol/vol) FBS, penicillin (100 U/mL), and streptomycin (100 μg/mL).

extract_protocol: Total RNA was isolated from UM-SCC-81B cells using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: DMEM complete medium (10% FBS) with glucose (25 mM) and DMEM complete medium (10% FBS) without glucose were used to prepare low-glucose (0.1 mM) medium. Tumor cells were split into 6-cm dishes the day before treatment. Before treatment, tumor cells were washed twice with PBS to remove residual medium and then treated with low glucose medium for 4 hours and 24 hours. Tumor cells cultured with DMEM complete medium were used as a non-treatment control.

tag: cell type

value: oral squamous cell carcinoma cells

value: low glucose (0.1 mM)

tag: treatment duration

value: 24 hrs


title: T79


title: UM-SCC-81B at T0

description:
UM-SCC-81B-NT
Gene expression data from UM-SCC-81B cells cultured under normal conditions (25 mM, glucose).

source_name: Head & Neck tumor UM-SCC-81B cells, without GD treatment

value: normal glucose


title: UM-SCC-81B at T4

description:
UM-SCC-81B-GD-4
Gene expression data from UM-SCC-81B cells cultured under low glucose (0.1 mM) for 4 hours.

source_name: Head & Neck tumor UM-SCC-81B cells, 4 hr GD treatment

value: 4 hrs


title: LM441

description:
LM001_525_AGE_1_LM441_07_31_09
Inclusion number in the clinical trial : 271

tag: egfr mutation

tag: kras mutation

value: Adenocarcinoma

value: No

value: Female

value: White

value: Never

tag: pfsc (1=progressed; 0=not progressed)

tag: pfsm (month)


title: LM422

description:
LM001_525_AGE_1_LM422_07_30_09
Inclusion number in the clinical trial : 236

tag: egfr index

value: IIIB

value: Former

value: 7:Shallow lymph nodes


title: parous-rep69-batch V.5

city: Philadelphia

first: Julia

last: Santucci-Pereira

state: PA

address: 333 Cottman Ave, P2051

institute: Fox Chase Cancer Center

description: gene expression

hyb_protocol: Hybridization was performed as described in the GeneChip Expression Analysis (701021 Rev.5) protocol from Affymetrix, following the instructions for 49 formta (standard)/64 format array.

scan_protocol: The scanner used was Affymetrix® GeneChip® Scanner 3000 and the software used was GCOS.

data_processing: The data were (1) RMA normalized; (2) filtered to exclude probesets present (P) in fewer than 25% of both parous & nulliparous samples; (3) batch normalized with ComBat (default parameters); (4) filtered to remove probesets with variance in the lowest quartile. The full set of RMA normalized and MAS5 calls data provided as a supplemetnary file on GSE26457.

source_name: Human breast tissue

label_protocol: The GeneChip Expression 3’-Amplification Two-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA) was used to prepare the cRNA for hybridization following the manufacturer’s protocol-GeneChip Expression Analysis (701021 Rev.5), initiating with 100ng of total RNA.

extract_protocol: Total RNA from core needle biopsies specimens was isolated using the Qiagen Allprep RNA/DNA Mini Kit according to manufacturer's instructions (Qiagen, Alameda, CA, USA)

tag: parity

value: parous

tag: phase

value: Validation

tag: batch

tag: gravida


title: parous-rep70-batch V.6

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-50

description:
Epithelial ovarian cancers
primary_data_description:Log relative ratio calclulated by Affymetric Genotyping Console

tag: histotype

value: clear cell


title: LM444

description:
LM001_525_AGE_1_LM444_08_19_09
Inclusion number in the clinical trial : 278

source_name: BATTLE_trial_core biopsy_chemorefractory non-small cell lung cancer

value: WT

tag: histology-iw revised

value: Squamous Cell Carcinoma

tag: egfr-iw type

tag: kras-iw mutation  (yes/no)

tag: gender

value: IB

tag: treatment

value: sorafenib


title: parous-rep71-batch V.8

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-94

source_name: Ovarian Cancer tissue


title: Ovarian cancer tissue from Japan JPKO-86


title: Ovarian cancer tissue from Japan JPKO-90


title: Ovarian cancer tissue from Japan JPKO-80

value: endometroid


title: parous-rep66-batch V.4

description: gene expression


title: LM326

description:
LM001_525_AGE_1_LM326_01_23_09
Inclusion number in the clinical trial : 230

value: Adenosquamous

tag: race

tag: biopsy site (grouped)

tag: markergroup

tag: 8-week disease control (1=yes, 0=no)


title: parous-rep64-batch V.3

description: gene expression


title: LM322

description:
LM001_525_AGE_1_LM322_01_23_09
Inclusion number in the clinical trial : 225

tag: egfr mutation

tag: kras mutation

value: Male

value: IIIA

tag: pfsc (1=progressed; 0=not progressed)


title: Ovarian cancer tissue from Japan JPKO-16


title: LM319

description:
LM001_525_AGE_1_LM319_01_22_09
Inclusion number in the clinical trial : 220

tag: egfr index

value: Adenocarcinoma

value: No

tag: pfsm (month)


title: parous-rep65-batch V.3

description: gene expression

tag: parity

tag: phase

tag: batch


title: Ovarian cancer tissue from Japan JPKO-57

tag: histotype


title: LM419

description:
LM001_525_AGE_1_LM419_07_30_09
Inclusion number in the clinical trial : 232

tag: histology-iw revised

tag: egfr-iw type

value: White

value: IV


title: LM424

description:
LM001_525_AGE_1_LM424_07_30_09
Inclusion number in the clinical trial : 241

tag: kras-iw mutation  (yes/no)

tag: gender

value: Former


title: Ovarian cancer tissue from Japan JPKO-53


title: LM316

description:
LM001_525_AGE_1_LM316_01_22_09
Inclusion number in the clinical trial : 215

value: NSCLC

tag: race

tag: treatment


title: Ovarian cancer tissue from Japan JPKO-79


title: Ovarian cancer tissue from Japan JPKO-32


title: parous-rep63-batch V.2

description: gene expression

value: parous

tag: gravida


title: parous-rep68-batch V.5

description: gene expression

value: Validation


title: parous-rep62-batch V.1

description: gene expression


title: parous-rep61-batch V.8

description: gene expression


title: parous-rep59-batch V.1

description: gene expression


title: LM315

description:
LM001_525_AGE_1_LM315_01_22_09
Inclusion number in the clinical trial : 212

tag: biopsy site (grouped)

value: 7:Shallow lymph nodes

tag: markergroup

tag: 8-week disease control (1=yes, 0=no)


title: parous-rep60-batch V.1

description: gene expression


title: parous-rep67-batch V.4

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-39

value: clear cell


title: parous-rep58-batch V.3

description: gene expression


title: parous-rep57-batch V.2

description: gene expression


title: parous-rep55-batch V.7

description: gene expression


title: parous-rep56-batch V.1

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-22


title: LM314

description:
LM001_525_AGE_1_LM314_01_22_09
Inclusion number in the clinical trial : 210

tag: egfr mutation

value: WT

tag: kras mutation

value: Female

value: BlackOrAfricanAmerican

value: IIIB

tag: pfsc (1=progressed; 0=not progressed)


title: LM313

description:
LM001_525_AGE_1_LM313_01_22_09
Inclusion number in the clinical trial : 209

tag: egfr index

value: 6:Bone/soft tissue component

value: sorafenib

tag: pfsm (month)


title: parous-rep53-batch V.6

description: gene expression

tag: parity

tag: phase

tag: batch


title: LM225

description:
LM001_525_AGE_1_LM225_10_08_08
Inclusion number in the clinical trial : 172

tag: histology-iw revised

tag: egfr-iw type

value: Male

value: Never


title: Ovarian cancer tissue from Japan JPKO-67

tag: histotype

value: serous-borderline


title: LM311

description:
LM001_525_AGE_1_LM311_01_22_09
Inclusion number in the clinical trial : 206

value: Adenocarcinoma

value: No

tag: kras-iw mutation  (yes/no)

tag: gender

tag: race


title: parous-rep51-batch V.6

description: gene expression

tag: gravida


title: parous-rep52-batch V.4

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-60

value: endometroid


title: LM219

description:
LM001_525_AGE_1_LM219_10_08_08
Inclusion number in the clinical trial : 161

value: White

value: IV

value: Former

tag: biopsy site (grouped)

tag: treatment

tag: markergroup


title: parous-rep49-batch V.2

description: gene expression

value: parous

value: Validation


title: parous-rep48-batch V.7

description: gene expression


title: parous-rep47-batch V.6

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-19


title: parous-rep46-batch V.5

description: gene expression


title: LM129

description:
Human Gene 1.0 ST_525_LM_129_06_17_08
Inclusion number in the clinical trial : 135

tag: egfr mutation

value: WT

tag: kras mutation

value: NSCLC

tag: 8-week disease control (1=yes, 0=no)


title: parous-rep50-batch V.8

description: gene expression


title: parous-rep44-batch V.3

description: gene expression


title: LM132

description:
Human Gene 1.0 ST_525_LM_132_06_24_08
Inclusion number in the clinical trial : 143

tag: egfr index

tag: pfsc (1=progressed; 0=not progressed)

tag: pfsm (month)


title: Ovarian cancer tissue from Japan JPKO-35

value: clear cell


title: parous-rep42-batch V.8

description: gene expression

tag: parity

tag: phase

tag: batch


title: parous-rep45-batch V.5

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-10

tag: histotype


title: parous-rep41-batch V.7

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-92

value: serous


title: parous-rep54-batch V.4

description: gene expression


title: LM123

description:
Human Gene 1.0 ST_525_LM_123_06_17_08
Inclusion number in the clinical trial : 125

tag: histology-iw revised

tag: egfr-iw type

tag: kras-iw mutation  (yes/no)

value: Female


title: LM128

description:
Human Gene 1.0 ST_525_LM_128_06_17_08
Inclusion number in the clinical trial : 130

tag: gender

tag: race

value: 7:Shallow lymph nodes

value: sorafenib


title: parous-rep40-batch V.6

description: gene expression

tag: gravida


title: parous-rep39-batch V.5

description: gene expression


title: parous-rep43-batch V.1

description: gene expression


title: Ovarian cancer tissue from Taiwan LD148

description:
probe_group_file:  HuGene-1_0-st-v1.r4.pgf
meta-probeset_file:  HuGene-1_0-st-v1.r4.mps

hyb_protocol: RNA was labeled and hybridized to each array according to the manufacturer's instructions.

data_processing: Data was pre-processed and RMA normalized using Affymetrix Gene Expression Console.

extract_protocol: Tumor RNAs were extracted by using Qiazol followed by column clean-up using miRNeasy kit (Qiagen).

value: Clear Cell


title: Ovarian cancer tissue from Taiwan LD100

value: Serous


title: Ovarian cancer tissue from Japan JPKO-51

description:
Epithelial ovarian cancers
primary_data_description:Log relative ratio calclulated by Affymetric Genotyping Console

value: serous-borderline


title: nulliparous-rep42-batch V.7

description: gene expression

value: nulliparous


title: nulliparous-rep40-batch V.6

description: gene expression


title: nulliparous-rep41-batch V.7

description: gene expression


title: Ovarian cancer tissue from Taiwan LD085


title: parous-rep38-batch V.2

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-74


title: nulliparous-rep38-batch V.5

description: gene expression


title: nulliparous-rep39-batch V.5

description: gene expression


title: Ovarian cancer tissue from Taiwan LB771


title: Ovarian cancer tissue from Japan JPKO-68


title: nulliparous-rep35-batch V.3

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-61


title: Ovarian cancer tissue from Taiwan LB957


title: nulliparous-rep36-batch V.4

description: gene expression


title: nulliparous-rep37-batch V.4

description: gene expression


title: nulliparous-rep34-batch V.3

description: gene expression


title: Ovarian cancer tissue from Taiwan LB625

value: Mucinous


title: Ovarian cancer tissue from Japan JPKO-111


title: Ovarian cancer tissue from Taiwan LB699


title: Ovarian cancer tissue from Japan JPKO-81


title: nulliparous-rep32-batch V.2

description: gene expression


title: Ovarian cancer tissue from Taiwan LB542


title: nulliparous-rep29-batch V.1

description: gene expression


title: nulliparous-rep30-batch V.6

description: gene expression


title: nulliparous-rep33-batch V.2

description: gene expression


title: nulliparous-rep28-batch V.3

description: gene expression


title: Ovarian cancer tissue from Taiwan LB165


title: nulliparous-rep31-batch V.1

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-83


title: Ovarian cancer tissue from Japan JPKO-25


title: nulliparous-rep27-batch V.7

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-110


title: Ovarian cancer tissue from Japan JPKO-59


title: nulliparous-rep26-batch V.4

description: gene expression


title: Ovarian cancer tissue from Taiwan LA805


title: nulliparous-rep23-batch V.5

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-56


title: nulliparous-rep24-batch V.6

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-66


title: Ovarian cancer tissue from Taiwan LA810


title: Ovarian cancer tissue from Taiwan LA243


title: Ovarian cancer tissue from Japan JPKO-55


title: Ovarian cancer tissue from Japan JPKO-17


title: Ovarian cancer tissue from Japan JPKO-12


title: nulliparous-rep21-batch V.1

description: gene expression


title: Ovarian cancer tissue from Taiwan LA097


title: nulliparous-rep25-batch V.2

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-42


title: parous-rep36-batch D.6

description: gene expression

value: Discovery


title: parous-rep37-batch D.8

description: gene expression


title: parous-rep35-batch D.5

description: gene expression


title: parous-rep34-batch D.3

description: gene expression


title: Ovarian cancer tissue from Taiwan L822


title: parous-rep32-batch D.3

description: gene expression


title: Ovarian cancer tissue from Taiwan L991


title: parous-rep31-batch D.3

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-23


title: parous-rep33-batch D.3

description: gene expression


title: Ovarian cancer tissue from Taiwan LD116


title: nulliparous-rep22-batch V.5

description: gene expression


title: parous-rep29-batch D.3

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-87


title: parous-rep30-batch D.3

description: gene expression


title: parous-rep26-batch D.4

description: gene expression


title: parous-rep27-batch D.4

description: gene expression


title: Ovarian cancer tissue from Taiwan LD108


title: parous-rep25-batch D.2

description: gene expression


title: Ovarian cancer tissue from Taiwan LD050


title: Ovarian cancer tissue from Japan JPKO-69


title: parous-rep24-batch D.6

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-46


title: Ovarian cancer tissue from Taiwan LD041


title: Ovarian cancer tissue from Taiwan LD048


title: parous-rep23-batch D.3

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-49


title: parous-rep28-batch D.5

description: gene expression


title: parous-rep22-batch D.3

description: gene expression


title: parous-rep21-batch D.6

description: gene expression


title: Ovarian cancer tissue from Taiwan LD029


title: parous-rep17-batch D.4

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-65


title: Ovarian cancer tissue from Taiwan LB630


title: parous-rep19-batch D.8

description: gene expression


title: parous-rep20-batch D.4

description: gene expression


title: parous-rep18-batch D.6

description: gene expression


title: parous-rep16-batch D.5

description: gene expression


title: Ovarian cancer tissue from Taiwan LB392


title: Ovarian cancer tissue from Japan JPKO-91


title: parous-rep15-batch D.3

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-1


title: Ovarian cancer tissue from Japan JPKO-6


title: Ovarian cancer tissue from Taiwan LB364


title: Ovarian cancer tissue from Taiwan LB761


title: Ovarian cancer tissue from Taiwan LB333


title: parous-rep13-batch D.7

description: gene expression


title: parous-rep11-batch D.3

description: gene expression


title: parous-rep10-batch D.5

description: gene expression


title: parous-rep12-batch D.3

description: gene expression


title: parous-rep9-batch D.5

description: gene expression


title: Ovarian cancer tissue from Taiwan LB271


title: parous-rep6-batch D.5

description: gene expression


title: parous-rep8-batch D.5

description: gene expression


title: parous-rep7-batch D.8

description: gene expression


title: 08246T1

first: Joanna

middle: Dawn

last: Holbrook

address: 30 Medical Drive

institute: Singapore Institute of Clinical Sciences

description: EA09054_0711-01F_GenomeWideSNP_6_08246T1.birdseed-v2.chp

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files were generated with GCOS, and further processed using default algorithms for normalization and genotype calling in Affymetrix Genotyping Consol.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Confidence' = strengh of the call (smaller is better); 'Signal A' = Summarized signal for allele A; 'Signal B' = Summarized signal for allele B;

extract_protocol: Acquired from Tissue Solutions Ltd

tag: tissue

value: Normal


title: 08257T1

description: EA09054_0711-01B_GenomeWideSNP_6_08257T1.birdseed-v2.chp


title: parous-rep14-batch D.5

description: gene expression


title: Ovarian cancer tissue from Taiwan LB044


title: 08255T1

description: EA09054_0711-01D_GenomeWideSNP_6_08255T1.birdseed-v2.chp


title: parous-rep5-batch D.7

description: gene expression


title: 08255T2

description: EA09054_0711-01C_GenomeWideSNP_6_08255T2.birdseed-v2.chp

value: Tumor


title: Ovarian cancer tissue from Taiwan LA731


title: parous-rep3-batch D.5

description: gene expression

value: parous


title: Ovarian cancer tissue from Japan JPKO-70


title: nulliparous-rep20-batch D.8

description: gene expression


title: 08257T2

description: EA09054_0711-01A_GenomeWideSNP_6_08257T2.birdseed-v2.chp


title: 08246T2

description: EA09054_0711-01E_GenomeWideSNP_6_08246T2.birdseed-v2.chp


title: parous-rep1-batch D.8

description: gene expression


title: nulliparous-rep19-batch D.3

description: gene expression


title: Ovarian cancer tissue from Taiwan LA590


title: parous-rep2-batch D.4

description: gene expression


title: nulliparous-rep18-batch D.3

description: gene expression


title: parous-rep4-batch D.5

description: gene expression


title: Ovarian cancer tissue from Taiwan LB310


title: nulliparous-rep17-batch D.3

description: gene expression


title: nulliparous-rep16-batch D.4

description: gene expression


title: Ovarian cancer tissue from Taiwan LA543


title: Ovarian cancer tissue from Taiwan LA554


title: 08259T1

description: EA09054_0710-12F_GenomeWideSNP_6_08259T1.birdseed-v2.chp


title: Ovarian cancer tissue from Taiwan LA527


title: 08274T2

description: EA09054_0710-12A_GenomeWideSNP_6_08274T2.birdseed-v2.chp


title: Ovarian cancer tissue from Taiwan LA473


title: Young GRK2+/- heart 2

city: Madrid

first: Lucas

last: Elisa

state: Madrid

address: Nicolas Cabrera 1

department: Molecular Biology

country: Spain

institute: Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM)

description:
4 mo GRK2+/- 2
331.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G System

data_processing: Analysis was performed using the affylmaGUI R package (Wettenhall et al., 2006). Robust Multi-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al., 2003). Next, differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (limma), included in the affylmGUI package. P-values were corrected for multiple-testing using the Benjamini-Hochberg’s method (False Discovery Rate) (Benjamini and Hochberg, 1995; Reiner et al., 2003).

organism: Mus musculus

source_name: Mouse young heart of 4 months of age

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The animals were bred and housed on a 12-hour light/dark cycle with free access to food and water.

extract_protocol: frozen heart tissue was lysed using metal beads (2 min, 30 Hz) in a Tissue Lyser (QUIAGEN), and total mRNA was extracted using Fibrous Tissue RNeasy Mini Kit (QIAGEN).Sampled with an adequate RNA quality (Bioanalyzer, Agilent 2100) were selected for analysis.

treatment_protocol: Mice were anesthetized by inhaling isoflurane and hearts were collected after heart arrest in diastole using cold intracardiac KCl injection. Hearts were rinsed with cold PBS and the third upper part was excised and treated with RNA later (QIAGEN) for 16 hours at 4ºC. Then samples were stored at -70ºC untill RNA extraction.

tag: genotype/variation

value: B6.129-Adrbk1tm1Mca/J backcrossed more than 20 generations onto C57BL/6J

value: Heart

tag: age

value: 4 months old; young


title: 08259T2

description: EA09054_0710-12E_GenomeWideSNP_6_08259T2.birdseed-v2.chp


title: 08269T1

description: EA09054_0710-12D_GenomeWideSNP_6_08269T1.birdseed-v2.chp


title: Ovarian cancer tissue from Taiwan LA269


title: Ovarian cancer tissue from Taiwan LB004


title: 08269T2

description: EA09054_0710-12C_GenomeWideSNP_6_08269T2.birdseed-v2.chp


title: nulliparous-rep15-batch D.4

description: gene expression


title: nulliparous-rep13-batch D.5

description: gene expression


title: Young GRK2+/- heart 1

description:
4 mo GRK2+/- 1
25.CEL


title: Ovarian cancer tissue from Taiwan LA073


title: nulliparous-rep14-batch D.2

description: gene expression


title: 08280T2

description: EA09054_0710-11G_GenomeWideSNP_6_08280T2.birdseed-v2.chp


title: Adult GRK2+/- heart 3 [re-analysis]

description:
9 mo GRK2+/- 3
289.CEL

value: 9 months old; adult


title: Ovarian cancer tissue from Taiwan L953


title: 08280T1

description: EA09054_0710-11H_GenomeWideSNP_6_08280T1.birdseed-v2.chp


title: Young GRK2+/- heart 3

description:
4 mo GRK2+/- 3
334.CEL


title: nulliparous-rep10-batch D.3

description: gene expression


title: Adult GRK2+/- heart 2 [re-analysis]

description:
9 mo GRK2+/- 2
280.CEL


title: 08310T1

description: EA09054_0710-11D_GenomeWideSNP_6_08310T1.birdseed-v2.chp


title: nulliparous-rep12-batch D.4

description: gene expression


title: Ovarian cancer tissue from Taiwan L609


title: Ovarian cancer tissue from Taiwan L553


title: nulliparous-rep9-batch D.7

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-2

value: serous


title: nulliparous-rep8-batch D.6

description: gene expression


title: Ovarian cancer tissue from Taiwan L513


title: nulliparous-rep7-batch D.1

description: gene expression


title: 08335T1

description: EA09054_0710-11B_GenomeWideSNP_6_08335T1.birdseed-v2.chp


title: 08310T2

description: EA09054_0710-11C_GenomeWideSNP_6_08310T2.birdseed-v2.chp


title: nulliparous-rep6-batch D.6

description: gene expression


title: Young WT heart 3

description:
4 mo WT 3
WT_335.CEL

source_name: young heart of 4 months of age

tag: genotype


title: 08335T2

description: EA09054_0710-11A_GenomeWideSNP_6_08335T2.birdseed-v2.chp


title: nulliparous-rep5-batch D.3

description: gene expression


title: Young WT heart 2

description:
4 mo WT 2
WT_332.CEL


title: Young WT heart 1

description:
4 mo WT 1
WT_24.CEL


title: Adult GRK2+/- heart 1 [re-analysis]

description:
9 mo GRK2+/- 1
273.CEL


title: Ovarian cancer tissue from Japan JPKO-64

description:
Gene Expression Data from Epithelial ovarian cancers
probe_group_file:  HuGene-1_0-st-v1.r4.pgf
meta-probeset_file:  HuGene-1_0-st-v1.r4.mps

value: mucinous-borderline


title: Ovarian cancer tissue from Japan JPKO-44


title: 08284T1

description: EA09054_0710-11F_GenomeWideSNP_6_08284T1.birdseed-v2.chp


title: nulliparous-rep4-batch D.5

description: gene expression


title: Ovarian cancer tissue from Japan JPKO-88


title: nulliparous-rep11-batch D.4

description: gene expression


title: Adult WT heart 3 [re-analysis]

description:
9 mo WT 3
WT_303.CEL

source_name: adult heart of 9 months of age


title: 08337T2

description: EA09054_0710-10G_GenomeWideSNP_6_08337T2.birdseed-v2.chp


title: 08337T1

description: EA09054_0710-10H_GenomeWideSNP_6_08337T1.birdseed-v2.chp


title: 08357T2

description: EA09054_0710-10E_GenomeWideSNP_6_08357T2.birdseed-v2.chp


title: nulliparous-rep2-batch D.7

description: gene expression


title: 08274T1

description: EA09054_0710-12B_GenomeWideSNP_6_08274T1.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-33


title: Adult WT heart 1 [re-analysis]

description:
9 mo WT 1
WT_276.CEL


title: Ovarian cancer tissue from Japan JPKO-62

value: mucinous


title: 08359T1

description: EA09054_0710-10D_GenomeWideSNP_6_08359T1.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-34


title: WT-male

city: shanghai

first: Jia-wei

last: Zhou

address: room. 319, building 23#, yueyang road No.320

country: China

institute: Institute of Neuroscience

description: Gene expression data from adult mice striatal tissue

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mus musculus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Gene array Scanner 3000.

data_processing: The data were analyzed with GCOS1.4, change gene choose standard is I or MI, ratio>=1

source_name: wild type

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from more than 10 ug total RNA using BioArray High Yield RNA Transcript Labeling kit (Expression Analysis Technical Manual, 2004, Affymetrix ).

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

treatment_protocol: Striatal tissues of the 2 months old male mice were manually selected under the dissecting scope.

tag: background strain

value: brain striatal

value: wild type


title: Ovarian cancer tissue from Japan JPKO-13


title: Drd2 KO-male

source_name: Dopamine receptor2 KO


title: Adult WT heart 2 [re-analysis]

description:
9 mo WT 2
WT_282.CEL


title: 08357T1

description: EA09054_0710-10F_GenomeWideSNP_6_08357T1.birdseed-v2.chp


title: 90715_08246T1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization

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

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


title: 90714_08246T2


title: 08359T2

description: EA09054_0710-10C_GenomeWideSNP_6_08359T2.birdseed-v2.chp


title: 90713_08255T1


title: 08360T1

description: EA09054_0710-10B_GenomeWideSNP_6_08360T1.birdseed-v2.chp


title: 90712_08255T2


title: Ovarian cancer tissue from Japan JPKO-60

value: endometroid


title: nulliparous-rep3-batch D.4

description: gene expression


title: 08362T1

description: EA09054_0710-09H_GenomeWideSNP_6_08362T1.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-31


title: Ovarian cancer tissue from Japan JPKO-63


title: Ovarian cancer tissue from Japan JPKO-80


title: 90711_08257T1


title: Ovarian cancer tissue from Japan JPKO-9


title: 90708_08259T2


title: 90707_08269T1


title: Ovarian cancer tissue from Japan JPKO-90

value: clear cell


title: 08366T2

description: EA09054_0710-09E_GenomeWideSNP_6_08366T2.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-86


title: 90710_08257T2


title: 08360T2

description: EA09054_0710-10A_GenomeWideSNP_6_08360T2.birdseed-v2.chp


title: nulliparous-rep1-batch D.1

description: gene expression

value: nulliparous


title: Ovarian cancer tissue from Japan JPKO-57


title: 90705_08274T1


title: 90706_08269T2


title: 08373T2

description: EA09054_0710-09C_GenomeWideSNP_6_08373T2.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-50


title: Ovarian cancer tissue from Japan JPKO-27


title: 08373T1

description: EA09054_0710-09D_GenomeWideSNP_6_08373T1.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-94


title: 08366T1

description: EA09054_0710-09F_GenomeWideSNP_6_08366T1.birdseed-v2.chp


title: 90703_08280T1


title: Ovarian cancer tissue from Japan JPKO-53

description:
Gene Expression Data from Epithelial ovarian cancers
probe_group_file:  HuGene-1_0-st-v1.r4.pgf
meta-probeset_file:  HuGene-1_0-st-v1.r4.mps


title: 90702_08280T2


title: 90701_08284T1


title: 90704_08274T2


title: 08375T1

description: EA09054_0710-09B_GenomeWideSNP_6_08375T1.birdseed-v2.chp


title: 08362T2

description: EA09054_0710-09G_GenomeWideSNP_6_08362T2.birdseed-v2.chp


title: 08375T2

description: EA09054_0710-09A_GenomeWideSNP_6_08375T2.birdseed-v2.chp


title: 90699_08310T1


title: 90700_08284T2


title: 90698_08310T2


title: Ovarian cancer tissue from Japan JPKO-79


title: Ovarian cancer tissue from Japan JPKO-35


title: 08379T1

description: EA09054_0710-08H_GenomeWideSNP_6_08379T1.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-16


title: 08380T1

description: EA09054_0710-08F_GenomeWideSNP_6_08380T1.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-32


title: Ovarian cancer tissue from Japan JPKO-39


title: 90697_08335T1


title: 08389T1

description: EA09054_0710-08B_GenomeWideSNP_6_08389T1.birdseed-v2.chp


title: 90696_08335T2


title: 90695_08337T1


title: Ovarian cancer tissue from Japan JPKO-67

value: serous-borderline


title: 08390T1

description: EA09054_0710-07H_GenomeWideSNP_6_08390T1.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-51


title: 08389T2

description: EA09054_0710-08A_GenomeWideSNP_6_08389T2_2.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-19


title: 90694_08337T2


title: Ovarian cancer tissue from Japan JPKO-22


title: 08380T2

description: EA09054_0710-08E_GenomeWideSNP_6_08380T2.birdseed-v2.chp


title: 90693_08357T1


title: 08384T1

description: EA09054_0710-08D_GenomeWideSNP_6_08384T1.birdseed-v2.chp


title: 08379T2

description: EA09054_0710-08G_GenomeWideSNP_6_08379T2.birdseed-v2.chp


title: 90691_08359T1


title: 90692_08357T2


title: Ovarian cancer tissue from Japan JPKO-25


title: 90689_08360T1


title: Ovarian cancer tissue from Japan JPKO-92


title: 08384T2

description: EA09054_0710-08C_GenomeWideSNP_6_08384T2.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-81


title: 90690_08359T2


title: HCC4017

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

hyb_protocol: 1.5 ug of the amplified and labeled cRNA probes was hybridized to the chip overnight at 58 degree C, then washed, blocked and detected by streptavidin-Cy3 per manufacturer's protocol.

scan_protocol: The chips were scanned by Illumina iScan system.

data_processing: Bead-level data were processed with the MBCB algorithm (Ding et al, Nucl Acids Res, 36:e58, 2008), which is a background-correction and summarization method, then quantile-normalized and log2-transformed

source_name: Lung cancer cell line

label_protocol: 500 ng of total RNA was used to label the cRNA probes by Ambion Illumina TotalPrep RNA Amplification kit (Cat# IL1791)

growth_protocol: RPMI 5% BFS

extract_protocol: Qiagen RNeasy kit including DNase1 treatment (lung cancer cell lines and HBECs); Trizol (HSAECs)

tag: cell line

value: NSCLC cell line

tag: cell line name

tag: histology

value: Large Cell

value: Caucasian

value: F


title: 08393T1

description: EA09054_0710-07D_GenomeWideSNP_6_08393T1.birdseed-v2.chp

value: Normal


title: 90688_08360T2

value: Tumor


title: 08284T2

description: EA09054_0710-11E_GenomeWideSNP_6_08284T2.birdseed-v2.chp


title: 08393T2

description: EA09054_0710-07C_GenomeWideSNP_6_08393T2.birdseed-v2.chp


title: 90687_08362T1


title: HCC4011

value: Adenocarcinoma

value: M


title: Ovarian cancer tissue from Japan JPKO-74

value: serous


title: Ovarian cancer tissue from Japan JPKO-70


title: HCC4018


title: HCC4006

tag: atcc alias


title: 08404T2

description: EA09054_0710-06G_GenomeWideSNP_6_08404T2.birdseed-v2.chp


title: 90686_08362T2


title: Ovarian cancer tissue from Japan JPKO-68

description:
Gene Expression Data from Epithelial ovarian cancers
probe_group_file:  HuGene-1_0-st-v1.r4.pgf
meta-probeset_file:  HuGene-1_0-st-v1.r4.mps


title: 08392T2

description: EA09054_0710-07E_GenomeWideSNP_6_08392T2.birdseed-v2.chp


title: HCC2935


title: 08402T1

description: EA09054_0710-07B_GenomeWideSNP_6_08402T1.birdseed-v2.chp


title: 90685_08366T1


title: 08404T1

description: EA09054_0710-06H_GenomeWideSNP_6_08404T1.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-111


title: Ovarian cancer tissue from Japan JPKO-10


title: 90684_08366T2


title: HCC2429

value: NSCLC (poorly diff)


title: 08402T2

description: EA09054_0710-07A_GenomeWideSNP_6_08402T2.birdseed-v2.chp


title: HCC2279

value: Asian


title: 90683_08373T1


title: Ovarian cancer tissue from Japan JPKO-61


title: 90682_08373T2


title: HCC2450

value: Squamous


title: Ovarian cancer tissue from Japan JPKO-83


title: HCC1833


title: 08406T2

description: EA09054_0710-06C_GenomeWideSNP_6_08406T2.birdseed-v2.chp


title: 08405T1

description: EA09054_0710-06F_GenomeWideSNP_6_08405T1.birdseed-v2.chp


title: 08405T2

description: EA09054_0710-06E_GenomeWideSNP_6_08405T2.birdseed-v2.chp


title: 90681_08375T1


title: Ovarian cancer tissue from Japan JPKO-59


title: Ovarian cancer tissue from Japan JPKO-66


title: 08406T1

description: EA09054_0710-06D_GenomeWideSNP_6_08406T1.birdseed-v2.chp


title: 90679_08379T1


title: Ovarian cancer tissue from Japan JPKO-110


title: 90680_08375T2


title: HCC1171


title: 08407T1

description: EA09054_0710-06B_GenomeWideSNP_6_08407T1.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-55


title: Ovarian cancer tissue from Japan JPKO-56


title: HCC827

value: Adenocarcinoma (BAC features)


title: HCC1359

value: Black


title: 08390T2

description: EA09054_0710-07G_GenomeWideSNP_6_08390T2.birdseed-v2.chp


title: 08410T1

description: EA09054_0710-05H_GenomeWideSNP_6_08410T1.birdseed-v2.chp


title: 90678_08379T2


title: 08411T2

description: EA09054_0710-05E_GenomeWideSNP_6_08411T2.birdseed-v2.chp


title: 08407T2

description: EA09054_0710-06A_GenomeWideSNP_6_08407T2.birdseed-v2.chp


title: 08410T2

description: EA09054_0710-05G_GenomeWideSNP_6_08410T2.birdseed-v2.chp


title: 08392T1

description: EA09054_0710-07F_GenomeWideSNP_6_08392T1.birdseed-v2.chp


title: HCC515


title: 08411T1

description: EA09054_0710-05F_GenomeWideSNP_6_08411T1.birdseed-v2.chp


title: 90676_08380T2


title: 90677_08380T1


title: HCC461


title: 90675_08384T1


title: Ovarian cancer tissue from Japan JPKO-12

description:
Gene Expression Data from Epithelial ovarian cancers
probe_group_file:  HuGene-1_0-st-v1.r4.pgf
meta-probeset_file:  HuGene-1_0-st-v1.r4.mps


title: HCC366

value: Adenosquamous


title: HCC1195

value: Adenocarcinoma (mixed)


title: Ovarian cancer tissue from Japan JPKO-17


title: 90674_08384T2


title: Ovarian cancer tissue from Japan JPKO-42


title: Ovarian cancer tissue from Japan JPKO-23


title: HCC364


title: 90673_08389T1


title: 08418T1

description: EA09054_0710-05D_GenomeWideSNP_6_08418T1.birdseed-v2.chp


title: HCC95


title: Ovarian cancer tissue from Japan JPKO-91


title: Ovarian cancer tissue from Japan JPKO-87


title: HCC44


title: Ovarian cancer tissue from Japan JPKO-69


title: Ovarian cancer tissue from Japan JPKO-65


title: 90671_08390T1


title: HCC15


title: 90672_08389T2


title: HCC78


title: Ovarian cancer tissue from Japan JPKO-49


title: H3255


title: 90670_08390T2


title: ZR7PXN47

description: EA09054_0710-05B_GenomeWideSNP_6_ZR7PXN47.birdseed-v2.chp


title: 90669_08392T1


title: ZR7PXAQH

description: EA09054_0710-05A_GenomeWideSNP_6_ZR7PXAQH.birdseed-v2.chp


title: W31ABNXB

description: EA09054_0710-04H_GenomeWideSNP_6_W31ABNXB.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-6


title: H3122

value: NSCLC


title: 08418T2

description: EA09054_0710-05C_GenomeWideSNP_6_08418T2.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-2


title: 90666_08393T2


title: H2882

value: NSCLC cell line


title: 90667_08393T1


title: 90665_08402T1


title: 90668_08392T2


title: Ovarian cancer tissue from Japan JPKO-46


title: TR9Y8A2B

description: EA09054_0710-04C_GenomeWideSNP_6_TR9Y8A2B.birdseed-v2.chp


title: H2347


title: W31ABA8F

description: EA09054_0710-04G_GenomeWideSNP_6_W31ABA8F.birdseed-v2.chp


title: H2126


title: VD1RLA6X

description: EA09054_0710-04E_GenomeWideSNP_6_VD1RLA6X.birdseed-v2.chp


title: Ovarian cancer tissue from Japan JPKO-1


title: H2887


title: VD1RLNUZ

description: EA09054_0710-04F_GenomeWideSNP_6_VD1RLNUZ.birdseed-v2.chp


title: 90664_08402T2


title: PGRZ1NVF

description: EA09054_0710-04B_GenomeWideSNP_6_PGRZ1NVF.birdseed-v2.chp


title: TR9Y8NRT

description: EA09054_0710-04D_GenomeWideSNP_6_TR9Y8NRT.birdseed-v2.chp


title: 90662_08404T2


title: H2106

value: Large Cell Neuroendocrine


title: H2077

value: Caucasian


title: 90663_08404T1


title: H2122

value: F


title: H2087


title: 90661_08405T1

value: Normal


title: 90660_08405T2

value: Tumor


title: N8FM1NI2

description: EA09054_0710-03H_GenomeWideSNP_6_N8FM1NI2.birdseed-v2.chp


title: 90659_08406T1


title: N8FM1ANF

description: EA09054_0710-03G_GenomeWideSNP_6_N8FM1ANF.birdseed-v2.chp


title: 90658_08406T2


title: PGRZ1AR6

description: EA09054_0710-04A_GenomeWideSNP_6_PGRZ1AR6.birdseed-v2.chp


title: N_CTR2_U18

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description:
CTR2
5859990059_B

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: BeadStudio software (v.1.8.0) was used to output the raw data and Bioconductor/R (v.2.8/v.2.13.1) packages were used for quantile normalization.

source_name: Control

label_protocol: Biotin

growth_protocol: IPSC-derived neuronal cultures were kept in neuron medium (Neurobasal medium supplemented with B27, BDNF, GDNF, ascorbic acid and cyclic AMP) for 2 weeks before total RNA extraction.

extract_protocol: Total RNA was extracted from neuronal cultures with RNeasy kit (Qiagen).

treatment_protocol: untreated

tag: condition

value: Control Sample

tag: cell type

value: iPSC-derived neuronal cultures


title: H2030

value: Adenocarcinoma

value: M


title: LR1SSNC6

description: EA09054_0710-03F_GenomeWideSNP_6_LR1SSNC6.birdseed-v2.chp


title: H2009


title: N_FTD1_U14

description:
FTD1
5859990059_F

source_name: Sporadic FTD

value: Sporadic frontotemporal dementia


title: N_FTD1_U30

description:
FTD1
5859990059_A


title: LR1SSALY

description: EA09054_0710-03E_GenomeWideSNP_6_LR1SSALY.birdseed-v2.chp


title: 90657_08407T1


title: N_FTD1_U1

description:
FTD1
5859990059_H


title: 90656_08407T2


title: IM3FEAP5

description: EA09054_0710-03C_GenomeWideSNP_6_IM3FEAP5.birdseed-v2.chp


title: N_CTR2_U15

description:
CTR2
5859990060_L


title: 90655_08410T1


title: N_CTR2_U21

description:
CTR2
5859990060_K


title: H1975


title: 90654_08410T2


title: 90653_08411T1


title: N_CTR2_U3

description:
CTR2
5859990060_G


title: 90652_08411T2


title: H1792


title: H1819


title: N_CTR2_U20

description:
CTR2
5859990060_E


title: DV41BABR

description: EA09054_0710-02G_GenomeWideSNP_6_DV41BABR.birdseed-v2.chp


title: CL9RTATE

description: EA09054_0710-02E_GenomeWideSNP_6_CL9RTATE.birdseed-v2.chp


title: H1993


title: R8

city: Barcelona

first: Laia

last: Agell

address: Passeig Maritim 25-29

department: Pathology

institute: FIMIM

description: Gene expression data from Human prostate cancer

hyb_protocol: Sample was hybridized to Affymetrix Human Exon 1.0 ST array using a Affymetrix GeneChip Hybridization Oven 645

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples and using core exons. The genome build was hg18.

source_name: Total RNA from human prostate cancer, Gleason 3+4

label_protocol: 100ng of total RNA from each sample, isolated from prostate biopsies included in OCT, was processed, labelled according to the Affymetrix GeneChip® Whole Transcript Sense Target Labelling Assay

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

value: prostate

tag: gleason score


title: H1781


title: FICJGAQV

description: EA09054_0710-03A_GenomeWideSNP_6_FICJGAQV.birdseed-v2.chp

source_name: FICJGAQV


title: CL9RTNUM

description: EA09054_0710-02F_GenomeWideSNP_6_CL9RTNUM.birdseed-v2.chp


title: DV41BNOH

description: EA09054_0710-02H_GenomeWideSNP_6_DV41BNOH.birdseed-v2.chp


title: R50

source_name: Total RNA from normal human prostate tissue

value: Normal human prostate tissue


title: N_FTD1_U31

description:
FTD1
5860114019_L


title: 90650_08418T2


title: R4


title: H1755


title: N_FTD1_U26

description:
FTD1
5860114019_E


title: 90651_08418T1


title: N_CTR2_U24

description:
CTR2
5859990060_C


title: H2052

value: Mesothelioma


title: H1693


title: N_FTD2_U16

description:
FTD2
5860114019_C

source_name: GRN FTD

value: Frontotemporal dementia due to GRN mutation


title: 90649_ZR7PXN47


title: H1666


title: B38W6NL3

description: EA09054_0710-02B_GenomeWideSNP_6_B38W6NL3.birdseed-v2.chp


title: B38W6ANP

description: EA09054_0710-02A_GenomeWideSNP_6_B38W6ANP.birdseed-v2.chp


title: B87XSA5V

description: EA09054_0710-02C_GenomeWideSNP_6_B87XSA5V.birdseed-v2.chp


title: R49

source_name: Total RNA from human prostate cancer, Gleason 4+5


title: H1650


title: 90648_ZR7PXAQH


title: R48


title: N_FTD1_U6

description:
FTD1
5872617023_L


title: H1437


title: N_FTD2_U4

description:
FTD2
5872617023_K


title: R46


title: R44


title: N_FTD2_U12

description:
FTD2
5872617023_J


title: 90647_W31ABNXB


title: 90646_W31ABA8F


title: H1648

value: Black


title: H1373


title: H1395


title: 3ENVANZC

description: EA09054_0710-01F_GenomeWideSNP_6_3ENVANZC.birdseed-v2.chp


title: 90644_VD1RLA6X


title: 3ENVAAQV

description: EA09054_0710-01E_GenomeWideSNP_6_3ENVAAQV.birdseed-v2.chp


title: 336MHN76

description: EA09054_0710-01D_GenomeWideSNP_6_336MHN76.birdseed-v2.chp


title: N_FTD2_U34

description:
FTD2
5872617023_B


title: R42


title: R3

source_name: Total RNA from human prostate cancer, Gleason 3+3


title: N_FTD2_U28

description:
FTD2
5872617029_L


title: R38


title: 90643_TR9Y8NRT


title: H1155


title: R37

source_name: Total RNA from human prostate cancer, Gleason 4+3


title: R40


title: 90642_TR9Y8A2B


title: IM3FENUT

description: EA09054_0710-03D_GenomeWideSNP_6_IM3FENUT.birdseed-v2.chp


title: N_FTD2_U27

description:
FTD2
5872617029_I


title: H1355


title: 336MHAXA

description: EA09054_0710-01C_GenomeWideSNP_6_336MHAXA.birdseed-v2.chp


title: 8IGVCAPM

description: EA09054_0710-01G_GenomeWideSNP_6_8IGVCAPM.birdseed-v2.chp


title: N_CTR2_U7

description:
CTR2
5872617029_K


title: 90640_PGRZ1AR6


title: 90641_PGRZ1NVF


title: N_FTD2_U5

description:
FTD2
5872617029_G


title: R34


title: H820


title: 90645_VD1RLNUZ


title: 90639_N8FM1NI2


title: 32LM7NVG

description: EA09054_0710-01B_GenomeWideSNP_6_32LM7NVG.birdseed-v2.chp


title: H661

value: Large Cell


title: 32LM7AKQ

description: EA09054_0710-01A_GenomeWideSNP_6_32LM7AKQ.birdseed-v2.chp


title: R30


title: R33


title: 90638_N8FM1ANF


title: H460

value: NSCLC cell line


title: H1299

value: Large Cell Neuroendocrine


title: 90637_LR1SSNC6


title: 90636_LR1SSALY


title: R21


title: R32


title: N_FTD1_U9

description:
FTD1
5860114010_C


title: 90635_IM3FENUT


title: 90634_IM3FEAP5


title: H647

value: Adenosquamous

value: Caucasian


title: H358


title: H441


title: N_FTD1_U2

description:
FTD1
5872617029_F


title: N_FTD2_U8

description:
FTD2
5860114010_B


title: N_CTR2_U22

description:
CTR2
5860114010_I


title: N_FTD2_U17

description:
FTD2
5860114010_E


title: 90633_FICJGNTY

source_name: FICJGNTY

value: Normal


title: N_FTD1_U19

description:
FTD1
5859990036_L


title: N_CTR2_U23

description:
CTR2
5872617023_I


title: H596


title: FICJGNTY

description: EA09054_0710-03B_GenomeWideSNP_6_FICJGNTY.birdseed-v2.chp


title: R20


title: 90632_FICJGAQV

value: Tumor


title: H290


title: A3-1 miRNA microarray - siLin28a rep2

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: A3-1 treated with siLin28a

hyb_protocol: Cy3-labelled RNA was hybridized for 20 hours at 55˚C in 20 rpm-set Agilent Hybridization Oven following the manufacturers instructions. On completion of hybridization, slides were washed with Agilent GE Wash Buffer 1 for 5 minutes at room temperature, then washed again with Agilent GE Wash Buffer 2 for 5 minutes at 37˚C.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner using one color scan setting for 8x15k array slides (Dye channel is set to Green and Green PMT is set to 100% High and 5% Low).

data_processing: The data were analyzed with Agilent Feature Extraction Software 9.5.3.1 using default analysis settings of miRNA-v1_95_May07.

source_name: cultured mouse embryonic stem cell

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 100 ng RNA using Agilent miRNA Complete Labeling and Hyb Kit according to the manufacturer's instructions.

growth_protocol: Mouse embryonic stem cell were incubated in DMEM media containing 20% FBS, non-essentail amino acid and LIF at 37˚C.

extract_protocol: Total RNA was purified with Trizol reagent (Invitrogen) according to manufacturer's protocol

treatment_protocol: Mouse embryonic stem cell were treated with siRNA for GFP or for Lin28a and incubated for 48 hours.

tag: sirna sequence


title: R13


title: H322


title: N_CTR2_U25

description:
CTR2
5859990036_J

value: Control Sample


title: R18

source_name: Total RNA from human prostate cancer, Gleason 5+4


title: A3-1 miRNA microarray - siLin28a rep1

description: A3-1 treated with siLin28a


title: N_CTR2_U11

description:
CTR2
5859990036_I

value: iPSC-derived neuronal cultures


title: N_FTD2_U13

description:
FTD2
5859990036_C


title: 90631_DV41BNOH


title: 90630_DV41BABR


title: R14


title: 90629_CL9RTNUM


title: H125


title: N_FTD1_U29

description:
FTD1
5859990036_A


title: 8IGVCNYA

description: EA09054_0710-01H_GenomeWideSNP_6_8IGVCNYA.birdseed-v2.chp


title: R19

description: Gene expression data from Human prostate cancer


title: N_CTR2_U10

description:
CTR2
5859990036_B


title: H157

value: Squamous


title: Calu-6

value: Adenocarcinoma

value: F


title: R15

value: prostate


title: H23

value: M


title: THP-1 VD+TsA 150min rep3

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
Sample name: 4790
replicate 3

data_processing: The data were normalized using VST transformation and RSN normalization used as standard approach for Illumina arrays with the R/lumi package

source_name: THP-1 cells, treated with VD+TsA for 150 min

growth_protocol: 24 h prior to the total RNA extraction one million cells were seeded in 1.5 ml phenol red-free RPMI 1640 medium supplemented with 5% activated charcoal-treated fetal calf serum (FCS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and the cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol: Total RNA was extracted using the Quick RNA Miniprep Kit (Zymo Research, HiSS Diagnostics, Freiburg, Germany) according to the manufacturers manual.

treatment_protocol: 90 min 300 nM Trichostatin A in vehicle (0.2% ethanol); 150 min 1α,25-dihydroxyvitamin D3 or TsA or 1α,25-dihydroxyvitamin D3+TsA in vehicle (0.2% ethanol)

tag: origin

value: monocytic leukemia

tag: agent

value: VD+TsA

tag: time

value: 150 min


title: H324

tag: race

value: Black

tag: gender


title: THP-1 VD+TsA 150min rep2

description:
Sample name: 4789
replicate 2


title: B87XSNUJ

description: EA09054_0710-02D_GenomeWideSNP_6_B87XSNUJ.birdseed-v2.chp

tag: tissue


title: A3-1 miRNA microarray - siGFP rep2

description: A3-1 treated with control siRNA


title: A3-1 miRNA microarray - siGFP rep1

description: A3-1 treated with control siRNA


title: 90628_CL9RTATE


title: T37

source_name: Peripheral blood

value: peripheral blood

source_name: Colorectal tumor tissue

value: colorectal tumor


title: THP-1 VD+TsA 150min rep1

description:
Sample name: 4788
replicate 1


title: THP-1 TsA 150min rep3

description:
Sample name: 4787
replicate 3

source_name: THP-1 cells, treated with TsA for 150 min

value: TsA


title: Calu-3

source_name: Lung cancer cell line

value: NSCLC cell line

tag: age

value: Caucasian


title: 90618_336MHAXA

value: Tumor


title: 90617_32LM7NVG

value: Normal


title: THP-1 TsA 150min rep2

description:
Sample name: 4786
replicate 2


title: THP-1 VD 150min rep3

description:
Sample name: 4784
replicate 3

source_name: THP-1 cells, treated with VD for 150 min

value: VD


title: 90626_B87XSA5V


title: Calu-1

value: Muco-epidermoid carcinoma


title: THP-1 TsA 150min rep1

description:
Sample name: 4785
replicate 1


title: THP-1 VD 150min rep1

description:
Sample name: 4782
replicate 1


title: THP-1 VD 150min rep2

description:
Sample name: 4783
replicate 2


title: THP-1 vehicle 150min rep3

description:
Sample name: 4781
replicate 3

source_name: THP-1 cells, treated with vehicle for 150 min

value: vehicle


title: 90624_B38W6ANP


title: THP-1 vehicle 150min rep1

description:
Sample name: 4779
replicate 1


title: T214


title: 90622_8IGVCAPM


title: 90621_3ENVANZC


title: A549

value: Adenocarcinoma


title: T213


title: 90620_3ENVAAQV


title: 90619_336MHN76


title: THP-1 TsA 90min rep3

description:
Sample name: 4775
replicate 3

source_name: THP-1 cells, treated with TsA for 90 min

value: 90 min


title: THP-1 TsA 90min rep2

description:
Sample name: 4774
replicate 2


title: T218


title: THP-1 vehicle 90min rep3

description:
Sample name: 4769
replicate 3

source_name: THP-1 cells, treated with vehicle for 90 min


title: THP-1 TsA 90min rep1

description:
Sample name: 4773
replicate 1


title: 90625_B38W6NL3


title: T114


title: 90616_32LM7AKQ


title: THP-1 vehicle 90min rep2

description:
Sample name: 4768
replicate 2


title: THP-1 vehicle 90min rep1

description:
Sample name: 4767
replicate 1


title: T112


title: Genomic DNA from 990090__N

status: Public on Oct 24 2012

first: Patrick

last: Tan

address: 8 College Rd.

institute: Duke-NUS Graduate Medical School

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridized to an Illumina HumanMethylation27 BeadChip using the standard Illumina protocol.

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

data_processing: BeadStudio software v3.2.

label: Cy5, Cy3

source_name: primary non-malignant gastric tissue

label_protocol: Standard Illumina labeling protocol.

extract_protocol: Genomic DNA was extracted from gastric tumors and gastric non-malignant samples using the Qiagen DNeasy Kit according to standard instructions.

value: primary non-malignant gastric tissue

tag: disease state

value: normal

tag: individual


title: Genomic DNA from 990396__N


title: Genomic DNA from 96141474__N


title: Genomic DNA from 990300__N


title: Genomic DNA from 32226415__N


title: Genomic DNA from 990070__N


title: Genomic DNA from 2000085__N


title: Genomic DNA from 990247__N


title: Genomic DNA from 73291145__N


title: Genomic DNA from 990046__N


title: Genomic DNA from 76629543__N


title: Genomic DNA from 980386__N


title: Genomic DNA from 990097__N


title: Genomic DNA from 990024__N


title: Genomic DNA from 46404174__N


title: Genomic DNA from 980417__N


title: Genomic DNA from 2000178__N


title: Genomic DNA from 990111__N


title: Genomic DNA from 990015__N


title: Genomic DNA from 990275__N


title: 90627_B87XSNUJ


title: Genomic DNA from 2000346__N


title: Genomic DNA from 990071__N


title: Genomic DNA from 2000201__N


title: Genomic DNA from 2000169__N


title: Genomic DNA from 2000303__N


title: Genomic DNA from 2000434__N


title: Genomic DNA from 2000441__N


title: Genomic DNA from 2000159__N


title: Genomic DNA from 2000286__N


title: Genomic DNA from 2000088__N


title: Genomic DNA from 2000040__N


title: Genomic DNA from 990413__N


title: Genomic DNA from 2000238__N


title: Genomic DNA from 2000068__N


title: Genomic DNA from 990515__N


title: Genomic DNA from 2000114__N


title: Genomic DNA from 990489__N


title: Genomic DNA from 2000479__N


title: Genomic DNA from 2000433__N


title: Genomic DNA from 990205__N


title: Genomic DNA from 2000256__N


title: Genomic DNA from 990475__N


title: Genomic DNA from 87622942__N


title: Genomic DNA from 2000362__N


title: Genomic DNA from 20263644__N


title: Genomic DNA from 58947266__N


title: Genomic DNA from 980029__N


title: Genomic DNA from 47492137__N


title: Genomic DNA from 990424__N


title: 90623_8IGVCNYA


title: Genomic DNA from 61669256__N


title: Genomic DNA from 66811693__N


title: Genomic DNA from 91596276__N


title: Genomic DNA from 990073__N


title: Genomic DNA from 57689477__N


title: Genomic DNA from 970005__N


title: Genomic DNA from 990060__N


title: Genomic DNA from 38877042__N


title: Genomic DNA from 980251__N


title: Genomic DNA from 990041__N


title: Genomic DNA from 980327__N


title: Genomic DNA from 57701999__N


title: Genomic DNA from 990412__N


title: Genomic DNA from 2000242__N


title: Genomic DNA from 980401__N


title: Genomic DNA from 980319__N


title: Genomic DNA from 970017__N


title: Genomic DNA from 980035__N


title: Genomic DNA from 990172__N


title: Genomic DNA from 980011__N


title: Genomic DNA from 990228__N


title: Genomic DNA from 990203__N


title: Genomic DNA from 980156__N


title: Genomic DNA from 980021__N


title: Genomic DNA from 980447__N


title: Genomic DNA from 990150__N


title: Genomic DNA from 990068__N


title: Genomic DNA from 2000403__N


title: Genomic DNA from 980442__N


title: Genomic DNA from 990044__N


title: Genomic DNA from 990098__N


title: Genomic DNA from 980369__N


title: Genomic DNA from 980344__N


title: Genomic DNA from 990089__N


title: Genomic DNA from 990010__N


title: Genomic DNA from 990069__N


title: Genomic DNA from 990355__N


title: Genomic DNA from 980437__N


title: Genomic DNA from 2000175__N


title: Genomic DNA from 990170__N


title: Genomic DNA from 980418__N


title: Genomic DNA from 49375233

source_name: primary gastric tumor

value: primary gastric tumor

value: gastric cancer


title: Genomic DNA from 990187


title: Genomic DNA from 980436__N


title: Genomic DNA from 990011


title: Genomic DNA from 980488


title: Genomic DNA from 2000601


title: Genomic DNA from 21080055


title: Genomic DNA from 990129__N


title: Genomic DNA from 26109694


title: Genomic DNA from 76629543


title: Genomic DNA from 73291145


title: Genomic DNA from 48982424


title: Genomic DNA from 990119__N


title: Genomic DNA from 87622942


title: Genomic DNA from 96141474


title: Genomic DNA from 32226415


title: Genomic DNA from 58947266


title: Genomic DNA from 2000721


title: Genomic DNA from 20020846


title: Genomic DNA from 68334421


title: Genomic DNA from 20020032


title: Genomic DNA from 980369


title: Genomic DNA from 46404174


title: Genomic DNA from 57689477


title: Genomic DNA from 2001123


title: Genomic DNA from 47492137


title: Genomic DNA from 990070


title: Genomic DNA from 29806547


title: Genomic DNA from 990228


title: Genomic DNA from 2000963


title: Genomic DNA from 990275


title: Genomic DNA from 2000734


title: Genomic DNA from 82973565


title: Genomic DNA from 2000892


title: Genomic DNA from 2000752


title: Genomic DNA from 20021007


title: Genomic DNA from 980327


title: Genomic DNA from 73813499


title: Genomic DNA from 2001120


title: Genomic DNA from 9432729


title: Genomic DNA from 74765340


title: Genomic DNA from 2000676


title: Genomic DNA from 2000521


title: Genomic DNA from NGCII022/CKH


title: Genomic DNA from TGCII064/SSB


title: Genomic DNA from TGCII037/LWY


title: Genomic DNA from 980442


title: Genomic DNA from TGCII068/QKW


title: Genomic DNA from 2000778


title: Genomic DNA from 990097


title: Genomic DNA from 980437


title: Genomic DNA from 990355


title: Genomic DNA from TGCII024/SWM


title: Genomic DNA from NGCII007/LKB


title: Genomic DNA from TGCII069/LYK


title: Genomic DNA from 2000986


title: Genomic DNA from NGCII017/TPC


title: Genomic DNA from 980453


title: Genomic DNA from 980447


title: Genomic DNA from NGCII047/WPK


title: THP-1 vehicle 150min rep2

description:
Sample name: 4780
replicate 2

tag: cell line

value: monocytic leukemia

value: 150 min


title: Genomic DNA from NGCII040/TLK


title: Genomic DNA from NGCII014/CKC


title: Genomic DNA from TGCII042/K-S


title: Genomic DNA from 990474__N


title: Genomic DNA from TGCII035/LGS


title: Genomic DNA from NGCII052/G-C


title: Genomic DNA from 2000618


title: Genomic DNA from TGCII033/KHK


title: Genomic DNA from NGCII011/LGE


title: Genomic DNA from NGCII035/PCC


title: Genomic DNA from NGCII055/KYF


title: Genomic DNA from NGCII038/LYC


title: Genomic DNA from TGCII039/TSC


title: Genomic DNA from NGCII050/I-Y


title: Genomic DNA from NGCII028/LGL


title: Genomic DNA from 990015


title: Genomic DNA from 7847924


title: Genomic DNA from 2000040


title: Genomic DNA from NGCII074/TWC


title: Genomic DNA from 990010


title: Genomic DNA from 990069


title: Genomic DNA from TGCII043/WKF


title: Genomic DNA from NGCII068/J-W


title: Genomic DNA from TGCII025/PHW


title: Genomic DNA from 990489


title: Genomic DNA from 990046


title: Genomic DNA from 990300


title: Genomic DNA from 990273


title: Genomic DNA from 2000085


title: Genomic DNA from 990412


title: Genomic DNA from 980417


title: Genomic DNA from 47149013


title: Genomic DNA from 78373410


title: Genomic DNA from 990044


title: Genomic DNA from 990024


title: Genomic DNA from 990089


title: Genomic DNA from 980401


title: Genomic DNA from 990071


title: Genomic DNA from 990119


title: Genomic DNA from 980386


title: Genomic DNA from 990339


title: Genomic DNA from 10390127


title: Genomic DNA from TGCII047/LAK


title: Genomic DNA from NGCII005/K-D


title: Genomic DNA from NGCII032/TKK


title: Genomic DNA from 980319


title: Genomic DNA from 990090


title: Genomic DNA from 98748381


title: Genomic DNA from 990041


title: Genomic DNA from 20020195


title: Genomic DNA from 20020361


title: Genomic DNA from 57701999


title: Genomic DNA from 990203


title: Genomic DNA from 990247


title: Genomic DNA from 2001241


title: Genomic DNA from 20020455


title: Genomic DNA from 20020999


title: Genomic DNA from 2000114


title: Genomic DNA from 31661621


title: Genomic DNA from 2000201


title: Genomic DNA from 2000256


title: Genomic DNA from 91515473


title: Genomic DNA from 990475


title: Genomic DNA from 2000242


title: Genomic DNA from 2000472


title: Genomic DNA from 2001086


title: Genomic DNA from 2000732


title: Genomic DNA from 2001190


title: Genomic DNA from 2000619


title: Genomic DNA from 77263387


title: Genomic DNA from 2000484


title: Genomic DNA from 2000159


title: Genomic DNA from 2000286


title: Genomic DNA from 2000403


title: Genomic DNA from 990413


title: Genomic DNA from 2000529


title: Genomic DNA from 2000708


title: Genomic DNA from 2000877


title: Genomic DNA from 990515


title: Genomic DNA from 2000362


title: Genomic DNA from 2000616


title: Genomic DNA from 990424


title: Genomic DNA from 2000068


title: Genomic DNA from 2000441


title: Genomic DNA from 2000238


title: Genomic DNA from TGCII021/LAH


title: Genomic DNA from 2000088


title: Genomic DNA from 2000433


title: Genomic DNA from 980436


title: Genomic DNA from 2000169


title: Genomic DNA from 990396


title: Genomic DNA from 990170


title: Genomic DNA from 2000346


title: Genomic DNA from 990111


title: Genomic DNA from TGCII046/CBP


title: Genomic DNA from 2000303


title: Genomic DNA from 2000479


title: Genomic DNA from 2001135


title: Genomic DNA from NGCII031/KCW


title: Genomic DNA from 2000175


title: Genomic DNA from NGCII006/LTE


title: Genomic DNA from 990172


title: Genomic DNA from 980418


title: Genomic DNA from TGCII045/TSL


title: Genomic DNA from 38877042


title: Genomic DNA from 990005


title: Genomic DNA from 2000178


title: Genomic DNA from 20263644


title: Genomic DNA from 61669256


title: Genomic DNA from 65256293


title: Genomic DNA from 66811693


title: Genomic DNA from 980028


title: Genomic DNA from 970032


title: Genomic DNA from 980161


title: Genomic DNA from 6412929


title: Genomic DNA from 63540193


title: Genomic DNA from 980097


title: Genomic DNA from 5218170


title: Actual Self1453 replicate 2 dye swap

city: College Station

first: Lindsay

middle: D.

last: Bennett

state: TExas

department: Biology

institute: Texas A&M University

description: WT/WT B

hyb_protocol: The washed arrays were quickly dried under a stream of nitrogen and then scanned using an Affymetrix (Santa Clara, CA) 428 array scanner.

scan_protocol: Image and data analysis were carried out with GenePix 6.1 and GeneSpring 7.3 software as previously described (PMID 12881511, 18454867).

data_processing:
Data analysis were carried out with GenePix 6.1 and GeneSpring 7.3 software as previously described (PMID 12881511, 18454867).
Data was normalized as such: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.
Data were filtered using the following criteria:  the wild type to wild type average value was required to be between 0.5 and 2.0. Genes that met these conditions were then subjected to the following restrictions: when comparing RNA from mak-1 to wild type in triplicate, values for each of the three experiments were required to be less than 0.67 or greater than 1.5 of wild type, or the average values of the 3 replicates were required to be statistically different from wild type using the student’s t-test with a p-value cutoff of 0.05  ['statistically_filtered_data.txt' available on Series records].

organism: Neurospora crassa

source_name: wild type_mycelial tissue

label_protocol: The arrays were pre-soaked and pre-hybridized to lower background fluorescence and then hybridized with the labeled cDNAs using reagents supplied in the Corning Pronto Universal Hybridization kit according to the manufacturer’s specifications.

growth_protocol: Mycelial mats of wild type and mak-1 strains were grown in constant light (LL) at 25C for 2 and 6 days, respectively,  in 1X Vogel’s, 2% glucose, 0.5% Arginine HCl, pH 6.0. A cork borer was used to cut plugs to inoculate 75mL of the same liquid media and cultures were grown in LL at 25C for 24h, transferred to constant darkness (DD) 25oC for 24 h before being harvested and total RNA extracted.

extract_protocol: RNA samples were treated with DNA-free (Ambion, Grand Island, NY) to remove residual genomic DNA, and then amplified using SenseAmp (Genisphere, Hatfield, PA). The high quality of the original and amplified RNA was confirmed with an Agilent Bioanalyzer (Santa Clara, CA) using RNA 6000 nano chips. The amplified RNA was used to prepare Cy-dye-labeled aminoallyl cDNA targets using the Pronto Indirect Labeling system (Promega, Madison, WI). Targets obtained from mutant and wild type cells at designated time points were labeled either with Cy5 or Cy3.

treatment_protocol: Mycelial tissue was harvested and ground in liquid Nitrogen. Tissue was resuspended in 0.1M Sodium Acetate, 1% sodium dodecyl sulfate (SDS), 10mM Ethylenediaminetetraacetic acid (EDTA) and RNA was extracted using acid phenol: choloroform.

tag: strain

tag: genotype/variation

value: WT

value: mycelial mats


title: Neurospora T0 M1 Cy3 WT Cy5 1412 dye swap

description: M1/WT C

source_name: mak mutant_mycelial tissue


title: Genomic DNA from 83507354


title: Genomic DNA from 980251


title: Genomic DNA from 980211


title: Genomic DNA from 980156


title: Swap 1479 replicate 2

description: M1/WT B


title: Genomic DNA from 980029


title: Genomic DNA from 15295992


title: Genomic DNA from 970024


title: Genomic DNA from 75554796


title: Genomic DNA from 31231321


title: Genomic DNA from 980095


title: Genomic DNA from 980056


title: Neurospora T0 M1 Cy5 - WT Cy3 1407 replicate 1

description: M1/WT A


title: Genomic DNA from 980011


title: Genomic DNA from 980255


title: Genomic DNA from 970017


title: Actual Self 1452 replicate 1

description: WT/WT A


title: Genomic DNA from 980252


title: Genomic DNA from 980307


title: Genomic DNA from 970005


title: Genomic DNA from 980035


title: Genomic DNA from 980148


title: Genomic DNA from 980305


title: Genomic DNA from 980184


title: Genomic DNA from 980021


title: Genomic DNA from 980025


title: Genomic DNA from 980269


title: Genomic DNA from 980002


title: Genomic DNA from 980048


title: LCH_7

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

hyb_protocol: Resulting double-stranded cDNA was used as a template to generate biotin-targeted cRNA following manufacturer’s specifications. Fifteen micrograms of the biotin labeled cRNA was fragmented to strands between 35 and 200 bases in length, 10 micrograms of which was hybridised onto the GeneChip® Human Genome U133 Plus 2.0 Array overnight in the GeneChip® Hybridisation oven 6400 using standard procedures. The arrays were washed and then stained in a GeneChip® Fluidics Station 45.

scan_protocol: Scanning was carried out with the GeneChip® Scanner 3000 and image analysis was performed using GeneChip® Operating Software.

data_processing: The data was analyzed in R statistical environment using Bioconductor packages. Normalization was done using the gcRMA algorithm

source_name: Langerhans cell histiocytosis lesion-bone

label_protocol: The preparation of labeled cRNA was performed according to the the GeneChip® Expression 3'-Amplification Reagents Two-cycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) to produce double-stranded cDNA.

extract_protocol: RNA was extrated usingTrizol according to the manufacturer's instructions.

tag: tissue origin

value: bone

value: sorted CD207+, CD1a+ LCH cells


title: Genomic DNA from 970010


title: pdC_3

source_name: peripheral blood-sorted plasmacytoid dendritic cell (pdC)

value: peripheral blood

tag: dendritic cell lineages

value: plasmacytoid dendritic cells (pDC)


title: LC_1

source_name: Skin- epidermal Langerhans cells

value: skin

value: epidermal Langerhans cells

tag: cell type

value: sorted CD1a+, epidermal Langerhans cells


title: pdC_1


title: LCH_5


title: mDC_2

source_name: peripheral blood- sorted myeloid dendritic cell (mDC1)

value: myeloid dendritic cells (mDC1)

value: sorted HLA-DR+/CD45RA hi/CD11c-/BDCA2+ cells


title: mDC_1


title: pdC_2


title: LCH_8

source_name: Langerhans cell histiocytosis lesion-mucosa

value: mucosa


title: LCH_1


title: LC_2

value: CD1a+, epidermal Langerhans cells


title: LCH_2


title: Genomic DNA from 970003

value: primary gastric tumor


title: Genomic DNA from 970001

value: gastric cancer


title: LCH_3


title: mDC_3


title: LCH_6

source_name: Langerhans cell histiocytosis lesion-skin


title: LCH_4


title: LC_3


title: human islets, ID73

status: Public on Oct 23 2012

city: Malmo

first: Anders

last: Rosengren

address: CRC 91-11 SUS

country: Sweden

institute: Lund University

description: Gene expression data from human pancreatic islets

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized onto the GeneChip® Human Gene 1.0 ST whole transcript based assay overnight in the GeneChip® Hybridization oven 6400 using standard procedures. The arrays were washed and stained in a GeneChip® Fluidics Station 450.

data_processing: The array data was summarized and normalized with Robust Multi-array Analysis (RMA) method using the software “Expression Console” (Affymetrix).

source_name: Islets from cadaver donor ID73

label_protocol: Briefly, 100-200 ng total RNA was processed as indicated by GeneChip® Expression 3’-Amplification Reagents Onecycle cDNA synthesis kit instructions (Affymetrix Inc, Santa Clara, CA, USA) was used to produce double-stranded cDNA. This was used as a template to generate biotintargeted cRNA following the manufacturer’s specifications.

extract_protocol: Total RNA was isolated with the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany). RNA quality and concentration were measured using an Agilent 2100 bioanalyzer (Bio-Rad, Hercules, CA, USA) and a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: The islets were cultured in CMRL 1066 (ICN Biomedicals, Costa Mesa, CA, USA) supplemented with 10 mM/l HEPES, 2 mM/l L-glutamine, 50 µg/ml gentamicin, 0.25 µg/ml Fungizone (GIBCO, BRL, Gaithersburg, MD, USA), 20 µg/ml ciprofloxacin (Bayer Healthcare, Leverkusen, Germany), and 10 mM/l nicotinamide at 37 °C (5% CO2) for 1–9 days prior to RNA preparation.

value: pancreatic islets

tag: Sex

value: Female

tag: bmi

tag: status

value: Non-diabetic donor


title: human islets, ID79

source_name: Islets from cadaver donor ID79

value: Male


title: human islets, ID72

source_name: Islets from cadaver donor ID72


title: human islets, ID71

source_name: Islets from cadaver donor ID71


title: human islets, ID76

source_name: Islets from cadaver donor ID75


title: human islets, ID67

source_name: Islets from cadaver donor ID67


title: human islets, ID62

source_name: Islets from cadaver donor ID62

value: Diabetic donor


title: human islets, ID80

source_name: Islets from cadaver donor ID80


title: human islets, ID66

source_name: Islets from cadaver donor ID66


title: human islets, ID58

source_name: Islets from cadaver donor ID58


title: human islets, ID69

source_name: Islets from cadaver donor ID69


title: human islets, ID51

source_name: Islets from cadaver donor ID51


title: human islets, ID59

source_name: Islets from cadaver donor ID59


title: human islets, ID54

source_name: Islets from cadaver donor ID54


title: human islets, ID60

source_name: Islets from cadaver donor ID60


title: human islets, ID78

source_name: Islets from cadaver donor ID78


title: human islets, ID61

source_name: Islets from cadaver donor ID61


title: human islets, ID70

source_name: Islets from cadaver donor ID70


title: human islets, ID64

source_name: Islets from cadaver donor ID64


title: human islets, ID77

source_name: Islets from cadaver donor ID77


title: human islets, ID56

source_name: Islets from cadaver donor ID56


title: human islets, ID55

source_name: Islets from cadaver donor ID55


title: human islets, ID74

source_name: Islets from cadaver donor ID74


title: human islets, ID63

source_name: Islets from cadaver donor ID63


title: human islets, ID65

source_name: Islets from cadaver donor ID65


title: human islets, ID50

source_name: Islets from cadaver donor ID50


title: human islets, ID68

source_name: Islets from cadaver donor ID68


title: human islets, ID57

source_name: Islets from cadaver donor ID57


title: human islets, ID52

source_name: Islets from cadaver donor ID52


title: human islets, ID53

source_name: Islets from cadaver donor ID53


title: human islets, ID49

source_name: Islets from cadaver donor ID49


title: human islets, ID43

source_name: Islets from cadaver donor ID43


title: human islets, ID47

source_name: Islets from cadaver donor ID47


title: human islets, ID45

source_name: Islets from cadaver donor ID45


title: human islets, ID36

source_name: Islets from cadaver donor ID36


title: human islets, ID42

source_name: Islets from cadaver donor ID42


title: human islets, ID32

source_name: Islets from cadaver donor ID32


title: human islets, ID37

source_name: Islets from cadaver donor ID37


title: human islets, ID46

source_name: Islets from cadaver donor ID46


title: human islets, ID35

source_name: Islets from cadaver donor ID35


title: human islets, ID31

source_name: Islets from cadaver donor ID31


title: human islets, ID38

source_name: Islets from cadaver donor ID38


title: human islets, ID48

source_name: Islets from cadaver donor ID48


title: human islets, ID29

source_name: Islets from cadaver donor ID29


title: human islets, ID44

source_name: Islets from cadaver donor ID44


title: human islets, ID30

source_name: Islets from cadaver donor ID30


title: human islets, ID39

source_name: Islets from cadaver donor ID39


title: human islets, ID40

source_name: Islets from cadaver donor ID40


title: human islets, ID41

source_name: Islets from cadaver donor ID41


title: human islets, ID26

source_name: Islets from cadaver donor ID26


title: human islets, ID33

source_name: Islets from cadaver donor ID33


title: human islets, ID27

source_name: Islets from cadaver donor ID27


title: human islets, ID34

source_name: Islets from cadaver donor ID34


title: human islets, ID28

source_name: Islets from cadaver donor ID28


title: human islets, ID23

source_name: Islets from cadaver donor ID23


title: human islets, ID22

source_name: Islets from cadaver donor ID22


title: human islets, ID24

source_name: Islets from cadaver donor ID24


title: human islets, ID25

source_name: Islets from cadaver donor ID25


title: human islets, ID16

source_name: Islets from cadaver donor ID16


title: human islets, ID20

source_name: Islets from cadaver donor ID20


title: human islets, ID19

source_name: Islets from cadaver donor ID19


title: human islets, ID21

source_name: Islets from cadaver donor ID21


title: human islets, ID13

source_name: Islets from cadaver donor ID13


title: human islets, ID12

source_name: Islets from cadaver donor ID12


title: human islets, ID14

source_name: Islets from cadaver donor ID14


title: human islets, ID6

source_name: Islets from cadaver donor ID6


title: human islets, ID5

source_name: Islets from cadaver donor ID5


title: human islets, ID11

source_name: Islets from cadaver donor ID11


title: human islets, ID7

source_name: Islets from cadaver donor ID7


title: MDA-MB-468, shTCF3-1 Wnt3A, biological rep2 [expt1]

city: Jerusalem

first: Ittai

last: Ben-Porath

address: Faculty of Medicine, Ein kerem

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University of Jerusalem

description: MDA-MB-468 cells stably infected with shRNA targeting TCF3 and treated with Wnt3A condition medium for 8 hours

hyb_protocol: 2ug ss cDNA in 80 ul were hybridized to a Mouse Gene 1.0 ST array using Affymetrix hybridization kit materials and hybridized for 17 hours at 45° at 60rpm. Post-hyb washes were done with Affymetrix wash solutions on the FS450 station using FS450_0007 protocol.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G

data_processing: Data was quantified using Affymetrix Expression Console, applying the RMA method

source_name: MDA-MB-468 Breast cancer cell line

label_protocol: 200ng TotalRNA were used. cDNA samples were generated and labeled using Affymetrix WT-cDNA synthesis and labeling kit

growth_protocol: Cells were grown under standard conditions as specified by the ATCC. 24 hours prior to RNA extraction cells were seeded at equal confluence. For mouse samples, mammary epithelium was isolated using enzimatic dissociation and total RNA was extracted

extract_protocol: Total RNA was extracted using the RNeasy Mini Plus kit (Qiagen). For mice samples, total RNA was extracted using TRI reagent (Sigma).

treatment_protocol: Infected cells were exposed to viral supernatants of specified vector in the presence of 6μg/ml polybrene. 48 hours post infection cells were placed under 1μg/ml puromycin selection. control or Wnt3A condition medium was collected from L-cells or L-Wnt3A cells receptively. Cells were treated for 8 hours prior to RNA extraction. For mouse samples, three transgenic mice K5-rtTA/tet-Tcf3 (or three tet-Tcf3 control mice) were induced for 2 days using doxycyclin.

value: MDA-MB-468 Breast cancer cell line

value: TCF3 knockdown

tag: treatment protocol

value: Wnt3A condition medium


title: human islets, ID15

source_name: Islets from cadaver donor ID15


title: human islets, ID4

source_name: Islets from cadaver donor ID4


title: human islets, ID2

source_name: Islets from cadaver donor ID2


title: human islets, ID9

source_name: Islets from cadaver donor ID9


title: human islets, ID3

source_name: Islets from cadaver donor ID3


title: MDA-MB-468, shCont Wnt3A, biological rep2 [expt1]

description: MDA-MB-468 cells stably infected with scrambled shRNA sequence and treated with Wnt3A condition medium for 8 hours

value: control


title: MDA-MB-468, shTCF3-2 Wnt3A,biological rep2 [expt1]


title: human islets, ID1

source_name: Islets from cadaver donor ID1


title: human islets, ID8

source_name: Islets from cadaver donor ID8


title: MDA-MB-468, shTCF3-2 L-cont, biological rep2 [expt1]

description: MDA-MB-468 cells stably infected with shRNA targeting TCF3 and treated with control condition medium for 8 hours

value: control condition medium


title: human islets, ID10

source_name: Islets from cadaver donor ID10


title: MDA-MB-468, shTCF3-1 Wnt3A, biological rep1 [expt1]


title: MDA-MB-468, shTCF3-2 L-cont, biological rep1 [expt1]

description: MDA-MB-468 cells stably infectedn with shRNA targeting TCF3 and treated with control condition medium for 8 hours


title: MDA-MB-468, shCont L-cont, biological rep2 [expt1]

description: MDA-MB-468 cells stably infected with scrambled shRNA sequence and treated with control condition medium for 8 hours


title: MDA-MB-468, shTCF3-2 Wnt3A, biological rep1 [expt1]


title: MDA-MB-468, shTCF3-1 L-cont, biological rep1 [expt1]


title: MDA-MB-468, shTCF3-1 L-cont, biological rep2 [expt1]


title: MDA-MB-468 shTCF3-1 untreated [expt1]

description: MDA-MB-468 cells stably infected with shRNA targeting TCF3

value: untreated


title: MDA-MB-468, shβ-catenin, untreated [expt1]

description: MDA-MB-468 cells stably infected with shRNA targeting β-catenin

value: β-catenin knockdown


title: MDA-MB-468, shCont Wnt3A, biological rep1 [expt1]


title: MDA-MB-468, shTCF3-2, untreated [expt1]


title: MDA-MB-468 shCont untreated [expt1]

description: MDA-MB-468 cells stably infected with scrambled shRNA sequence