title: HMEC rep1

description:
HMEC cells cultured in MEGM (Lonza)
HGU133(+2.0)_01_3A.CEL

tag: cell line

value: Human breast cancer-derived cell line HMEC

tag: culture medium

value: MEGM


title: LM227

status: Public on Jun 01 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_LM227_10_08_08
Inclusion number in the clinical trial : 175

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: 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.

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: WT

tag: kras mutation

value: Mutant

tag: egfr index

tag: histology-iw revised

value: Adenocarcinoma

tag: egfr-iw type

value: No

tag: kras-iw mutation  (yes/no)

value: Yes

tag: codon kras mut

tag: type of kras mut

tag: base change

value: G to A

tag: transition/transversion

value: Transition

tag: type kras aa change

value: ASP

tag: glyc replaced by c, d, v and a

value: D

tag: aa change cys vs. other

value: Other

tag: gender

value: Male

tag: race

value: White

value: IIIB

value: Former

tag: biopsy site (grouped)

tag: treatment

value: sorafenib

tag: markergroup

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

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

tag: pfsm (month)


title: LM218

description: RNA was extracted and purified from OCT-embedded core biopsies using the RNeasy Mini Kit (Qiagen) including on-column DNase (Qiagen) digestion as described by the manufacturer's 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. 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. Gene chips were scanned using a 7 G scanner (Affymetrix) and images (DAT files) were converted to CEL files using GCOS software (Affymetrix).

tag: egfr mutation

tag: kras mutation

tag: egfr index

value: erlotinib

tag: randomization date

tag: date of progression

tag: progression-free survival status

tag: progression-free survival time (months)

tag: disease

value: non small cell lung cancer

value: G to T

value: Transversion

value: VAL

value: V


title: LM237

value: WT

value: Mutant

value: Yes


title: LM131

tag: egfr activating mutation

value: unknown

tag: egfr mutation exon

value: Exon 21

tag: egfr mutation pattern

value: G to A

value: Transition

value: ASP


title: 3349

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: sham-operated rats (S), 6h after MCAO

hyb_protocol: Purified and labeled cRNA (28 pmol of Cy3 labeled cRNA) was hybridised on the Agilent followed by (manual) washing, according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 9.1.1.1).

data_processing: Data as processed by the Agilent’s Feature Extraction software (version 9.1.1.1 - feature gProcessedSignal).

organism: Rattus norvegicus

source_name: brain cortex_sham_6h_rep3

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 1 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

extract_protocol: Total RNA was extracted with Trizol followed by silica column purification (Trizol Plus RNA purification kit, cat. N 12183-555, Life Technologies, Carlsbad, CA)

tag: strain

tag: gender

value: male

tag: weight

tag: tissue

value: brain cortex

tag: time

value: 6h after MCAO


title: common lymphoblastic leukemia [common_06]

city: Padua

first: Lara

last: Mussolin

address: via Giustiniani 3

country: Italy

institute: Department of Pediatrics

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the  HG-U133 Plus2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the  GeneChip Scanner 3000.

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

source_name: common lymphoblastic leukemia bone marrow

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: tumor biopsies were send to our lab in colture medium and bone marrow aspirates in Na-citrate anticoagulant

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

value: bone marrow

tag: diagnosis


title: common lymphoblastic leukemia [common_05]

value: common  lymphoblastic leukemia bone marrow


title: LM126

tag: egfr mutation

value: non small cell lung cancer

value: G to T

value: CYS

value: C


title: common lymphoblastic leukemia [common_04]


title: common lymphoblastic leukemia [common_02]


title: 3348

description: ischemic rats undergoing MCAO with EPO treatment (IE), 2h after MCAO

source_name: brain cortex_ischemia_EPO_2h_rep3

value: 2h after MCAO

tag: treatment

value: erythropoietin


title: 3350

description: ischemic rats undergoing MCAO with saline treatment (I), 6h after MCAO

source_name: brain cortex_ischemia_6h_rep3

value: saline


title: LM229

value: Mutant

value: unknown

value: Exon 20

tag: kras mutation

tag: egfr index

value: Yes

value: GT to TA

value: Transversion

value: VAL

value: V

value: Other


title: LM118

description:
Human Gene 1.0 ST_525_LM_118_05_13_08
Inclusion number in the clinical trial : 138

value: WT

tag: histology-iw revised

value: Adenocarcinoma

tag: egfr-iw type

value: No

tag: kras-iw mutation  (yes/no)

tag: codon kras mut

tag: type of kras mut

tag: base change

tag: transition/transversion

tag: type kras aa change

tag: glyc replaced by c, d, v and a

tag: aa change cys vs. other

value: Male

tag: race

value: White

value: IV

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: common lymphoblastic leukemia [common_03]

tag: tissue

value: bone marrow

tag: diagnosis

value: common  lymphoblastic leukemia bone marrow


title: LM124

tag: egfr mutation

tag: kras mutation

value: Mutant

tag: egfr index

tag: treatment

value: erlotinib

tag: randomization date

tag: date of progression

tag: progression-free survival status

tag: progression-free survival time (months)

tag: disease

value: non small cell lung cancer

value: G to T

value: CYS

value: C


title: 3346

description: sham-operated rats (S), 2h after MCAO

source_name: brain cortex_sham_2h_rep3

tag: strain

tag: gender

value: male

tag: weight

value: brain cortex

tag: time

value: 2h after MCAO


title: 3347

description: ischemic rats undergoing MCAO with saline treatment (I), 2h after MCAO

source_name: brain cortex_ischemia_2h_rep3

value: saline


title: T-cell acute lymphoblastic leukemia [TALL_10]

source_name: T-cell acute lymphoblastic leukemia bone marrow_diagnosis


title: U373-MAML1-dn, rep 2

city: Basel

first: Roland

middle: Martin

last: Huber

state: BS

address: Hebelstrasse 20

department: Biomedicine

country: Switzerland

institute: University of Basel

description: Human glioma cell line U373 stably transfected with an MAML1-dominant-negative expression vector.

hyb_protocol: Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip(r) Scanner 3000 with autolaoader.

data_processing: Probesets were summarized and probeset-level values normalized with the justRMA() function from the R (version 2.9.0)/Bioconductor package affy (version 2.5) using the CDF environment HuGene-1_0-st-v1.r3.cdf.

source_name: glioma cell line U373, MAML1-dn expressing

label_protocol: RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix.

growth_protocol: Cells were grown in DMEM supplemented with fetal calf serum and Glutamax in 5% CO2 in a humified incubator at 37°C.

extract_protocol: Trizol extraction of total RNA followed by a purification step using Qiagen RNeasy Mini Kit was performed according to the manufacturer's instructions.

treatment_protocol: Cells were transfected by CaCl2 precipitation, selected with Geniticin and maintained in low Geneticin concentrations.

tag: cell line

tag: cell type

value: glioma

tag: vector

value: MAML1 dominant-negative


title: common lymphoblastic leukemia [common_01]

tag: tissue

tag: diagnosis


title: U373-DTX1-myc, rep 3

description: Human glioma cell line U373 stably transfected with an DTX1-myc expression vector.

source_name: glioma cell line U373, DTX1 over-expressing

value: Deltex1 (Myc-tagged)


title: T-cell acute lymphoblastic leukemia [TALL_08]

value: T-cell acute lymphoblastic leukemia bone marrow


title: U373-EGFP, rep 3

description: Human glioma cell line U373 stably transfected with an EGFP expression vector.

source_name: glioma cell line U373, EGFP expressing

value: EGFP


title: U373-DTX1-myc, rep 2


title: 3345

description: ischemic rats undergoing MCAO with EPO treatment (IE), 6h after MCAO

source_name: brain cortex_ischemia_EPO_6h_rep2

value: 6h after MCAO

value: erythropoietin


title: U373-MAML1-dn, rep 1


title: 3344

source_name: brain cortex_ischemia_6h_rep2


title: 3343

description: sham-operated rats (S), 6h after MCAO

source_name: brain cortex_sham_6h_rep2


title: T-cell acute lymphoblastic leukemia [TALL_09]

value: bone marrow


title: U373-DTX1-myc, rep 1


title: U373-EGFP, rep 2


title: T-cell acute lymphoblastic leukemia [TALL_06]


title: 3342

source_name: brain cortex_ischemia_EPO_2h_rep2


title: Malova study, patient 3548

type: genomic

city: London

first: Christopher

last: Jones

address: Paul O'Gorman Building, 72 Huntley Street

department: Gynaecological Oncology

country: United Kingdom

institute: UCL EGA Institute for Women's Health

description: Malignant ovarian tumour

hyb_protocol: Test and reference DNA samples (50 microlitres each) were combined, precipitated together with 100 micrograms of human Cot1 DNA (1 microgram/microlitre, Invitrogen) and resuspended in 100 microlitres of hybridization buffer (50% formamide, 10% dextran sulphate, 2X SSC, 2% SDS, 4 microgram/microlitre yeast tRNA). The samples were denatured at 70oC for 15mins and pre-hybridized at 37oC for 60mins. Meanwhile, array slides were denatured at 95oC for 2mins, allowed to cool and pre-hybridized in blocking buffer (25% formamide, 0.1% SDS, 5X SSC, 1g BSA) at 42oC for 60mins. The array slides were gently washed in 0.1X SSC for 30secs and spun dry at 2000rpm for 3mins. The pre-hybridized test and reference DNA samples were applied onto cover slips and hybridized onto the array slides. The slides were then transferred into a small hybridization chamber containing Whatmann 3MM paper saturated with dH20 and incubated in a rocking hybridization oven at 42oC for 24hrs. Post hybridization, slides were washed in 2X SSC, 0.1% SDS at 45oC for 15mins, then 2X SSC, 50% formamide at 45oC for 15mins, then 2X SSC, 0.1% SDS at 45oC for 30mins and finally followed by 0.2X SSC for 15mins at room temperature. Slides were spun dry in a centrifuge for 3mins at 2000rpm and stored in a dark dry container until scanning.

scan_protocol: Scanner - ScanArray Express; Collection software - ScanArray Express, Microarray Analysis System 3.0.0.16; Resolution - 5 micrometers.

data_processing: Spot identification and signal extraction using BlueFuse software (BlueGnome, Cambridge UK); spots are filtered using a BlueFuse confidence score > 0.3; spatial normalisation using MANOR; signal normalisation using LIMMA; segmentation using DNAcopy; copy number status calling using CGHcall. MANOR, LIMMA, DNAcopy and CGHcall are all Bioconductor packages (www.bioconductor.org).

label: Alexa 3

molecule: genomic DNA

source_name: Patient peripheral blood DNA

label_protocol: BioPrime Total kit (Invitrogen) using Alexa 3 and Alexa 5 dyes (Invitrogen).

extract_protocol: Desalting protocol.

tag: sample type

value: reference (normal female control)

value: female

value: peripheral blood

label: Alexa 5

source_name: FFPE tumour section

extract_protocol: Proteinase K extraction.

value: test (tumour genomic DNA)

tag: patient survival probability

tag: Stage

value: IIIC

tag: tumour type

value: serous adenocarcinoma


title: Malova study, patient 461

description: Malignant ovarian tumour


title: 3339

source_name: brain cortex_ischemia_EPO_6h_rep1

value: male

value: brain cortex

tag: treatment


title: U373-MAML1-dn, rep 3


title: T-cell acute lymphoblastic leukemia [TALL_05]


title: 3340

description: sham-operated rats (S), 2h after MCAO

source_name: brain cortex_sham_2h_rep2

value: 2h after MCAO


title: 3341

source_name: brain cortex_ischemia_2h_rep2

value: saline


title: Malova study, patient 1447

description: Malignant ovarian tumour

source_name: Pooled normal female DNA

extract_protocol: Commercial preparation.


title: Malova study, patient 715

description: Malignant ovarian tumour


title: Malova study, patient 1996

description: Malignant ovarian tumour


title: T-cell acute lymphoblastic leukemia [TALL_02]


title: 3338

source_name: brain cortex_ischemia_6h_rep1


title: Malova study, patient 3719

description: Malignant ovarian tumour


title: T-cell acute lymphoblastic leukemia [TALL_07]


title: Malova study, patient 58122

description: Malignant ovarian tumour


title: T-cell acute lymphoblastic leukemia [TALL_04]


title: T-cell acute lymphoblastic leukemia [TALL_01]


title: U373-EGFP, rep 1

value: glioma


title: 3334

description: sham-operated rats (S), 2h after MCAO

source_name: brain cortex_sham_2h_rep1


title: T lymphoblastic tumor biopsy_diagnosis [TLL_21]

source_name: lymphoblastic tumor biopsy_diagnosis

value: nodal tumor

value: lymphoblastic tumor biopsy


title: T lymphoblastic tumor biopsy_diagnosis [TLL_19]


title: Malova study, patient 4109

description: Malignant ovarian tumour


title: Malova study, patient 670

description: Malignant ovarian tumour


title: Malova study, patient 213

description: Malignant ovarian tumour


title: T lymphoblastic tumor biopsy_diagnosis [TLL_18]


title: Malova study, patient 843

description: Malignant ovarian tumour


title: Malova study, patient 1875

description: Malignant ovarian tumour


title: Malova study, patient 58256

description: Malignant ovarian tumour


title: Malova study, patient 439

description: Malignant ovarian tumour


title: Malova study, patient 1329

description: Malignant ovarian tumour


title: Malova study, patient 1551

description: Malignant ovarian tumour


title: Malova study, patient 58227

description: Malignant ovarian tumour


title: 3335

source_name: brain cortex_ischemia_2h_rep1


title: Malova study, patient 4095

description: Malignant ovarian tumour


title: Malova study, patient 1084

description: Malignant ovarian tumour


title: Day 14 vs. Day 1 Chondrocyte Comparison A

city: Lexington

first: Michael

middle: J.

last: Mienaltowski

email: M.Mski@uky.edu, mmienalt@health.usf.edu

state: KY

address: 108 Gluck Equine Research Center

department: Veterinary Science

institute: University of Kentucky

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Day 14-1 532
Source_name_ch2 = Day 1-1 635
Source_name_ch1 = Day 1-1 532
Source_name_ch2 = Day 14-1 635

hyb_protocol: Samples were labeled with an indirect labeling protocol using amino-allyl dUTP and hybridized 48 hours at 42C.

scan_protocol: Slides were scanned with a Molecular Devices GenePix Personal 4100A Scanner using GenePix Pro 5.0.

data_processing: Data analyzed by LOWESS normalization, followed by SAS-based one sample t-test.

label: AlexaFluor555, AlexaFluor647

organism: Equus caballus

source_name: Day 14 Chondrocytes (A)

label_protocol: Invitrogen Indirect PLUS Labeling

extract_protocol: Amplified RNA from total RNA

tag: Chondrocytes isolated from adult Standardbred and maintained in monolayer culture for 14 days

label: AlexaFluor647, AlexaFluor555

source_name: Day 1 Chondrocytes (A)

tag: Chondrocytes isolated from adult Standardbred and maintained in monolayer culture for 1 day


title: Day 14 vs. Day 1 Chondrocyte Comparison C

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Day 14-3 532
Source_name_ch2 = Day 1-3 635
Source_name_ch1 = Day 1-3 532
Source_name_ch2 = Day 14-3 635

source_name: Day 14 Chondrocytes (C)

source_name: Day 1 Chondrocytes (C)


title: Day 14 vs. Day 1 Chondrocyte Comparison B

description:
This "sample" represents an average of two dye swap slides. The actual channel assignments were as follows:
Source_name_ch1 = Day 14-2 532
Source_name_ch2 = Day 1-2 635
Source_name_ch1 = Day 1-2 532
Source_name_ch2 = Day 14-2 635

source_name: Day 14 Chondrocytes (B)

source_name: Day 1 Chondrocytes (B)


title: Malova study, patient 1260

description: Malignant ovarian tumour


title: T lymphoblastic tumor biopsy_diagnosis [TLL_16]


title: T lymphoblastic tumor biopsy_diagnosis [TLL_15]


title: Malova study, patient 1618

description: Malignant ovarian tumour

scan_protocol: Scanner - GenePix 4000B; Collection software - AxImageIO 2.0.2.4; Resolution - 5 micrometers.


title: Malova study, patient 58700

description: Malignant ovarian tumour


title: T lymphoblastic tumor biopsy_diagnosis [TLL_13]


title: T lymphoblastic tumor biopsy_diagnosis [TLL_17]


title: T lymphoblastic tumor biopsy_diagnosis [TLL_14]


title: Malova study, patient 1000

description: Malignant ovarian tumour


title: Malova study, patient 4179

description: Malignant ovarian tumour


title: Malova study, patient 254

description: Malignant ovarian tumour


title: Malova study, patient 1404

description: Malignant ovarian tumour


title: Malova study, patient 1886

description: Malignant ovarian tumour


title: Malova study, patient 1427

description: Malignant ovarian tumour


title: Malova study, patient 57824

description: Malignant ovarian tumour


title: T lymphoblastic tumor biopsy_diagnosis [TLL_12]


title: Malova study, patient 460

description: Malignant ovarian tumour


title: T lymphoblastic tumor biopsy_diagnosis [TLL_11]


title: Malova study, patient 4188

description: Malignant ovarian tumour


title: T-cell acute lymphoblastic leukemia [TALL_03]

source_name: T-cell acute lymphoblastic leukemia bone marrow_diagnosis


title: Malova study, patient 4006

description: Malignant ovarian tumour


title: T lymphoblastic tumor biopsy_diagnosis [TLL_10]


title: Malova study, patient 1093

description: Malignant ovarian tumour

source_name: Patient peripheral blood DNA


title: T1D lymphocytes H3K27me3

city: Duarte

first: Nancy

last: Chen

state: CA

address: 1500 Duarte Road

department: Diabetes

institute: City of Hope

description:
H3K27me3_T1D
H3K27me3 profile with pooled type 1 diabetes samples.

hyb_protocol: According to the NimbleGen kit.

scan_protocol: NimbleScan's default procedures using an Agilent Scanner.

data_processing: Mean-centered log2 ratios (Cy5/Cy3) (NimbleScan).

source_name: H3K27me3 ChIP with pooled type 1 diabetes samples

label_protocol: According to the standard NimbleGen protocol.

growth_protocol: None.

extract_protocol: Peripheral blood lymphocytes were freshly isolated from normal and T1D subjects and then crosslinked in 1% formaldehyde, sonicated to shear DNA, and immunoprecipitated with antibodies to histone PTMs. IP with no antibody was used as the Input control.

treatment_protocol: None.

value: peripheral blood lymphocytes

tag: disease status

value: type 1 diabetes

tag: chip antibody

tag: antibody vendor

value: Millipore

tag: antibody catalog #

source_name: lymphocytes, no antibody control


title: Normal lymphocytes H3K27me3

description:
H3K27me3_NORMAL
H3K27me3 profile with pooled normal samples.

source_name: H3K27me3 ChIP with pooled normal samples

value: healthy, non-diabetic


title: T1D lymphocytes H4k16Ac

description:
H4K16ac_T1D
H4K16Ac profile with pooled type 1 diabetes samples.

source_name: H4K16Ac ChIP with pooled type 1 diabetes samples


title: Normal lymphocytes H4K16Ac

description:
H4K16ac_NORMAL
H4K16Ac profile with pooled normal samples.

source_name: H4K16Ac ChIP with pooled normal samples


title: T1D lymphocytes H3K9me3

description:
H3K9me3_T1D
H3K9me3 profile with pooled type 1 diabetes samples.

source_name: H3K9me3 ChIP with pooled type 1 diabetes samples

value: Abcam


title: T1D lymphocytes H3K4me3

description:
H3K4me3_T1D
H3K4me3 profile with pooled type 1 diabetes samples.

source_name: H3K4me3 ChIP with pooled type 1 diabetes samples


title: Malova study, patient 57988

description: Malignant ovarian tumour

value: reference (normal female control)

tag: gender

value: female

source_name: FFPE tumour section


title: Malova study, patient 57911

description: Malignant ovarian tumour

source_name: Pooled normal female DNA

value: test (tumour genomic DNA)


title: Normal lymphocytes H3K9me3

description:
H3K9me3_NORMAL
H3K9me3 profile with pooled normal samples.

source_name: H3K9me3 ChIP with pooled normal samples


title: Normal lymphocytes H3K4me3

description:
H3K4me3_NORMAL
H3K4me3 profile with pooled normal samples.

source_name: H3K4me3 ChIP with pooled normal samples


title: Yoked Saline STR (1901185011_K)

city: Baltimore

first: Jean Lud

last: Cadet

state: MD

address: 251 Bayview Blvd, Suite 200

department: Molecular Neuropsychiatry Research Branch

institute: NIDA, IRP

description:
1901185011_K
Yoked Saline STR

hyb_protocol: Microarray hybridization was done using RatRef-12 Expression BeadChips arrays (22 523 probes) (Illumina Inc., San Diego, CA). 750 ng of each cRNA sample were hybridized to Illumina arrays at 55°C overnight according to the Gene Expression Protocol for BeadStation (Illumina Inc.). Hybridized cRNA was detected with cyanine3-streptavidin (GE Healthcare, Piscataway, NJ) and quantified using Illumina's BeadStation 500GX scanner.

scan_protocol: Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.

data_processing: The microarray data reported in the manuscript are in accordance with MIAME guidelines. Gene expression changes caused by METH self-administration were analyzed using GeneSpring 11.0.2 software (Silicon Genetics, Redwood City, CA). Raw data were transformed using median normalization followed by unpaired t test. Functional annotation and gene classification analyses for significantly changed genes were performed using DAVID Annotation Tool (http://david.abcc.ncifcrf.gov)16 and were supported by literature searches. To concentrate on changes that could be related to gene function, we included only genes classified using DAVID Annotation Tool in further analyses and excluded all undefined (LOC and RGD) genes. Microarray results were extensively validated by qRT-PCR as described in the manuscript.

source_name: dorsal striata

label_protocol: 600 ng of total RNA from each sample was amplified using Illumina RNA Amplification kit (Ambion, Austin, TX). Single-stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP (Roche Diagnostics, Indianapolis, IN).

extract_protocol: Separate groups of rats were euthanized at 2 h, 24 h and 1 month after the last METH self-administration session. Dorsal striata were dissected from the brains and stored at -80ºC. Western blot experiments were conducted as described previously. Proteins were extracted from individual samples by sonication of the tissue in lysis buffer A (10 mM HEPES, 10mM KCl, 1.5 mM MgCl2, 1% Igepal CA) containing protease and phosphatase inhibitors (Roche Diagnostics) and centrifugation at 14 000g for 5 min at 4oC. Total RNA was isolated from the samples using RNeasy Mini Kit (QIAGEN, Valencia, CA). RNA concentration and integrity was determined using Agilent BioAnalyzer (Agilent, Santa Clara, CA). Samples were stored at -80ºC.

treatment_protocol: Male Sprague-Dawley rats (Charles River, Raleigh, NC), weighing 350-420 g, were housed individually under a reversed lighting 12-h light/dark cycle (lights on at 7:00 pm) with free access to food and water. All animal procedures were performed according to the NIH Guide for the Care and Use of Laboratory Animals and were approved by the Animal Care and Use Committee of NIDA-IRP (ASP #09-BNRB-31)

tag: strain

value: Sprague Dawley

tag: weight

value: dorsal striata

value: yoke saline


title: Malova study, patient 58044

description: Malignant ovarian tumour

value: peripheral blood

value: IIIC

value: serous adenocarcinoma


title: Malova study, patient 58072

description: Malignant ovarian tumour


title: Malova study, patient 1085

description: Malignant ovarian tumour


title: T lymphoblastic tumor biopsy_diagnosis [TLL_09]

source_name: lymphoblastic tumor biopsy_diagnosis


title: Malova study, patient 57842

description: Malignant ovarian tumour


title: T lymphoblastic tumor biopsy_diagnosis [TLL_07]


title: T lymphoblastic tumor biopsy_diagnosis [TLL_08]


title: T lymphoblastic tumor biopsy_diagnosis [TLL_05]


title: T lymphoblastic tumor biopsy_diagnosis [TLL_03]


title: Yoked Saline STR (1901185011_G)

description:
1901185011_G
Yoked Saline STR


title: T lymphoblastic tumor biopsy_diagnosis [TLL_06]


title: METH STR 24h (1901185011_A)

description:
1901185011_A
METH STR 24h

value: METH (0.1 mg/kg/injection, i.v.) during 15 h sessions for 8 d and were euthanized after 24 h


title: Yoked Saline STR (1901185009_I)

description:
1901185009_I
Yoked Saline STR


title: METH STR 24h (1901185009_J)

description:
1901185009_J
METH STR 24h


title: T lymphoblastic tumor biopsy_diagnosis [TLL_02]

value: nodal tumor


title: METH STR 24h (1901185011_I)

description:
1901185011_I
METH STR 24h


title: METH STR 24h (1901185009_F)

description:
1901185009_F
METH STR 24h


title: T1D lymphocytes H3K9Ac

description:
H3K9ac_T1D
H3K9Ac profile with pooled type 1 diabetes samples.

source_name: H3K9Ac ChIP with pooled type 1 diabetes samples

tag: cell type


title: Yoked Saline STR (1901185009_A)

description:
1901185009_A
Yoked Saline STR

tag: tissue


title: T lymphoblastic tumor biopsy_diagnosis [TLL_01]

tag: diagnosis

value: lymphoblastic tumor biopsy


title: Normal lymphocytes H3K9Ac

description:
H3K9ac_NORMAL
H3K9Ac profile with pooled normal samples.

source_name: H3K9Ac ChIP with pooled normal samples

value: peripheral blood lymphocytes


title: Yoke Saline (1897673047_K)

description:
1897673047_K
Yoke Saline


title: Meth 2hr STR (1897673047_L)

description:
1897673047_L
Meth 2hr STR

value: METH (0.1 mg/kg/injection, i.v.) during 15 h sessions for 8 d and were euthanized after 2 h


title: Yoked Saline STR (1901185009_E)

description:
1901185009_E
Yoked Saline STR


title: Yoked Saline STR (1901185011_C)

description:
1901185011_C
Yoked Saline STR


title: METH STR 24h (1901185009_B)

description:
1901185009_B
METH STR 24h


title: Yoke Saline (1897673047_I)

description:
1897673047_I
Yoke Saline


title: Malova study, patient 1118

description: Malignant ovarian tumour

tag: sample type


title: t=48,b4

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protoco

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)

source_name: FOXR1 B4 shRNA, harvested 48 hr

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: HOS cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37C

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol,

treatment_protocol: Cells were infected with viruses containing control shRNA (SHC002) or FOXR1 shRNA (B4 and B8) at an MOI of 3 and harvested at the indicated time points.  Time point 0 is a 'No Virus' control profile of HOS

tag: cell line

value: Human Osteosarcoma (HOS)

tag: transduced with

value: FOXR1 B4 shRNA (B4)

tag: harvest time point

value: 48 hr


title: Meth 2hr STR (1897673047_J)

description:
1897673047_J
Meth 2hr STR

tag: treatment


title: Meth 2hr STR (1897673047_H)

description:
1897673047_H
Meth 2hr STR


title: Meth 2hr STR (1897673047_F)

description:
1897673047_F
Meth 2hr STR


title: t=48,SHC002

source_name: Control shRNA, harvested 48 hr

value: Control shRNA (SHC002)


title: t=24,b8

source_name: FOXR1 B8 shRNA, harvested 24 hr

value: FOXR1 B8 shRNA (B8)

value: 24 hr


title: Yoke Saline (1897673047_G)

description:
1897673047_G
Yoke Saline

value: Sprague Dawley


title: Meth 2hr STR (1897673047_B)

description:
1897673047_B
Meth 2hr STR

value: dorsal striata


title: t=24,b4

source_name: FOXR1 B4 shRNA, harvested 24 hr


title: Yoke Saline (1897673047_E)

description:
1897673047_E
Yoke Saline

value: yoke saline


title: t=16,b8

source_name: FOXR1 B8 shRNA, harvested 16 hr

value: 16 hr


title: Meth 2hr STR (1897673047_D)

description:
1897673047_D
Meth 2hr STR


title: METH STR 24h (1901185011_E)

description:
1901185011_E
METH STR 24h


title: t=24,SHC002

source_name: Control shRNA, harvested 24 hr


title: Yoke Saline (1897673047_A)

description:
1897673047_A
Yoke Saline


title: Malova study, patient 58113

description: Malignant ovarian tumour

hyb_protocol: Test and reference DNA samples (50 microlitres each) were combined, precipitated together with 100 micrograms of human Cot1 DNA (1 microgram/microlitre, Invitrogen) and resuspended in 100 microlitres of hybridization buffer (50% formamide, 10% dextran sulphate, 2X SSC, 2% SDS, 4 microgram/microlitre yeast tRNA). The samples were denatured at 70oC for 15mins and pre-hybridized at 37oC for 60mins. Meanwhile, array slides were denatured at 95oC for 2mins, allowed to cool and pre-hybridized in blocking buffer (25% formamide, 0.1% SDS, 5X SSC, 1g BSA) at 42oC for 60mins. The array slides were gently washed in 0.1X SSC for 30secs and spun dry at 2000rpm for 3mins. The pre-hybridized test and reference DNA samples were applied onto cover slips and hybridized onto the array slides. The slides were then transferred into a small hybridization chamber containing Whatmann 3MM paper saturated with dH20 and incubated in a rocking hybridization oven at 42oC for 24hrs. Post hybridization, slides were washed in 2X SSC, 0.1% SDS at 45oC for 15mins, then 2X SSC, 50% formamide at 45oC for 15mins, then 2X SSC, 0.1% SDS at 45oC for 30mins and finally followed by 0.2X SSC for 15mins at room temperature. Slides were spun dry in a centrifuge for 3mins at 2000rpm and stored in a dark dry container until scanning

scan_protocol: Scanner - ScanArray Express; Collection software - ScanArray Express, Microarray Analysis System 3.0.0.16; Resolution - 5 micrometers

data_processing: Spot identification and signal extraction using BlueFuse software (BlueGnome, Cambridge UK); spots are filtered using a BlueFuse onfidence score > 0.3; spatial normalisation using MANOR; signal normalisation using LIMMA; segmentation using DNAcopy; copy number status calling using CGHcall; MANOR, LIMMA, DNAcopy and CGHcall are all Bioconductor packages (www.bioconductor.org)

source_name: Patient peripheral blood DNA

label_protocol: BioPrime Total (Invitrogen)

extract_protocol: Desalting protocol

tag: status

value: Reference (normal female control)

extract_protocol: Proteinase K extraction

value: Test (tumour genomic DNA)

tag: patient survival probability

tag: Stage

value: IIC

tag: tumour type

value: Serous adenocarcinoma


title: Malova study, patient 58689

description: Malignant ovarian tumour

extract_protocol: Commercial preparation

value: IC


title: Malova study, patient 58841

description: Malignant ovarian tumour

value: IIB


title: Malova study, patient 58709

description: Malignant ovarian tumour


title: Malova study, patient 1521

description: Malignant ovarian tumour

tag: patient survival probability:

value: IIIC

value: Papillary adenocarcinoma


title: Malova study, patient 57989

description: Malignant ovarian tumour


title: WT PILECs, rep1

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

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

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

data_processing: RMA by software Partek

organism: Mus musculus

source_name: TC1 Embryonic Stem Cells

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

extract_protocol: Total RNA was extracted using RNAeasy kit (Qiagen)

tag: genetic background

tag: genotype

value: Wild-type

value: ES cells were differentiated into pancreatic islet-like endocrine cells (PILECs)


title: t=16,b4

source_name: FOXR1 B4 shRNA, harvested 16 hr

value: Human Osteosarcoma (HOS)

value: FOXR1 B4 shRNA (B4)


title: t=72,b8

source_name: FOXR1 B8 shRNA, harvested 72 hr

value: FOXR1 B8 shRNA (B8)

value: 72 hr


title: WT PILECs, rep2


title: Malova study, patient 58550

description: Malignant ovarian tumour

source_name: Pooled normal female DNA

source_name: FFPE tumour section

value: IA


title: t=16,SHC002

source_name: Control shRNA, harvested at 16 hr

value: Control shRNA (SHC002)


title: Men1-KO PILECs, rep2

source_name: 3.2N Menin-null Embryonic Stem Cells


title: Malova study, patient 58193

description: Malignant ovarian tumour


title: t=72,SHC002

source_name: Control shRNA, harvested at 72 hr


title: Malova study, patient 83

description: Malignant ovarian tumour


title: Malova study, patient 58419

description: Malignant ovarian tumour


title: Yoke Saline (1897673047_C)

description:
1897673047_C
Yoke Saline

source_name: dorsal striata

tag: strain

value: Sprague Dawley

value: dorsal striata

value: yoke saline


title: Men1-KO PILECs, rep1


title: Malova study, patient 4053

description: Malignant ovarian tumour

value: Reference (normal female control)

value: Test (tumour genomic DNA)


title: t=48,b8

source_name: FOXR1 B8 shRNA, harvested 48 hr

value: 48 hr


title: t=72,b4

source_name: FOXR1 B4 shRNA, harvested 72 hr


title: Men1-KO ES cells, rep2

value: ES cell


title: Men1-KO ES cells, rep1


title: WT ES Cells (Men1), rep2


title: Malova study, patient 1323

description: Malignant ovarian tumour

value: IB

value: Serous adenocarcinoma


title: Malova study, patient 4169

description: Malignant ovarian tumour

value: IIC


title: t=0,no virus

source_name: No Virus

value: No Virus


title: Malova study, patient 1872

description: Malignant ovarian tumour


title: Malova study, patient 528

description: Malignant ovarian tumour

value: IC


title: CD34+ cells GAR-treated 7 days rep1

city: Tokyo

first: Taito

last: Nishino

address: 7-1, Kanda-nishikicyo 3-chome, Chiyodaku

country: Japan

institute: Nissan Chemical Industries, LTD

description: Gene expression data from CD34+ CD38- cells which were isolated from celtured CD34+ cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 with Hybridization, Wash and Stain Kit.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

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

source_name: CD34+ CD38- cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (3' IVT Express Kit User Manual, 2008,

growth_protocol: CD34+ cells were cultured in serum-free medium for 7 days at 37 degrees C with DMSO (Blank) or Garcinol (GAR)

extract_protocol: Extraction of total RNA was performed with Quiagen RNeasy mini kit according to the manufacturer's instructions.

treatment_protocol: 0.1% (v/v) of DMSO (Blank) or 10uM of Garcinol (GAR) was added in medium.

value: cultured CD34+ cells from cord blood

value: Garcinol


title: WT ES cells (Men1), rep1

value: Wild-type


title: Malova study, patient 3712

description: Malignant ovarian tumour


title: MMTV-iFGFR1 48 hours pool 2

city: Minneapolis

first: Kaylee

last: Schwertfeger

state: MN

address: 420 Delaware St. SE MMC 609

department: Lab Medicine and Pathology

institute: University of Minnesota

description: Gene expression data from pooled samples of macrophages (from 3 MMTV-iFGFR1 transgenic mice) following 48 hours of dimerizer treatment

hyb_protocol: standard Affymetrix hybridization protocol

scan_protocol: standard GeneChip Scanner 3000 protocol

data_processing: Microarray Suite version 5.0

source_name: Mammary gland macrophages fromMMTV-iFGFR1 transgenic mice treated with dimerizer for 48 hours

label_protocol: standard Affymetrix small sample labeling protocol

growth_protocol: 6-week-old female mice were housed under standard conditions

extract_protocol: Total RNA was isolated from the sorted cells using the PicoPure RNA isolation kit (Arcturus), following by mRNA amplification using a T7 global amplification method (Two-cycle Target Labeling kit; Affymetrix)

treatment_protocol: 6-week-old MMTV-iFGFR1 transgenic mice and non-transgenic littermates on an inbred FVB background, were injected with dimerizer to activate inducible FGFR1 for 48 hours or 4 weeks, mammary glands were harvested and digested with 2 mg/ml collagenase A for 45 minutes, Cells were washed, stained with Cd11b-PE and sorted, Samples from 3 mice were pooled for RNA extraction

value: Mammary gland macrophages

value: FVB

value: MMTV-iFGFR1 transgenic

tag: time


title: Control 4 weeks pool 2

description: Gene expression data from pooled samples of macrophages (from 3 non-transgenic mice) following 4 weeks of dimerizer treatment

source_name: Mammary gland macrophages from non-transgenic mice treated with dimerizer for 4 weeks

tag: cell type

value: control

value: 4 w


title: CD34+ cells DMSO-treated 7 days rep1

value: DMSO


title: Malova study, patient 1653

description: Malignant ovarian tumour

value: Reference (normal female control)

value: Test (tumour genomic DNA)


title: Malova study, patient 696

description: Malignant ovarian tumour


title: Malova study, patient 1451

description: Malignant ovarian tumour


title: Malova study, patient 1972

description: Malignant ovarian tumour


title: Patient-matched non-tumor control V608N

city: Brussels

first: Gil

last: Tomas

address: 808 route de Lennik

department: IRIBHM

institute: ULB

description: Patient-matched nontumor control

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files were normalized with RMA using the affy Bioconductor package

source_name: patient-matched nontumor control

label_protocol: standard Affymetrix protocol

extract_protocol: All tissues were immediately dissected, placed on ice, snap-frozen in liquid nitrogen, and stored at –80°C until processing. The ethics committees of the involved institutions approved the protocol. RNAs were prepared using TRIzol Reagent and RNeasy columns (Qiagen), followed by a verification of their quality. The Affymetrix protocol with two cycles of amplification was used and hybridizations were performed following manufacturer’s instructions.

tag: origin

value: Chernobyl

tag: dominant variant

tag: invasion capsule

tag: extra-thyroid invasion

tag: regional metastasis

tag: age at operation

tag: age at incident

tag: height (cm)

tag: weight (g)

tag: Sex

value: F

tag: braf

tag: braf delph

tag: lymphocyte infiltration

tag: sample id

tag: tissue

value: Patient-matched nontumor control


title: Malova study, patient 122

description: Malignant ovarian tumour

source_name: Patient peripheral blood DNA

tag: status

tag: patient survival probability

tag: Stage

tag: tumour type

value: Serous adenocarcinoma


title: MMTV-iFGFR1 4 weeks pool 2

source_name: Mammary gland macrophages fromMMTV-iFGFR1 transgenic mice treated with dimerizer for 4 weeks

tag: cell type

tag: genetic background

tag: genotype

tag: treatment

tag: time


title: Malova study, patient 1272

description: Malignant ovarian tumour

value: IIC


title: Malova study, patient 58105

description: Malignant ovarian tumour

value: IIA


title: Malova study, patient 4073

description: Malignant ovarian tumour

value: IC


title: T lymphoblastic tumor biopsy_diagnosis [TLL_04]

source_name: lymphoblastic tumor biopsy_diagnosis

value: nodal tumor

tag: diagnosis

value: lymphoblastic tumor biopsy


title: Papillary thyroid carcinoma V519T

description: Papillary thyroid carcinoma

source_name: tumor

tag: origin

tag: dominant variant

value: papillary

tag: invasion capsule

value: no

tag: extra-thyroid invasion

tag: regional metastasis

value: yes

tag: age at operation

tag: age at incident

tag: height (cm)

tag: weight (g)

value: Papillary thyroid carcinoma


title: Papillary thyroid carcinoma V608T

description: Papillary thyroid carcinoma

tag: Sex

tag: braf

tag: braf delph

tag: lymphocyte infiltration

tag: sample id

tag: tissue


title: Control 48 hours pool 2

description: Gene expression data from pooled samples of macrophages (from 3 non-transgenic mice) following 48 hours of dimerizer treatment

source_name: Mammary gland macrophages from non-transgenic mice treated with dimerizer for 48 hours

tag: cell type

value: Mammary gland macrophages

tag: genetic background

value: FVB

tag: genotype

value: control

tag: treatment

tag: time


title: Malova study, patient 3668

description: Malignant ovarian tumour

tag: status

value: Reference (normal female control)

source_name: FFPE tumour section

value: Test (tumour genomic DNA)

tag: patient survival probability

tag: Stage

tag: tumour type


title: Control 4 weeks pool 1

value: 4 w


title: Patient-matched non-tumor control V519N

description: Patient-matched nontumor control

tag: origin

value: Chernobyl

tag: dominant variant

tag: invasion capsule

tag: extra-thyroid invasion

tag: regional metastasis

tag: age at operation

tag: age at incident

tag: height (cm)

value: F

value: Patient-matched nontumor control


title: Malova study, patient 650

description: Malignant ovarian tumour

source_name: Pooled normal female DNA

value: Serous adenocarcinoma


title: Malova study, patient 1348

description: Malignant ovarian tumour

value: IB


title: Malova study, patient 1062

description: Malignant ovarian tumour


title: Control 48 hours pool 1

tag: cell type


title: MMTV-iFGFR1 48 hours pool 1

tag: genetic background

value: MMTV-iFGFR1 transgenic


title: Malova study, patient 1764

description: Malignant ovarian tumour

value: IA


title: Patient-matched non-tumor control S425N

description: Patient-matched nontumor control

tag: weight (g)

tag: Sex

value: M

tag: braf

tag: braf delph

tag: lymphocyte infiltration

tag: sample id

tag: tissue


title: Malova study, patient 111

description: Malignant ovarian tumour

tag: status

tag: patient survival probability

tag: Stage

tag: tumour type


title: Malova study, patient 262

description: Malignant ovarian tumour

tag: patient survival probability:

value: IV

value: Papillary adenocarcinoma


title: Papillary thyroid carcinoma S422T

description: Papillary thyroid carcinoma

tag: origin

tag: dominant variant

value: papillary

tag: invasion capsule

value: yes

tag: extra-thyroid invasion

value: no

tag: regional metastasis

tag: age at operation

value: Papillary thyroid carcinoma


title: Papillary thyroid carcinoma S423T

description: Papillary thyroid carcinoma

tag: age at incident

tag: height (cm)

tag: weight (g)

tag: Sex


title: Malova study, patient 330

description: Malignant ovarian tumour

value: Reference (normal female control)


title: Malova study, patient 1078

description: Malignant ovarian tumour

value: Test (tumour genomic DNA)

value: IIC


title: Patient-matched non-tumor control S423N

description: Patient-matched nontumor control

value: Chernobyl

tag: braf

tag: braf delph

tag: lymphocyte infiltration

tag: sample id


title: Malova study, patient 27

description: Malignant ovarian tumour

tag: status

tag: Stage

value: IIIC


title: Malova study, patient 346

description: Malignant ovarian tumour

tag: patient survival probability

tag: tumour type


title: Malova study, patient 965

description: Malignant ovarian tumour

tag: patient survival probability:


title: Malova study, patient 1421

description: Malignant ovarian tumour

value: IIIB


title: Malova study, patient 3748

description: Malignant ovarian tumour


title: Malova study, patient 3612

description: Malignant ovarian tumour


title: Patient-matched non-tumor control S422N

description: Patient-matched nontumor control

tag: origin

tag: dominant variant

tag: invasion capsule

tag: tissue

value: Patient-matched nontumor control


title: Papillary thyroid carcinoma S425T

description: Papillary thyroid carcinoma

value: follicular

tag: extra-thyroid invasion

tag: regional metastasis

tag: age at operation

tag: age at incident


title: Papillary thyroid carcinoma S420T

description: Papillary thyroid carcinoma

value: solitary

tag: height (cm)

tag: weight (g)

tag: Sex

value: F

tag: braf


title: Patient-matched non-tumor control S420N

description: Patient-matched nontumor control

tag: braf delph

tag: lymphocyte infiltration

tag: sample id


title: Malova study, patient 1982

description: Malignant ovarian tumour

tag: status

tag: Stage

tag: tumour type


title: Malova study, patient 1496

description: Malignant ovarian tumour

tag: patient survival probability:


title: Malova study, patient 58102

description: Malignant ovarian tumour


title: Malova study, patient 151

description: Malignant ovarian tumour


title: Malova study, patient 1234

description: Malignant ovarian tumour

tag: patient survival probability

value: IIB

value: Serous adenocarcinoma


title: Malova study, patient 1681

description: Malignant ovarian tumour

value: Papillary adenocarcinoma


title: Malova study, patient 4012

description: Malignant ovarian tumour


title: Papillary thyroid carcinoma S418T

description: Papillary thyroid carcinoma

tag: origin

tag: dominant variant

tag: invasion capsule

value: M

tag: tissue


title: Papillary thyroid carcinoma S415T

description: Papillary thyroid carcinoma

value: papillary

value: yes

tag: extra-thyroid invasion

tag: regional metastasis

tag: age at operation

tag: age at incident


title: Malova study, patient 57909

description: Malignant ovarian tumour

tag: sample type

value: reference (normal female control)

tag: gender

value: female

value: peripheral blood

value: test (tumour genomic DNA)

value: IV

value: serous adenocarcinoma


title: Patient-matched non-tumor control S418N

description: Patient-matched nontumor control

value: Chernobyl

tag: height (cm)

tag: weight (g)

tag: Sex

tag: braf

tag: braf delph

tag: lymphocyte infiltration


title: Papillary thyroid carcinoma S409T

description: Papillary thyroid carcinoma

value: no

tag: sample id

value: Papillary thyroid carcinoma


title: Malova study, patient 3563

description: Malignant ovarian tumour

tag: patient survival probability

tag: Stage

value: IIIB

tag: tumour type


title: Malova study, patient 3778

description: Malignant ovarian tumour

tag: tissue


title: Patient-matched non-tumor control S409N

description: Patient-matched nontumor control

tag: origin

tag: dominant variant

tag: invasion capsule

tag: extra-thyroid invasion

value: F

value: Patient-matched nontumor control


title: Papillary thyroid carcinoma PTC23

description: Papillary thyroid carcinoma

value: sporadic

value: follicular

tag: regional metastasis

tag: age at operation

tag: age at incident


title: Patient-matched non-tumor control S415N

description: Patient-matched nontumor control

tag: height (cm)

tag: weight (g)

value: M


title: Malova study, patient 4019

description: Malignant ovarian tumour

tag: status

value: Reference (normal female control)

value: Test (tumour genomic DNA)

tag: patient survival probability:

value: IIIC

value: Papillary adenocarcinoma


title: Papillary thyroid carcinoma S405T

description: Papillary thyroid carcinoma

value: papillary

value: yes

tag: Sex

tag: braf

tag: braf delph

tag: lymphocyte infiltration


title: Papillary thyroid carcinoma PTC26

description: Papillary thyroid carcinoma

tag: sample id


title: Malova study, patient 1059

description: Malignant ovarian tumour

tag: patient survival probability

tag: Stage

value: IC

tag: tumour type

value: Serous adenocarcinoma


title: Patient-matched non-tumor control S405N

description: Patient-matched nontumor control

tag: origin

value: Chernobyl

tag: dominant variant

tag: invasion capsule

tag: tissue


title: Malova study, patient 3500

description: Malignant ovarian tumour

tag: sample type

value: reference (normal female control)

tag: gender

value: female

value: peripheral blood

value: test (tumour genomic DNA)

value: IV

value: serous adenocarcinoma


title: Malova study, patient 496

description: Malignant ovarian tumour

value: IIIB


title: Papillary thyroid carcinoma PTC20

description: Papillary thyroid carcinoma

value: sporadic

value: no

tag: extra-thyroid invasion

tag: regional metastasis

tag: age at operation

tag: age at incident

tag: height (cm)

tag: weight (g)

value: F

value: Papillary thyroid carcinoma


title: Malova study, patient 1839

description: Malignant ovarian tumour

value: IIIC


title: Malova study, patient 58589

description: Malignant ovarian tumour


title: Papillary thyroid carcinoma PTC18

description: Papillary thyroid carcinoma

value: papillary

tag: Sex

tag: braf

tag: braf delph

tag: lymphocyte infiltration


title: Malova study, patient 1149

description: Malignant ovarian tumour

tag: patient survival probability

tag: Stage

tag: tumour type


title: MMTV-iFGFR1 4 weeks pool 1

description: Gene expression data from pooled samples of macrophages (from 3 MMTV-iFGFR1 transgenic mice) following 4 weeks of dimerizer treatment

tag: cell type

value: Mammary gland macrophages

tag: genetic background

value: FVB

tag: genotype

value: MMTV-iFGFR1 transgenic

tag: treatment

tag: time

value: 4 w


title: Malova study, patient 1123

description: Malignant ovarian tumour

tag: sample type

value: reference (normal female control)

tag: gender

tag: tissue


title: Malova study, patient 485

description: Malignant ovarian tumour

value: female


title: Malova study, patient 4068

description: Malignant ovarian tumour


title: Malova study, patient 58680

description: Malignant ovarian tumour


title: Malova study, patient 4047

description: Malignant ovarian tumour


title: Malova study, patient 977

description: Malignant ovarian tumour

value: peripheral blood


title: Malova study, patient 464

description: Malignant ovarian tumour

value: test (tumour genomic DNA)

value: IIIA


title: Malova study, patient 4027

description: Malignant ovarian tumour

value: IV

value: serous adenocarcinoma


title: Malova study, patient 969

description: Malignant ovarian tumour


title: Malova study, patient 4191

description: Malignant ovarian tumour


title: Papillary thyroid carcinoma PTC8

description: Papillary thyroid carcinoma

tag: origin

value: sporadic

tag: dominant variant

tag: invasion capsule

tag: extra-thyroid invasion

tag: regional metastasis

value: yes

tag: age at operation

tag: age at incident

tag: height (cm)

value: M

tag: sample id


title: Papillary thyroid carcinoma PTC9

description: Papillary thyroid carcinoma

value: no

tag: weight (g)

tag: Sex

value: F

tag: braf

tag: braf delph

tag: lymphocyte infiltration

value: Papillary thyroid carcinoma


title: Malova study, patient 58730

description: Malignant ovarian tumour

tag: sample type

tag: patient survival probability

tag: Stage

value: IIIB

tag: tumour type


title: Malova study, patient 4178

description: Malignant ovarian tumour

tag: gender

value: IIIC


title: Papillary thyroid carcinoma PTC19

description: Papillary thyroid carcinoma

tag: origin

tag: dominant variant

value: follicular

tag: invasion capsule

tag: tissue


title: Papillary thyroid carcinoma PTC14

description: Papillary thyroid carcinoma

tag: extra-thyroid invasion

tag: regional metastasis

tag: age at operation

tag: age at incident


title: Malova study, patient 420

description: Malignant ovarian tumour


title: Malova study, patient 4059

description: Malignant ovarian tumour


title: Malova study, patient 397

description: Malignant ovarian tumour


title: Malova study, patient 57830

description: Malignant ovarian tumour


title: Malova study, patient 472

description: Malignant ovarian tumour

tag: status

value: Reference (normal female control)

value: Test (tumour genomic DNA)

value: IC

value: Serous adenocarcinoma


title: Malova study, patient 321

description: Malignant ovarian tumour

value: reference (normal female control)

value: female

value: test (tumour genomic DNA)


title: Malova study, patient 4078

description: Malignant ovarian tumour

value: serous adenocarcinoma


title: Malova study, patient 3717

description: Malignant ovarian tumour

value: peripheral blood


title: Malova study, patient 1726

description: Malignant ovarian tumour

value: IV


title: Papillary thyroid carcinoma PTC6

description: Papillary thyroid carcinoma

value: sporadic

value: papillary

value: yes

tag: height (cm)

tag: weight (g)

tag: Sex

value: M

tag: braf

tag: sample id


title: Patient-matched non-tumor control NPTC26

description: Patient-matched nontumor control

value: F

tag: braf delph

tag: lymphocyte infiltration

value: Patient-matched nontumor control


title: Papillary thyroid carcinoma PTC7

description: Papillary thyroid carcinoma

value: no

value: Papillary thyroid carcinoma


title: Malova study, patient 229

description: Malignant ovarian tumour

tag: sample type

tag: gender

tag: patient survival probability

tag: Stage

value: IIIC

tag: tumour type


title: Malova study, patient 1193

description: Malignant ovarian tumour

tag: tissue

value: IIIB


title: Malova study, patient 640

description: Malignant ovarian tumour


title: Malova study, patient 1466

description: Malignant ovarian tumour

value: IIIA


title: Malova study, patient 57926

description: Malignant ovarian tumour

value: reference (normal female control)


title: Patient-matched non-tumor control NPTC23

description: Patient-matched nontumor control

tag: origin

tag: dominant variant

tag: invasion capsule

tag: extra-thyroid invasion

tag: regional metastasis


title: A2AR KO Tregs + vehicle 18 hr biological rep 1

city: Charlottesville

first: Gilbert

middle: R

last: Kinsey

state: Virginia

institute: University of Virginia

description:
Gene expression in unactivated adenosine 2A receptor KO Tregs
Treg KO Veh 1

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

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

data_processing: The data were analyzed with GCOS (GeneChip Operating Software) using Affymetrix default analysis settings.

source_name: A2AR KO Tregs + DMSO_18 hr

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChip 3'-IVT Express Kit Manual, 2008-2009, Affymetrix).

growth_protocol: Isolated Tregs were incubated in a 5% CO2 incubator at 37C for 18 hr in RPMI 1640, 10% FBS, 10 mM HEPES, 1 mM NaPyruvate, 55 mM b-mercaptoethanol with penicillin and streptomycin.

extract_protocol: Total RNA was extracted from Tregs using the Qiagen Rneasy kit according to the manufacturer's protocol.

treatment_protocol: Vehicle (DMSO) or the adenosine 2A receptor selective agonist ATL1222 (10 nM final concentration) were added at the beginning of culture.

tag: background strain

tag: genotype/variation

value: A2AR knockout (KO), A2AR-/-FoxP3GFP

tag: age

value: spleen and lymph nodes

tag: cell type

value: FACS-sorted CD4+CD25+FoxP3+ cells


title: Malova study, patient 1938

description: Malignant ovarian tumour

value: female

value: peripheral blood

value: test (tumour genomic DNA)

value: serous adenocarcinoma


title: Malova study, patient 1989

description: Malignant ovarian tumour

value: IV


title: WT Tregs + vehicle 18 hr biological rep 2

description:
Gene expression in unactivated WT Tregs
Treg WT Veh 2

source_name: WT Tregs + DMSO_18 hr

value: wild type, A2AR+/+FoxP3GFP


title: Patient-matched non-tumor control NPTC18

description: Patient-matched nontumor control

tag: age at operation

tag: age at incident

tag: height (cm)

tag: weight (g)

tag: Sex

value: F

tag: braf

tag: braf delph

tag: sample id


title: WT Tregs + ATL1222 18 hr biological rep 1

description:
Gene expression in WT Tregs after selective activation of the adenosine 2A receptor
Treg WT ATL 1

source_name: WT Tregs + ATL1222_18 hr

tag: tissue


title: Malova study, patient 1096

description: Malignant ovarian tumour

tag: sample type

tag: gender

tag: patient survival probability

tag: Stage

tag: tumour type


title: Patient-matched non-tumor control NPTC20

description: Patient-matched nontumor control

tag: origin

tag: dominant variant

tag: invasion capsule

tag: extra-thyroid invasion

tag: regional metastasis

tag: lymphocyte infiltration

value: Patient-matched nontumor control


title: WT Tregs + ATL1222 18 hr biological rep 2

description:
Gene expression in WT Tregs after selective activation of the adenosine 2A receptor
Treg WT ATL 2

tag: background strain

tag: genotype/variation

tag: age

tag: cell type


title: Patient-matched non-tumor control NPTC14

description: Patient-matched nontumor control

tag: age at operation

tag: age at incident

tag: height (cm)

tag: weight (g)

tag: Sex

value: M

tag: braf

tag: braf delph

tag: sample id


title: Malova study, patient 615

description: Malignant ovarian tumour

tag: sample type

tag: gender

tag: patient survival probability

tag: Stage

tag: tumour type


title: A2AR KO Tregs + vehicle 18 hr biological rep 2

description:
Gene expression in unactivated adenosine 2A receptor KO Tregs
Treg KO Veh 2

tag: background strain

tag: tissue


title: Malova study, patient 57880

description: Malignant ovarian tumour


title: Malova study, patient 950

description: Malignant ovarian tumour


title: WT Tregs + vehicle 18 hr biological rep 1

description:
Gene expression in unactivated WT Tregs
Treg WT Veh 1

tag: genotype/variation

tag: age


title: Malova study, patient 3730

description: Malignant ovarian tumour


title: Patient-matched non-tumor control NPTC19

description: Patient-matched nontumor control

tag: origin

tag: dominant variant

tag: invasion capsule

tag: extra-thyroid invasion

tag: regional metastasis

tag: age at operation

tag: lymphocyte infiltration


title: Malova study, patient 4061

description: Malignant ovarian tumour


title: Malova study, patient 388

description: Malignant ovarian tumour


title: Malova study, patient 3725

description: Malignant ovarian tumour


title: Patient-matched non-tumor control NPTC9

description: Patient-matched nontumor control

tag: age at incident

tag: height (cm)

tag: weight (g)

tag: Sex

tag: braf

tag: braf delph

tag: sample id


title: Patient-matched non-tumor control NPTC8

description: Patient-matched nontumor control

tag: tissue


title: M0112-3_KO-1

city: Chiba

first: ATSUSHI

last: IWAMA

address: 1-8-1 Inohana, Chuo-ku

department: Department of Cellular and Molecular Medicine

institute: Graduate School of Medicine, Chiba University

description: Gene expression data of Ezh2 KO leukemic cells

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: The arrays were scanned on the GCS 3000 Affymetrix high resolution scanner and analyzed using the GeneChip Operating Software v1.4 (GCOS; Affymetrix) and GeneSpring v7.3.1 (Agilent Technologies).

data_processing: Expression Console (affymetrix-algorithm-name = ExpressionStat, affymetrix-algorithm-version = 5.0)

source_name: Ezh2 KO leukemic cell (Purified leukemic cells from BM of recipient mice)

label_protocol: Biotinylated cRNA were prepared  from the purified total RNA equivalent to 10,000 cells according to the standard Affymetrix protocol.

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

tag: strain (of recipient mice)

tag: cell type (transplanted into recipient)

value: leukemic cell

tag: genotype/variation (of transplanted cells)

value: Ezh2 KO

tag: protocol

value: C57BL/6 recipient mice repopulated with Ink4a-/-Arf-/- BM cells


title: Anaplastic thyroid carcinoma ATC10

description: Anaplastic thyroid carcinoma

tag: origin

tag: dominant variant

tag: invasion capsule

value: Anaplastic thyroid carcinoma


title: Malova study, patient 1689

description: Malignant ovarian tumour

tag: sample type

value: reference (normal female control)

tag: gender

tag: patient survival probability

tag: Stage

value: IIIC

tag: tumour type


title: M0112-2_WT-2

description: Gene expression data of wild-type leukemic cells

source_name: Wild-type leukemic cell (Purified leukemic cells from BM of recipient mice)

value: Wild type

value: C57BL/6 recipient mice repopulated with wild-type BM cells


title: Malova study, patient 58267

description: Malignant ovarian tumour

value: female


title: Malova study, patient 58713

description: Malignant ovarian tumour


title: Malova study, patient 1748

description: Malignant ovarian tumour

value: peripheral blood


title: M0112-4_KO-2


title: Malova study, patient 1710

description: Malignant ovarian tumour

value: test (tumour genomic DNA)

value: IIIB


title: Patient-matched non-tumor control NPTC6

description: Patient-matched nontumor control

tag: extra-thyroid invasion

tag: regional metastasis

tag: age at operation

tag: age at incident

tag: height (cm)

tag: weight (g)

tag: Sex

tag: lymphocyte infiltration


title: Malova study, patient 1762

description: Malignant ovarian tumour

tag: tissue

value: serous adenocarcinoma


title: Anaplastic thyroid carcinoma ATC8

description: Anaplastic thyroid carcinoma

tag: origin

tag: braf

tag: braf delph

tag: sample id


title: Patient-matched non-tumor control NPTC7

description: Patient-matched nontumor control

tag: dominant variant

tag: invasion capsule


title: Malova study, patient 1269

description: Malignant ovarian tumour

tag: sample type

tag: gender

tag: patient survival probability

tag: Stage


title: Malova study, patient 4097

description: Malignant ovarian tumour

tag: tumour type


title: Malova study, patient 4001

description: Malignant ovarian tumour


title: Malova study, patient 58425

description: Malignant ovarian tumour


title: sorted duct cells, biological rep 2

city: Los Angeles

first: Brigitte

last: Gomperts

address: 10833 Le Conte Ave., A2-410 MDCC

department: Pediatrics

institute: UCLA

hyb_protocol: Standard Afffymetrix protocol

scan_protocol: Standard Afffymetrix protocol

data_processing: Affymetrix AGCC

source_name: TROP-2+ sorted cells from tracheal tissue after surface epithelium removed with pronase

label_protocol: Standard Afffymetrix protocol

growth_protocol: Single cell suspensions were generated from enzymatic digestion and manual dissection of proximal airways.

extract_protocol: Qiagen RNeasy kit

treatment_protocol: Cells from proximal airway surface epithelium were stained for TROP-2 and ITGA6 conjugated to PE or APC (eBioscience and Biolegend) and cells from SMG were stained for TROP-2 by incubation with the antibody for 15 minutes at room temperature followed by washing and incubation in donkey anti-goat Alexa Fluor 488 or PE.  Sorting was performed on a FACS Aria and the data analyzed with FACS Diva software (BD Biosciences).

tag: cell type

value: proximal airway duct cell

tag: tracheal section

value: upper third

tag: strain


title: Malova study, patient 212

description: Malignant ovarian tumour

extract_protocol: Desalting protocol.


title: Malova study, patient 68

description: Malignant ovarian tumour

extract_protocol: Proteinase K extraction.


title: M0112-1_WT-1

tag: strain (of recipient mice)

tag: cell type (transplanted into recipient)

tag: genotype/variation (of transplanted cells)

tag: protocol


title: Anaplastic thyroid carcinoma ATC7

description: Anaplastic thyroid carcinoma

tag: origin

tag: extra-thyroid invasion

tag: regional metastasis

tag: age at operation

tag: age at incident

tag: height (cm)

tag: weight (g)

tag: Sex

tag: braf

tag: lymphocyte infiltration

tag: tissue


title: Malova study, patient 1673

description: Malignant ovarian tumour

tag: sample type

tag: gender

tag: patient survival probability

tag: Stage

tag: tumour type


title: Anaplastic thyroid carcinoma ATC6

description: Anaplastic thyroid carcinoma

tag: dominant variant

tag: invasion capsule

tag: braf delph

tag: sample id


title: sorted duct cells, biological rep 3

tag: cell type

tag: tracheal section

tag: strain


title: Anaplastic thyroid carcinoma ATC5

description: Anaplastic thyroid carcinoma

tag: origin

tag: extra-thyroid invasion

tag: regional metastasis

tag: age at operation

tag: age at incident

tag: height (cm)

tag: weight (g)


title: Malova study, patient 3632

description: Malignant ovarian tumour

tag: sample type

tag: gender

tag: tissue

tag: patient survival probability


title: Malova study, patient 505

description: Malignant ovarian tumour

tag: Stage

tag: tumour type


title: Spleen WT

city: Salt Lake City

first: John

middle: H

last: Weis

state: UT

address: 15 North Medical Drive

department: Pathology

institute: Univ of Utah

data_processing:
per manufacturer  http://www.agilent.com/
Comparison analysis was performed using Genesifter, and ratio tables are provided as supplementary files on the Series record.

source_name: B220 B cells

label_protocol: Single color

growth_protocol: naïve mice

extract_protocol: Qiagen Rneasy kit

treatment_protocol: freshly isolated

value: Spleen


title: Anaplastic thyroid carcinoma ATC2

description: Anaplastic thyroid carcinoma

tag: dominant variant

tag: invasion capsule

tag: Sex

tag: braf

tag: braf delph

tag: lymphocyte infiltration

tag: sample id


title: Malova study, patient 4046

description: Malignant ovarian tumour

extract_protocol: Commercial preparation.

value: IV


title: Malova study, patient 4123

description: Malignant ovarian tumour


title: Malova study, patient 660

description: Malignant ovarian tumour


title: Anaplastic thyroid carcinoma ATC3

description: Anaplastic thyroid carcinoma

tag: origin

tag: extra-thyroid invasion

tag: regional metastasis

tag: age at operation


title: sorted basal cells, biological rep 1

source_name: TROP-2+ITGA6+ sorted cells from dispase digested surface epithelium

tag: cell type

value: proximal airway basal cell

tag: tracheal section

value: lower two-thirds

tag: strain


title: sorted duct cells, biological rep 1


title: Anaplastic thyroid carcinoma ATC4

description: Anaplastic thyroid carcinoma

tag: age at incident

tag: height (cm)

tag: weight (g)

tag: tissue


title: Malova study, patient 1403

description: Malignant ovarian tumour

tag: sample type

tag: gender

tag: patient survival probability

tag: Stage

tag: tumour type


title: sorted basal cells, biological rep 2


title: Spleen KO

hyb_protocol: per manufacturer  http://www.agilent.com/

value: Mef2c KO


title: Malova study, patient 402

description: Malignant ovarian tumour


title: Anaplastic thyroid carcinoma ATC1

description: Anaplastic thyroid carcinoma

tag: dominant variant

tag: invasion capsule

tag: Sex

tag: braf

tag: braf delph

tag: lymphocyte infiltration

tag: sample id

value: Anaplastic thyroid carcinoma


title: Malova study, patient 727

description: Malignant ovarian tumour

value: reference (normal female control)


title: Malova study, patient 145

description: Malignant ovarian tumour


title: Malova study, patient 4200

description: Malignant ovarian tumour


title: Bone marrow KO

scan_protocol: per manufacturer  http://www.agilent.com/

tag: strain

value: Bone Marrow


title: Malova study, patient 4008

description: Malignant ovarian tumour

value: IIIC


title: Malova study, patient 1502

description: Malignant ovarian tumour


title: Malova study, patient 957

description: Malignant ovarian tumour


title: Malova study, patient 399

description: Malignant ovarian tumour


title: Mantle cell lymphoma cells resistant to the drug at 17 hrs sample 4

city: Chicago

first: Samuel

last: McBrayer

address: 303 E Superior

institute: Northwestern University

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Quantile normalization with variance stabilizing transformation using 'lumi' R package.

label: Biotin

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

tag: cell type

value: Mantle cell lymphoma

tag: cell line

value: Granta


title: Malova study, patient 58107

description: Malignant ovarian tumour

value: female

value: peripheral blood


title: Bovine 61PP, biological rep1

city: Kagoshima

first: Dorji

last: Dorji

address: Korimoto

department: Faculty of Agriculture

institute: Kagoshima University

description: PP1 (BLASTO)

hyb_protocol: Microarray hybridizations, wash and stain were performed on the Amplified, fragmented and biotin labeled cDNA targets in triplicate for each of the experimental groups using Hybridization Wash Stain (HWS) Kit as per the manufacturer's recommendations (Affymetrix Santa Clara, CA, USA). Hybridization cocktails were made according to the NuGEN specifications. Briefly, the amplified biotin-labeled cDNA from prepubertal and adult 8- to 16-cell and day 7 blastocysts were hybridized to individual Affymetrix bovine genome arrays in a hybridization oven, set to 45°C and rotations of 60 rpm for 18 h. The genechips/arrays were washed and stained following the standard Affymetrix protocol for eukaryotic targets by using fluidics protocols FS450_0002 on Genechip Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: After hybridization, wash and stain protocol, arrays were scanned on Affymetrix GeneChip Scanner 3000.

data_processing: Affymetrix GeneChip Command Console Software (AGCC) (Affymetrix Inc., USA) was used to process image and process data files. In order to compensate for systematic technical differences between chips and to see more clearly the systematic biological differences between samples, raw data (CEL files) was normalized using Affymetrix GeneChip Microarray Suite (MAS 5.0) implemented in the AGCC software. Expression data from each array after normalization were analyzed using Rank Products (RP) incorporated in MultiExperiment Viewer (MeV) software. RP is a novel test for determining differential expressed genes with multiple replicates (Breitling et al., 2004). Expression Analysis Systematic Explorer (EASE) (Hosack et al., 2003) incorporated in MeV was used to classify the differentially expressed gene lists according to their gene ontology (GO); biological process, molecular function and cellular location.

organism: Bos taurus

source_name: Blastocysts from prepubertal heifers

label_protocol: Total RNA was amplified using WT-Ovation Pico RNA amplification system (NuGEN Technologies, Inc., San Carlos, CA, USA) following the manufacturer’s instruction. Following amplification, the synthesized cDNA was fragmented and biotin labeled using NuGEN FL-Ovation cDNA biotin module V2 (NuGEN Technologies, Inc., San Carlos, CA, USA), in accordance with the manufacturer's protocol. All samples were stored at –20°C until use. The Thermo Scientific NanoDrop 8000 spectrophotometer (NanoDrop Technologies; Wilmington, DE, USA) was used to determine the yield and purity of amplified cDNA prior to and following fragmentation/biotinylation. Only those samples yielding biotin labeled cDNA of consistent size range and quantity across samples were utilized in subsequent microarray experiments.

growth_protocol: The maturation medium used was TCM 199 (Invitrogen, Gibco, NY, USA) supplemented with 10% heat-inactivated fetal bovine serum. The COC were cultured in maturation medium at 38.5°C in a humidified atmosphere of 5% CO2 in air for 20 to 22 h for in vitro maturation (IVM). In vitro fertilization (IVF) was carried out using thawed frozen semen in Brackett-Oliphant (BO) medium. For in vitro development (IVD), presumptive zygotes were cultured in CR1aa medium supplemented with fatty acid-free BSA (Sigma) for 2 days and cultured in CR1aa medium supplemented with 10% (v/v) fetal bovine serum (FBS) for next 5 days at 38.5 °C in 5% CO2, 5% O2 and 90% N2  with high humidity.

extract_protocol: In vitro produced embryos were individually selected under a stereomicroscope for normal morphology and pooled in batches for total RNA extraction according to their developmental stages. 8- to 16-cell refers to day 3, 70 to 72 hours post insemination( hpi) preimplantation embryo stage containing 8 to 16 cells, while blastocyst refer to pre-hatching day 7 expanded blastocysts. RNA yield is lower in oocytes and cleavage stage embryos compared to blastocyst stage embryos therefore, 50 embryos per sample were collected for the early stages while 10 blastocysts were pooled for every sample.Pools of 8- to 16- cell embryos (50 in each sample) and blastocysts (10 in each sample) from prepubertal and adult groups were washed twice in Hepes-TLP-PVA by centrifugation (200 × g, 5 min each) and once in phosphate buffer saline (PBS) by centrifugation (200 x g, 5 min). The pellets were used for total RNA extraction. Total RNA was extracted from pooled 8- to 16-cell (n=50) and Blastocysts (n=10) of adult and prepubertal groups using FastPure RNA Kit (Takara Bio, Otsu, Japan), following the manufacturer’s recommended protocol. In brief, lysate was prepared from the pooled samples by homogenization using lysis and solubilization buffers. The total RNA was collected by centrifugation of the lysate through a cartridge containing the polymer filter. DNase treatment was performed in all extracted samples by DNase I (TaKaRa) while the RNA is bound to the filter to remove Residual genomic DNA to eliminate all DNA contamination. The filter was then washed several times and RNA eluted with the elution buffer. The eluted total RNA was stored at -80°C until.

tag: breed

value: Japanese black cattle

value: Prehatched expanded Blastocysts obtained at Day 7

tag: tissue source

value: prepubertal heifers


title: Mantle cell lymphoma cells resistant to the drug at 17 hrs sample 1


title: wild type, sample 1

city: Philadelphia

first: Nina

middle: Michelle

last: Bowens

state: Pennsylvania

address: 3400 Spruce Street

department: Cardiology

institute: University of Pennsylvania

description: Undifferentiated wild type embryonic stem cells

hyb_protocol: The standard hybridization protocol was used as recommended by Affymterix.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000

data_processing: Affymetrix Expression Console v1.1 RMA normalization log2

source_name: wild type, embryonic stem cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix

growth_protocol: Embryonic Stem Cells were cultured on gelatin and a MEF feeder layer in the presence 20 percent fetal bovine serum containing LIF, as previously described (Doetschman et al. 1985). Media was changed dialy.

extract_protocol: Qiagen RNeasy Mini Kit

treatment_protocol: ES cells were trypsinized  and separated from MEF cells by placing all cells in culture  with ES media for one hour. During this period MEF cells adhere while ES cells remain in suspension. ES cells in suspension were aspirated and centrifuged to form a pellet used for total RNA extraction.

value: Embryonic Stem Cell

tag: genotype

value: wild type


title: Malova study, patient 35

description: Malignant ovarian tumour

hyb_protocol: Test and reference DNA samples (50 microlitres each) were combined, precipitated together with 100 micrograms of human Cot1 DNA (1 microgram/microlitre, Invitrogen) and resuspended in 100 microlitres of hybridization buffer (50% formamide, 10% dextran sulphate, 2X SSC, 2% SDS, 4 microgram/microlitre yeast tRNA). The samples were denatured at 70oC for 15mins and pre-hybridized at 37oC for 60mins. Meanwhile, array slides were denatured at 95oC for 2mins, allowed to cool and pre-hybridized in blocking buffer (25% formamide, 0.1% SDS, 5X SSC, 1g BSA) at 42oC for 60mins. The array slides were gently washed in 0.1X SSC for 30secs and spun dry at 2000rpm for 3mins. The pre-hybridized test and reference DNA samples were applied onto cover slips and hybridized onto the array slides. The slides were then transferred into a small hybridization chamber containing Whatmann 3MM paper saturated with dH20 and incubated in a rocking hybridization oven at 42oC for 24hrs. Post hybridization, slides were washed in 2X SSC, 0.1% SDS at 45oC for 15mins, then 2X SSC, 50% formamide at 45oC for 15mins, then 2X SSC, 0.1% SDS at 45oC for 30mins and finally followed by 0.2X SSC for 15mins at room temperature. Slides were spun dry in a centrifuge for 3mins at 2000rpm and stored in a dark dry container until scanning.

scan_protocol: Scanner - ScanArray Express; Collection software - ScanArray Express, Microarray Analysis System 3.0.0.16; Resolution - 5 micrometers.

data_processing: Spot identification and signal extraction using BlueFuse software (BlueGnome, Cambridge UK); spots are filtered using a BlueFuse confidence score > 0.3; spatial normalisation using MANOR; signal normalisation using LIMMA; segmentation using DNAcopy; copy number status calling using CGHcall. MANOR, LIMMA, DNAcopy and CGHcall are all Bioconductor packages (www.bioconductor.org).

source_name: Patient peripheral blood DNA

label_protocol: BioPrime Total kit (Invitrogen) using Alexa 3 and Alexa 5 dyes (Invitrogen).

tag: sample type

tag: gender

tag: tissue

value: test (tumour genomic DNA)

value: serous adenocarcinoma


title: Malova study, patient 4195

description: Malignant ovarian tumour

tag: patient survival probability

tag: Stage

tag: tumour type


title: Mkl2-/-, sample 3

description: Undifferentiated Mkl2-/- embryonic stem cells

source_name: Mkl2-/-, embryonic stem cells


title: Ptc003

description: papillary thyroid carcinoma

extract_protocol: All patients undergoing thyroid surgery by one of the authors (TJF) had thyroid tumor samples collected at the time of surgery. Tumor tissue was dissected by a pathologist and snap frozen in liquid nitrigen and stored at -80C. RNA was extracted, following the manufacturer's protocol, from each sample after homogeneization in TRIzol reagent and RNA clean-up was performed using RNeasy MiniKit.

tag: clinical description

value: papillary thyroid carcinoma


title: Bovine 68A, biological rep3

description: A3 (BLASTO)

source_name: Blastocysts from adult cows

value: adult cows


title: Mantle cell lymphoma cells resistant to the drug at 17 hrs sample 2


title: Mantle cell lymphoma cells resistant to the drug at 17 hrs sample 3


title: wild type, sample 2


title: Mantle cell lymphoma cells resistant to the drug at 5 hrs sample 3


title: Mkl2-/-, sample 1


title: Malova study, patient 57837

description: Malignant ovarian tumour


title: Bovine 67PP, biological rep3

description: PP3 (BLASTO)


title: Bovine 65A, biological rep2

description: A2 (BLASTO)


title: Mkl2-/-, sample 2


title: Bovine 63A, biological rep1

description: A1 (BLASTO)


title: Mantle cell lymphoma cells resistant to the drug at 5 hrs sample 4


title: Bovine 64PP, biological rep2

description: PP2 (BLASTO)


title: Bone marrow WT

value: Bone marrow


title: Mantle cell lymphoma cells resistant to the drug at 5 hrs sample 2


title: PTC011

description: papillary thyroid carcinoma

source_name: tumor


title: PTC010

description: papillary thyroid carcinoma


title: Mantle cell lymphoma cells resistant to the drug at 5 hrs sample 1


title: PTC006

description: papillary thyroid carcinoma


title: PTC005

description: papillary thyroid carcinoma


title: PTC009

description: papillary thyroid carcinoma


title: PTC007

description: papillary thyroid carcinoma


title: PTC004

description: papillary thyroid carcinoma


title: Hurthle013

description: Hurthle cell adenoma

value: Hurthle cell adenoma


title: Bovine 95PP, biological rep3

description: PP3 (8-16 cell)

source_name: 8- to 16-cell stage embryos from prepubertal heifers

value: Embryos obtained at Day 3 after IVF


title: Bovine 93PP, biological rep2

description: PP2 (8-16 cell)


title: Hurthle010

description: Hurthle cell adenoma


title: Hurthle008

description: Hurthle cell adenoma


title: Mantle cell lymphoma cells resistant to the drug at start point sample 4


title: Malova study, patient 1145

description: Malignant ovarian tumour

value: reference (normal female control)

source_name: FFPE tumour section

value: IIIC


title: Hurthle012

description: Hurthle cell adenoma


title: PTC008

description: papillary thyroid carcinoma


title: Hurthle009

description: Hurthle cell adenoma


title: Hurthle011

description: Hurthle cell adenoma


title: Bovine 94A, biological rep3

description: A3 (8-16 cell)

source_name: 8- to 16-cell stage embryos from adult cows


title: Mantle cell lymphoma cells resistant to the drug at start point sample 2

value: Mantle cell lymphoma

value: Granta


title: Mantle cell lymphoma cells resistant to the drug at start point sample 3


title: Bovine 90A, biological rep1

description: A1 (8-16 cell)


title: Bovine 92PP, biological rep1

description: PP1 (8-16 cell)


title: Bovine 91A, biological rep2

description: A2 (8-16 cell)


title: Mantle cell lymphoma cells resistant to the drug at start point sample 1


title: Bovine 70 A, biological rep2

description: A2 MII

hyb_protocol: Microarray hybridizations, wash and stain were performed on the Amplified, fragmented and biotin labeled cDNA targets in triplicate for each of the experimental groups using Hybridization Wash Stain (HWS) Kit as per the manufacturer's recommendations (Affymetrix Santa Clara, CA, USA). Hybridization cocktails were made according to the NuGEN specifications. Briefly, the amplified biotin-labeled cDNA from prepubertal and adult GV and MII oocytes were hybridized to individual Affymetrix bovine genome arrays in a hybridization oven, set to 45°C and rotations of 60 rpm for 18 h. The genechips/arrays were washed and stained following the standard Affymetrix protocol for eukaryotic targets by using fluidics protocols FS450_0002 on Genechip Fluidics Station 450 (Affymetrix Inc., USA).

data_processing: Affymetrix GeneChip Command Console Software (AGCC) (Affymetrix Inc., USA) was used to process image and process data files.  In order to compensate for systematic technical differences between chips and to see more clearly the systematic biological differences between samples, raw data (CEL files) was normalized using Affymetrix GeneChip Microarray Suite (MAS 5.0) implemented in the AGCC software. Expression data from each array after normalization were analyzed using Rank Products (RP) incorporated in MultiExperiment Viewer (MeV) software. RP is a novel test for determining differential expressed genes with multiple replicates (Breitling et al., 2004).  Expression Analysis Systematic Explorer (EASE) (Hosack et al., 2003) incorporated in MeV was used to classify the differentially expressed gene lists according to their gene ontology (GO); biological process, molecular function and cellular location.

source_name: MII stage oocytes from adult cattle

growth_protocol: The Germinal Vesicle (GV) stage oocytes showing clear cytoplasm were obtained immediately after aspiration from the ovarian follicles, while MII oocytes were selected after 20 to 22 h In vitro maturation (IVM) by the presence of clearly extruded first polar body. For IVM, The COCs (70 to 80) were placed in 200 µL drop of the maturation medium (TCM 199 + 10% FBS) in petri dish (35x10mm, Becton Dickinson Labware, Oxnard, CA, USA) covered with paraffin liquid (Nacalai Tesque Inc, Kyoto, Japan) and cultured at 38.5°C in a humidified atmosphere of 5% CO2 in air for 20 to 22 h.

extract_protocol: The COCs at GV and MII stages were denuded of surrounding cumulus cells by gentle pipetting in a solution of 0.1% (w/v) hyaluronidase (Sigma, St. Louis, MO, USA). Oocytes completely denuded of cumulus cells were then individually selected under a stereomicroscope and pooled. The oocytes were washed twice in Hepes-TLP-PVA by centrifugation (200 × g, 5 min each) and once in phosphate buffer saline (PBS) by centrifugation (200 x g, 5 min). The pellets were used for total RNA extraction. Total RNA was extracted from pooled (n=50) GV and M-II oocytes  of adult and prepubertal groups using FastPure RNA Kit (Takara Bio, Otsu, Japan), according to the manufacturer's recommendations. In brief, lysate was prepared from the pooled samples by homogenization using lysis and solubilization buffers. The total RNA was collected by centrifugation of the lysate through a cartridge containing the polymer filter. DNase treatment was performed while the RNA is bound to the filter to remove even trace amounts of genomic DNA to eliminate all DNA contamination. The filter was then washed several times and RNA eluted with the elution buffer. The eluted total RNA was stored at -80°C until used for cDNA synthesis. Concentration and purity of isolated RNA were determined using Thermo Scientific NanoDrop 8000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

tag: protocol

value: Oocytes obtained after 20 to 22 h IVM

tag: group

value: Adult cow

value: MII


title: Mantle cell lymphoma cells sensitive to the drug at 17 hrs sample 4

value: Jeko


title: Hurthle007

description: Hurthle cell adenoma


title: HYP007

description: hyperplasia

value: hyperplasia


title: HYP010

description: hyperplasia


title: Hurthle002

description: Hurthle cell adenoma


title: HYP008

description: hyperplasia


title: Mantle cell lymphoma cells sensitive to the drug at 17 hrs sample 3


title: HYP009

description: hyperplasia


title: Mantle cell lymphoma cells sensitive to the drug at 17 hrs sample 2


title: HYP006

description: hyperplasia


title: Bovine 71 A, biological rep3

description: A3 MII


title: Bovine 57 PP, biological rep3

description: PP3 MII

source_name: MII stage oocytes from prepubertal heifers

value: Prepubertal heifer


title: Mantle cell lymphoma cells sensitive to the drug at 17 hrs sample 1


title: HYP005

description: hyperplasia


title: Hurthle001

description: Hurthle cell adenoma


title: HYP001

description: hyperplasia


title: HS004

description: hashimoto thyroiditis

value: hashimoto thyroiditis


title: HS006

description: hashimoto thyroiditis


title: HYP002

description: hyperplasia


title: Bovine 59 A, biological rep1

description: A1 MII


title: Bovine 81 A, biological rep3

description: A3 GV

source_name: GV stage oocytes from Adult cattle

value: Oocytes obtained immediately after aspiration from follicles

value: GV


title: Bovine 7 PP, biological rep1

description: PP1 MII


title: Bovine 53 PP, biological rep2

description: PP2 MII


title: Bovine 80b A, biological rep2

description: A2 GV


title: Mantle cell lymphoma cells sensitive to the drug at 5 hrs sample 3


title: Mantle cell lymphoma cells sensitive to the drug at 5 hrs sample 2


title: Mantle cell lymphoma cells sensitive to the drug at 5 hrs sample 1


title: Mantle cell lymphoma cells sensitive to the drug at 5 hrs sample 4


title: HS003

description: hashimoto thyroiditis


title: HS001

description: hashimoto thyroiditis


title: Ftc007

description: follicular thyroid carcinoma

value: follicular thyroid carcinoma


title: HS002

description: hashimoto thyroiditis


title: Ftc006

description: follicular thyroid carcinoma


title: FVPTC013

description: follicular variant of papillary thyroid carcinoma


title: HS005

description: hashimoto thyroiditis


title: FVPTC011

value: follicular variant of papillary thyroid carcinoma


title: FVPTC010


title: FVPTC007


title: Mantle cell lymphoma cells sensitive to the drug at start point sample 4


title: Bovine 74b A, biological rep1

description: A1 GV


title: Bovine 4b PP, biological rep1

description: PP1 GV

source_name: GV stage oocytes from prepubertal heifers


title: FVPTC006


title: FVPTC004


title: Bovine 79 PP, biological rep3

description: PP3 GV


title: FVPTC005


title: FVPTC012


title: Mantle cell lymphoma cells sensitive to the drug at start point sample 2


title: Bovine 78b PP, biological rep2

description: PP2 GV


title: FVPTC003


title: HTR-8/SVneo_IL6

city: New Delhi

first: Satish

middle: Kumar

last: Gupta

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institue of Immunology

description: Gene expression data from HTR-8/SVneo cells cultured for 24 h in medium without fetal bovine serum and stimulated with IL-6 (100 ng/ml).

hyb_protocol: Fragmented and labeled cDNAs were hybridized to Affymetrix Exon 1.0 ST GeneChips (Affymetrix, Santa Clara, CA) at 45ºC for 17 h in a hybridization oven at 60 rpm according to Affymetrix protocols.

scan_protocol: The chips were read using a GeneChip Scanner 3000.

data_processing: Raw images after scannning were converted to signal intensities, detection calls, comparison files, signal log ratios, and change calls. For normalizing and summarizing probe-level intensity measurements from GeneChips, GCRMA was used which converts .CEL files into an expression set using the Robust Multi-array Average (RMA) with the help of probe sequence and with GC-content background correction.

source_name: HTR-8/SVneo cells stimulated with IL-6 (100 ng/ml) for 24 h

label_protocol: Sense strand cDNA was prepared using the Ambion WT expression kit (Ambion Inc., Austin, Texas, USA), and then it was fragmented and biotin-labeled using the Affymetrix GeneChip WT terminal labeling kit (Affymetrix, High Wycombe, UK), according to the manufacturers’ recommendations.

growth_protocol: JEG-3 and HTR-8/SVneo cells were maintained in medium supplemented with 10% foetal bovine serum containing an antibiotic and antimycotic cocktail. For growth, cells were kept at 37⁰C in a humidified atmosphere containing 5% CO2 in air.

treatment_protocol: Cells (~0.1 million) were seeded onto six-well culture plates and cultured for 24 h in medium containing 10% foetal bovine serum. Cells were serum starved for 4 h before addition of LIF (50 ng/ml) or IL-6 (100 ng/ml) for 24 h, keeping the appropriate controls.

tag: treatment


title: Mantle cell lymphoma cells sensitive to the drug at start point sample 1


title: HTR-8/SVneo_LIF

description: Gene expression data from HTR-8/SVneo cells cultured for 24 h in medium without fetal bovine serum and stimulated with LIF (50 ng/ml).

source_name: HTR-8/SVneo cells stimulated with LIF (50ng/ml) for 24 h

value: LIF


title: Myeloma cells resistant to the drug at 17 hrs sample 3

value: Myeloma


title: Myeloma cells resistant to the drug at 17 hrs sample 4


title: HTR-8/SVneo_Control_24h

description: Gene expression data from HTR-8/SVneo cells cultured for 24 h in medium without fetal bovine serum.

source_name: HTR-8/SVneo cells cultured for 24 h without any kind of exogenous treatment


title: Myeloma cells resistant to the drug at 17 hrs sample 2


title: Myeloma cells resistant to the drug at 5 hrs sample 4


title: FVPTC001


title: FVPTC002


title: FVPTC008


title: FVPTC009


title: Mantle cell lymphoma cells sensitive to the drug at start point sample 3


title: JEG-3_IL6

description: Gene expression data from JEG-3 cells cultured for 24 h in medium without fetal bovine serum and stimulated with IL-6 (100 ng/ml).

source_name: JEG-3 cells stimulated with IL-6 (100ng/ml) for 24 h


title: FTC003

description: follicular thyroid carcinoma


title: FA017

description: follicular adenoma

value: follicular adenoma


title: FTC001

description: follicular thyroid carcinoma


title: JEG-3_LIF

description: Gene expression data from JEG-3 cells cultured for 24 h in medium without fetal bovine serum and stimulated with LIF (50 ng/ml).

source_name: JEG-3 cells stimulated with LIF (50 ng/ml) for 24 h


title: JEG-3_Control

description: Gene expression data from JEG-3 cells cultured for 24 h in medium without fetal bovine serum.

source_name: JEG-3 cells cultured for 24 h without any kind of exogenous treatment


title: FTC002

description: follicular thyroid carcinoma


title: FA016

description: follicular adenoma


title: Myeloma cells resistant to the drug at start point sample 4


title: FA015

description: follicular adenoma


title: Myeloma cells resistant to the drug at start point sample 3


title: FTC009

description: follicular thyroid carcinoma


title: Myeloma cells resistant to the drug at 5 hrs sample 2


title: FTC008

description: follicular thyroid carcinoma


title: Myeloma cells resistant to the drug at 5 hrs sample 3


title: Myeloma cells sensitive to the drug at 17 hrs sample 4