title: P3.VII

city: Utrecht

first: Wigard

last: Kloosterman

address: Universiteitsweg 100

institute: University Medical Center Utrecht

description:
SAMPLE 30
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining, BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on an iScan (Illumina).

data_processing: Data processing was done using GenomeStudio (Illumina).

label: Biotin (C, G), DNP (A,T)

source_name: adenocarcinoma of the ovary, peritoneal metastasis

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (MSM) and primer/neutralization mix (MA1-MA2-0.1N NaOH). After incubation, the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen tissue was performed using QIAGEN Genomic DNA kit.

tag: gender

value: female

tag: disease status

value: ovarian cancer

tag: tumor stage

value: IV

value: peritoneal metastasis

value: no treatment

tag: patient identifier


title: NF-11 DNA

status: Public on Jun 05 2013

type: genomic

city: Atlanta

first: William

last: Lewis

state: Georgia

address: 101 Woodruff Circle

department: Pathology

country: USA

institute: Emory University

hyb_protocol: Hybridization was completed using NimbleGen Hybridization Kit (Cat # 05583683001)following their standard operating protocol.

scan_protocol: Scanning was performed using Roche NimbleGen MS200 Microarray Scanner following the manufacturer's standard protocol

data_processing: Each sample was processed utilizing NimbleScan software default values, including analysis of the 635/532 ratio utilizing a 500bp sliding window KS test according to manufacturer instructions.

molecule: genomic DNA

organism: Homo sapiens

source_name: Methylated Genomic DNA from NF sample

label_protocol: DNA labeling was completed using NimbleGen Dual-Color DNA labeling Kit (Cat # 06370250001) following their standard operating protocol.

extract_protocol: DNA was extracted  using a MagNAPure DNA Extraction System (Roche), quantiated, sonicated and enriched using the MethylCollector Ultra Kit (Active Motif) following the manufacturer's protocol. Both methylated and input DNA was amplified using whole genome amplification (Sigma-Aldrich).

tag: tissue

value: heart left ventricle

tag: dna type

value: Methylaed Genomic DNA

source_name: Total Genomic DNA from NF Sample

value: total Genomic DNA


title: pre-iPSC- siRNA to luciferase- biological replicate2

type: RNA

city: Madison

first: Rupa

last: Sridharan

address: 2118 Wisconsin Institute for Discovery

institute: UW-Madison

description: pre-iPSC-control 2

hyb_protocol: Hybridisation was performed using Affymetrix protocol

scan_protocol: Gene ChiPs were scanned with a Gene Array Scanner

data_processing: CEL files generated were normalized by RMA normalization from the R statistical package

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Standard Affymetrix protocol

growth_protocol: pre-iPSCs we re grown in standard embryonic stem cell media

extract_protocol: Trizol extraction was carried out according to manufacturer's instructions

treatment_protocol: pre-iPSCs were treated with indicated siRNA for 3 days and then RNA was extracted

tag: cell type

value: pre-iPSCs

tag: sirna mediated knockdown

value: control


title: 24 h ABA imbibed after-ripened, biological rep2

city: Winnipeg

first: Belay

middle: T.

last: Ayele

state: MB

address: 222 Agriculture Building

department: Plant Science

country: Canada

institute: University of Manitoba

description: Gene expression data from after-ripened seeds imbibed in ABA for 24 h.

hyb_protocol: Following fragmentation, labelled cRNA samples were hybridized for 16 hr at 45C on GeneChip Wheat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix Scanner 3000.

data_processing: The data were analyzed with Robust Multi-array Average methodology (RMA).

organism: Triticum aestivum

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT Labelling Kit and the GeneChip Sample Cleanup Module

growth_protocol: Wheat plants were grown in a greenhouse at 18-22oC/14-18oC (day/night) under a 16/8 h photoperiod until harvest. Spikes were harvested at maturity.

extract_protocol: mRNA isolation using PolyATtract kit according to the manufacturer's instructions.

treatment_protocol: After-ripened seeds were imbibed in 50 µM ABA for for 24 h.

value: seed

tag: genotype

value: AC Domain

tag: age

value: mature


title: NF-4 DNA


title: NF-2 DNA


title: P3.V

country: Netherlands

description:
SAMPLE 28
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: adenocarcinoma of the ovary, omental lesion

value: omental lesion

tag: treatment


title: 24 h ABA imbibed after-ripened, biological rep1

source_name: after-ripened seeds imbibed in ABA for 24 h


title: 12 imbibed after-ripened, biological rep3

description: Gene expression data from after-ripened seeds imbibed for 12 h.

source_name: after-ripened seeds imbibed for 12 h

treatment_protocol: One-half of the seeds were stored at -80oC to retain dormancy.To obtain AR seeds, the remaining portion of the seeds was stored at room temperature for 10 months.


title: copt2-1 seedlings versus Col 0 seedlings in Fe and Cu sufficient medium replicate 2

city: Valencia

first: Francisco

last: Vera-Sirera

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: IBMCP (UPV-CSIC)

hyb_protocol: DNA onto slides was rehydrated by placing the slide upside-down over a water bath at 60°C for 10 s, and snap dry onto a heat block at 65°C. Rehydratation was repeated 3 times. DNA was immobilized by UV light by exposing the slides DNA-side-up to 65 mJ in a UV cross-linker (Stratagene). Slides were then washed twice in 0.1% SDS and 4 times in water, 2 min each wash at RT, and finally dipped in 96% ethanol for 1 min and dried by centrifugation at 2000 rpm 1 min at RT. Slides were prehybridized for 30 min at 42°C with 100 µL of prehybridization solution (6x SSC (Sigma), 1% BSA (Sigma) and 0.5% SDS (Sigma)), under a 60x22 mm coverslip LifterSlip (Erie Scientific) in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were rinsed 5 times in H2O in a slide rack at RT and dried by centrifugation at 2000 rpm 1 min at RT. Slides were hybridized immediately.  Both coupled aa-aRNA (Cy3 and Cy5) were mixed and fragmented in the presence of 20 µg of tRNA (Ambion) and 20 µg of poly(A) (Roche) using the RNA fragmentation Reagent (Ambion) as described by the manufacturer, in a final volume of 10 µL. Fragmented aa-aRNA was used directly in the hybridization mix, which contains of 50 µL deionized formamide (Sigma), 30 µL 20x SSC, 5 µL 100x Denhardt´s solution (Sigma), and 5 µL 10% SDS in a final volume of 100 µL. Hybridization mixture was denatured at 95 °C for 5 min, spun briefly, and applied by capillary between a pre-treated slide (see above) and a 60x42 mm coverslip LifterSlip. Slides were incubated o/n at 37°C in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were washed sequentially once in 1x SSC 0.1% SDS 5 min at 30°C; once in 0.2x SSC 0.1% SDS 5 min at 30°C; twice in 0.1x SSC 2 min each at 30°C; and finally 0.01x SSC 10 sec at RT. Slides were dried by centrifugation at 2000 rpm 1 min at RT.

scan_protocol: Hybridized microarray slides were scanned at 532-nm for the Cy3 and 635-nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA), at 5-nm resolution and 100% laser power.

data_processing:
Spot intensities were quantified using GenePix Pro 6.0 microarray-analysis software (Axon Molecular Devices, Sunnyvale CA). Spots with a net intensity in both channels lower than the median signal background plus twice standard deviations were removed as low signal spots.  Data were normalized by median global intensity using the GenePix Pro 6.0 software.
Linear normalized log2 ratio (copt2-1/Col-0). Values for copt2-1 vs Col 0 +Fe +Cu Rep 3, copt2-1 vs Col 0 +Fe +Cu Rep 4, copt2-1 vs Col 0 -Fe +Cu Rep 3, copt2-1 vs Col 0 -Fe +Cu Rep 4, copt2-1 vs Col 0 -Fe -Cu Rep 3 and copt2-1 vs Col 0 -Fe -Cu Rep 4  have been dye-swap corrected at Matrix table.

organism: Arabidopsis thaliana

source_name: 7 days seedlings of copt2-1 mutant in Fe and Cu sufficient medium

label_protocol: RNA was amplified using the MessageAmp II aRNA Amplification kit (Ambion), basically as described by the manufacturer. 5-(3-aminoallyl)-UTP (aa-UTP) (Ambion) was incorporated into the amplified RNA (aRNA) at ratio 1:1 with UTP. After purification 7.5 µg of aminoallyl-aRNA (aa-aRNA) were used in a coupling reaction with either fluorescent Cy3 or Cy5 as reactive N-hydroxyl succinimidal dyes (NHS-dyes) (Amersham Pharmacia Biotech, Piscataway, NJ). For this, each aliquot of Cy3 or Cy5 were dissolved in 20 µL of DMSO and used in four coupling reactions. aa-aRNA was dissolved in 15 µL of freshly-made 0.1 M NaCO3 pH 9.0, and mixed with 5 µl of either Cy-3 or Cy-5 dye. Coupling was allowed for 1 h at RT in the dark. Reaction was stopped with 35 µL of 100 mM sodium acetate pH 5.2 and incubated 5 min in the dark. Fluorescent aa-aRNA was purified using a MegaClear purification column (Ambion) as described by the manufacturer. Coupled aa-aRNA (250-300 pmol Cy dye in 5-7 µg aa-aRNA) was dried in a speedvac and dissolved in 2.5 µL of filtered water.

growth_protocol: Seeds were surface sterilized by treatment with 70% ethanol for 20 min, followed by commercial bleach (2.5 % sodium hypochlorite) containing 0.05 % Triton X-100 for 10 min, and finally, four washes with sterile distilled water. Stratification of the seeds was conducted in the dark at 4ºC for 2 days. Seeds were sowed in  ½ MS medium (see specifications in treatment protocol) and grown for 7 days under  12 hours of light + 12 hours of darkness photoperiod conditions.

extract_protocol: Seedlings were frozen in liquid nitrogen, and grounded in mortars dipped in liquid nitrogen. Total RNA was extracted using the Quiagen Plant RNeasy Mini Kit followong the manufacturer´s recommendations

treatment_protocol: Seedlings in the Fe and Cu sufficient medium were grown in a ½ MS medium that includes macronutrients (10mM NH4NO3, 9.4mM KNO3, 0.37mM MgSO4.7H20, 0.62mM KH2PO4 and 1.13mM CaCl2), micronutrients (50μM H3BO3, 36.6μM MnSO4.2H20, 15μM ZnSO4.7H20, 0.57μM NaMoO4.2H2O and 0.05μM CoCl2.6H20), 50μM Fe-EDTA, 0.25mM KI, 1μM CuSO4, 0.05% MES, 1% sucrose and 0.8% phytoagar; pH 5.7-5.8. For the Fe deficient and Cu sufficient medium,  300μM ferrozine was added to the medium and Fe-EDTA was removed from it. For the Fe and Cu deficient medium, 300μM ferrozine was added to the medium and Fe-EDTA and CuSO4 were removed from it.

value: 7 days seedlings

tag: ecotype

value: copt2-1 mutant

tag: growth condition

value: Fe and Cu sufficient medium

source_name: 7 days seedlings of Col-0 mutant in Fe and Cu sufficient medium

value: wildtype


title: P3.VI

description:
SAMPLE 29
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

value: female

value: ovarian cancer


title: copt2-1 seedlings versus Col 0 seedlings in Fe and Cu sufficient medium replicate 3


title: copt2-1 seedlings versus Col 0 seedlings Fe deficient and Cu sufficient medium replicate 1

source_name: 7 days seedlings of copt2-1 mutant in Fe deficient and Cu sufficient medium

value: Fe deficient and Cu sufficient medium

source_name: 7 days seedlings of Col-0 mutant in Fe deficient and Cu sufficient medium


title: 12 imbibed after-ripened, biological rep2


title: P3.III

description:
SAMPLE 26
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: adenocarcinoma of the ovary, right ovary

value: IV

value: right ovary

value: no treatment


title: copt2-1 seedlings versus Col 0 seedlings in Fe and Cu sufficient medium replicate 1


title: copt2-1 seedlings versus Col 0 seedlings Fe deficient and Cu sufficient medium replicate 3


title: 12 h imbibed dormant, biological rep3

description: Gene expression data from dormant seeds imbibed for 12 h.

source_name: dormant seeds imbibed for 12 h


title: 24 h ABA imbibed after-ripened, biological rep3


title: P3.I

description:
SAMPLE 24
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: adenocarcinoma of the ovary, peritoneal metastasis left lower pelvic region


title: P3.IV

description:
SAMPLE 27
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: adenocarcinoma of the ovary, mesenteric lesion

value: mesenteric lesion


title: P3.VIII

description:
SAMPLE 31
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: normal muscle tissue

value: normal muscle


title: copt2-1 seedlings versus Col 0 seedlings in Fe and Cu sufficient medium replicate 4


title: anti-miR-27a

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

country: Japan

institute: Kanazawa University

description: Gene expression data from Huh-7.5 cells transfected with anti-miR-27a

hyb_protocol: Biotin-labeled cDNA was suspended in 220 ul of hybridization cocktail (NuGen) and 200 ul was used for hybridization to the Affymetrix Human 133 Plus 2.0 microarray chip containing 54,675 probes.GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: After stringent washing, the microarray chips were stained with streptavidin-phycoerythrin and probe hybridization was determined using a GeneChip Scanner 3000 (Affymetrix).

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 arbitrarily set to 100.

label_protocol: Aliquots of total RNA (50 ng) isolated from cells were subjected to amplification using the WT-Ovation Pico RNA Amplification System (NuGen, San Carlos, CA, USA) according to the manufacturer’s instructions. Approximately 10 ug of cDNA was amplified from 50 ng of total RNA, and 5 ug of cDNA was used for fragmentation and biotin labeling using the FL-Ovation cDNA Biotin Module V2 (NuGen) according to the manufacturer’s instructions.

extract_protocol: RNeasy Mini Kit (QIAGEN) for total RNA was performed according to the manufacturer's instructions.

tag: cell line

value: Huh-7.5 cells


title: pre-miR-control

description: Gene expression data from Huh-7.5 cells transfected with pre-miR-control

source_name: pre-miR-control

value: pre-miR-control


title: 12 h imbibed dormant, biological rep1

value: seed

value: AC Domain


title: pre-miR-27a

description: Gene expression data from Huh-7.5 cells transfected with pre-miR-27a


title: 24 imbibed after-ripened, biological rep3

description: Gene expression data from after-ripened seeds imbibed for 24 h.

source_name: after-ripened seeds imbibed for 24 h

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT Labelling Kit and the GeneChip Sample Cleanup Module.

growth_protocol: Wheat plants were grown in a greenhouse at 16-22oC/14-18oC (day/night) under a 16/8 h photoperiod until harvest. Spikes were harvested at maturity.

value: mature


title: P2.VII-1

description:
SAMPLE 21
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: carcinosarcoma of the ovary, omental lesion, adipose tissue infiltrated with tumor cells

value: IIIC


title: Cumulus cells from oocyte at MI stage , biological rep3

city: Yan tai

first: Xin

last: Huang

state: Shan dong

address: Yuhuangding east street 20

department: Reproduction Medical Centre

country: China

institute: Yuhuangding hospital of Yantai

description: Gene expression data from cumulus cells isolated from oocyte at MI stage

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

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 to analyze the hybridization data.

source_name: Cumulus cells isolated from oocyte at stage metaphase I (MI) of PCOS patients

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

growth_protocol: All patients with PCOS fulfilled the 1990 National Institutes of Health and the revised 2003 Rotterdam consensus diagnostic criteria for PCOS, and the patients which average age was 32 years (range 25-38 years) were enrolled in the study.

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

treatment_protocol: All the PCOS participants included in the study were women undergoing in vitro fertilization.Ovarian stimulation and oocyte retrieval protocols were carried out as below.pituitary down-regulation was started with mid-luteal phase GnRH agonist (Diphereline 3.75mg, PharmaBiotech, Paris, France). Once adequate pituitary down-regulation was confirmed [absence of ovarian cysts>=18mm in diameter and serum estradiol (E2) levels of <50 pg/ml]. Controlled ovarian stimulation was conducted with recombinant FSH (Follitropin Alfa, Serono, London, UK). Human chorionic gonadotropin (hCG; 10,000 IU, Profasi; Serono Laboratories) was given in when two or more follicles were at least 18mm in diameter and the serum E2 levels were at least 300pg/ml per dominant follicle. Oocyte retrieval was performed 36h after hCG administration. Cumulus cells were separated from the oocyte with strippers mechanically and washed twice in cold phosphate buffer saline (Dubelcco’s medium) (Gibco, invitrogen, Paris, France) then centrifuged at 200g for 10 min. The supernatant was removed and the pellet was resuspended in RLT buffer of the Reasy Mini Kit.

value: Cumulus cells

tag: cell cyle

value: metaphase I

tag: disease state

value: Polycystic ovary syndrome


title: 24 imbibed after-ripened, biological rep2


title: 24 imbibed after-ripened, biological rep1


title: P2.VI-3

description:
SAMPLE 20
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: carcinosarcoma of the ovary, lesser pelvis

value: female

value: lesser pelvis


title: dry after-ripened, biological rep3

description: Gene expression data from dry after-ripened seeds, before imbibition.

source_name: dry after-ripened seeds


title: dry after-ripened, biological rep2


title: anti-miR-control

description: Gene expression data from Huh-7.5 cells transfected with anti-miR-control

source_name: anti-miR-control

value: anti-miR-control


title: dry after-ripened, biological rep1


title: P2.VI-2

description:
SAMPLE 19
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

value: ovarian cancer


title: Cumulus cells from oocyte at MI stage , biological rep2


title: P3.II

description:
SAMPLE 25
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: adenocarcinoma of the ovary, right fallopian tube

value: IV

value: right fallopian tube


title: P2.V-1

description:
SAMPLE 17
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: carcinosarcoma of the ovary, peritoneal metastasis on bladder

value: peritoneal metastasis on bladder

value: no treatment


title: P2.VII-2

description:
SAMPLE 22
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

value: adipose tissue infiltrated with tumor cells


title: P2.IV-1

description:
SAMPLE 16
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: carcinosarcoma of the ovary, peritoneal metastasis left pelvis

value: peritoneal metastasis left pelvis


title: 24 imbibed dormant, biological rep3

description: Gene expression data from dormant seeds imbibed for 24 h.

source_name: dormant seeds imbibed for 24 h

value: seed


title: NF-7 DNA

source_name: Methylated Genomic DNA from NF sample

value: heart left ventricle

value: Methylaed Genomic DNA

source_name: Total Genomic DNA from NF Sample

value: total Genomic DNA


title: P2.III-1

description:
SAMPLE 15
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: carcinosarcoma of the ovary, peritoneal metastasis right pelvis

value: IIIC

value: peritoneal metastasis right pelvis


title: P2.II-2

description:
SAMPLE 14
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: carcinosarcoma of the ovary, right ovary

value: right ovary


title: 24 imbibed dormant, biological rep1

value: AC Domain

value: mature


title: 12 h imbibed dormant, biological rep2

description: Gene expression data from dormant seeds imbibed for 12 h.

source_name: dormant seeds imbibed for 12 h


title: dry dormant, biological rep3

description: Gene expression data from dry dormant seeds, before imbibition.

source_name: air-dry dormant seeds


title: dry dormant, biological rep1


title: P2.I-5

description:
SAMPLE 13
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: normal stroma of the ovary

value: female

value: normal stroma of the ovary


title: Placebo_responder_24hr_person58

status: Public on Jun 04 2013

city: Munich

first: Divya

last: Mehta

country: Germany

institute: MPI

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Microarray expression analysis was performed in R, using beadarray (providing routines to handle Illumina BeadStudio data) , limma (for statistical routines) and vsn (for normalization) packages. Raw microarray scan files were exported using the Illumina Beadstudio program and loaded into R for downstream analysis. The data were transformed and normalized using the variance stabilizing normalization method. Of the 48804 probes present on the Human HT-12v3, probes were selected which fulfilled the criteria of Illumina probe detection p-value of <0.01 in the individuals leaving 16962  transcripts after normalization and filtering for analysis. Raw qPCR data from the Roche LightCycler 480 System was extracted and the crossing thresholds (CT) from the technical replicates were averaged across all samples. Transcripts were normalized to housekeeping gene TBP.

source_name: whole blood

label_protocol: standard Illumina protocol

extract_protocol: TempusTM Spin RNA Isolation Kit

value: Placebo

tag: group

value: responder

tag: time

tag: subject

tag: Sex

value: Female

tag: bmi

tag: medication status

value: whole blood


title: Infliximab_responder_2week_person57

value: Infliximab

tag: tissue


title: P2.I-4

description:
SAMPLE 12
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

tag: gender

tag: disease status

value: ovarian cancer

tag: tumor stage

value: no treatment

tag: patient identifier


title: Placebo_responder_baseline_person58

tag: treatment

value: baseline


title: Infliximab_responder_baseline_person57


title: Placebo_responder_6hr_person58


title: Infliximab_responder_24hr_person57


title: Placebo_responder_2week_person58


title: Infliximab_responder_6hr_person57


title: 24 imbibed dormant, biological rep2

value: seed

tag: genotype

tag: age


title: P2.I-1

description:
SAMPLE 11
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: carcinosarcoma of the ovary, left ovary

value: left ovary


title: Placebo_responder_2week_person56


title: Placebo_responder_6hr_person56


title: P1.IV-2

description:
SAMPLE 8
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: adenocarcinoma of the ovary, metastasis omentum

value: IIIC

value: metastasis omentum


title: 12 imbibed after-ripened, biological rep1

description: Gene expression data from after-ripened seeds imbibed for 12 h.

source_name: after-ripened seeds imbibed for 12 h


title: Placebo_responder_2week_person55

value: Male


title: Placebo_responder_baseline_person56


title: P1.IV-3

description:
SAMPLE 9
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.


title: Infliximab_nonresponder_2week_person54

value: nonresponder


title: Placebo_responder_6hr_person55


title: P1.IV-1

description:
SAMPLE 7
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.


title: Infliximab_nonresponder_baseline_person53


title: Placebo_responder_24hr_person56


title: P2.VII-3

description:
SAMPLE 23
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: carcinosarcoma of the ovary, omental lesion, adipose tissue infiltrated with tumor cells


title: Infliximab_nonresponder_6hr_person54


title: P1.II-1

description:
SAMPLE 4
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: adenocarcinoma of the ovary, left ovary


title: P1.II-3

description:
SAMPLE 6
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: normal tuba tissue

value: normal tuba


title: Infliximab_nonresponder_24hr_person54


title: Infliximab_nonresponder_2week_person52


title: dry dormant, biological rep2

value: AC Domain

value: mature


title: Placebo_responder_24hr_person55

value: Placebo


title: Infliximab_nonresponder_24hr_person52


title: Infliximab_nonresponder_baseline_person54


title: Infliximab_nonresponder_baseline_person52


title: Placebo_responder_2week_person51

value: responder


title: P2.VI-1

description:
SAMPLE 18
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: carcinosarcoma of the ovary, lesser pelvis

value: female

value: lesser pelvis


title: Placebo_responder_2week_person50

value: Female

value: whole blood


title: Placebo_responder_baseline_person51


title: Placebo_responder_24hr_person51


title: Placebo_responder_6hr_person51


title: Placebo_responder_24hr_person50


title: P1.II-2

description:
SAMPLE 5
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

value: ovarian cancer

value: no treatment


title: P1.I-1

description:
SAMPLE 1
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: adenocarcinoma of the ovary, right ovary

value: right ovary


title: P1.V-1

description:
SAMPLE 10
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

source_name: adenocarcinoma of the ovary, peritoneal metastasis

value: peritoneal metastasis


title: P1.I-3

description:
SAMPLE 3
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.

value: IIIC


title: P1.I-2

description:
SAMPLE 2
Genomic DNA extracted from sample was genotyped using Illumina HumanCytoSnp-12 Beadchip version 2.0.


title: Infliximab_nonresponder_6hr_person47

value: Infliximab


title: Placebo_responder_6hr_person50


title: Infliximab_nonresponder_24hr_person47


title: Infliximab_nonresponder_2week_person47


title: Placebo_responder_baseline_person50

value: baseline


title: Infliximab_responder_24hr_person49


title: Infliximab_nonresponder_baseline_person48

value: nonresponder


title: Placebo_responder_24hr_person45


title: Placebo_responder_2week_person45


title: Placebo_responder_6hr_person45


title: Infliximab_nonresponder_baseline_person47


title: Infliximab_responder_2week_person49


title: Placebo_responder_baseline_person46

value: Male


title: Placebo_responder_24hr_person46


title: Placebo_responder_24hr_person44


title: Placebo_responder_6hr_person44


title: Placebo_responder_baseline_person44


title: Placebo_responder_2week_person46


title: Placebo_nonresponder_2week_person43


title: Placebo_responder_6hr_person46


title: Placebo_responder_baseline_person45


title: Placebo_nonresponder_24hr_person43


title: Placebo_responder_2week_person44


title: Placebo_nonresponder_6hr_person43


title: Placebo_nonresponder_baseline_person43


title: Infliximab_responder_baseline_person49


title: Placebo_responder_2week_person42


title: Placebo_responder_24hr_person42


title: Placebo_responder_baseline_person42


title: Infliximab_responder_2week_person41


title: Placebo_responder_6hr_person39


title: Infliximab_nonresponder_baseline_person40


title: Infliximab_nonresponder_6hr_person52


title: Infliximab_responder_24hr_person41


title: Infliximab_responder_baseline_person41


title: Placebo_responder_2week_person39


title: Placebo_responder_baseline_person55


title: Infliximab_nonresponder_baseline_person38


title: Placebo_responder_6hr_person42


title: Placebo_responder_baseline_person39


title: Infliximab_nonresponder_24hr_person38


title: Infliximab_nonresponder_6hr_person40


title: Infliximab_nonresponder_6hr_person38


title: Placebo_responder_24hr_person39


title: Infliximab_responder_baseline_person37


title: Infliximab_nonresponder_2week_person40


title: Infliximab_responder_6hr_person41


title: Infliximab_nonresponder_24hr_person40


title: Infliximab_responder_6hr_person37


title: Infliximab_nonresponder_2week_person38


title: Placebo_nonresponder_2week_person36


title: Infliximab_responder_24hr_person37


title: Infliximab_responder_2week_person37


title: Placebo_nonresponder_24hr_person36


title: Placebo_nonresponder_6hr_person36


title: Placebo_nonresponder_baseline_person36


title: Infliximab_nonresponder_2week_person35


title: Infliximab_nonresponder_24hr_person35


title: Infliximab_nonresponder_baseline_person35


title: Infliximab_nonresponder_baseline_person34


title: Infliximab_nonresponder_6hr_person35


title: Infliximab_nonresponder_24hr_person34


title: Infliximab_responder_6hr_person33


title: Infliximab_responder_24hr_person32


title: Infliximab_nonresponder_6hr_person34


title: Infliximab_responder_2week_person32


title: Placebo_nonresponder_24hr_person28


title: Infliximab_responder_baseline_person32


title: Infliximab_responder_6hr_person32


title: Placebo_nonresponder_2week_person31


title: Placebo_nonresponder_6hr_person28


title: Infliximab_nonresponder_baseline_person29


title: Placebo_nonresponder_baseline_person30


title: Placebo_nonresponder_6hr_person31


title: Infliximab_responder_24hr_person33


title: Placebo_nonresponder_baseline_person27


title: Placebo_nonresponder_2week_person28


title: Placebo_nonresponder_6hr_person27


title: Placebo_nonresponder_baseline_person31


title: Infliximab_responder_2week_person33


title: Placebo_nonresponder_24hr_person31


title: Placebo_nonresponder_2week_person27


title: Infliximab_responder_baseline_person33


title: Placebo_nonresponder_24hr_person27


title: Placebo_nonresponder_baseline_person28


title: Infliximab_nonresponder_24hr_person26


title: Infliximab_nonresponder_baseline_person26


title: Infliximab_nonresponder_6hr_person26


title: Placebo_nonresponder_6hr_person22


title: Placebo_nonresponder_24hr_person24


title: Placebo_nonresponder_baseline_person25


title: Placebo_nonresponder_6hr_person24


title: Placebo_responder_24hr_person23


title: Placebo_nonresponder_6hr_person21


title: Placebo_responder_6hr_person23


title: Placebo_nonresponder_24hr_person25


title: Placebo_nonresponder_6hr_person25


title: Placebo_responder_baseline_person23


title: Placebo_nonresponder_2week_person25


title: Placebo_nonresponder_24hr_person22


title: Placebo_nonresponder_baseline_person21


title: Placebo_responder_2week_person23


title: Placebo_nonresponder_2week_person24


title: Infliximab_responder_2week_person18


title: Placebo_nonresponder_2week_person21


title: Placebo_nonresponder_baseline_person24


title: Placebo_nonresponder_2week_person22


title: Infliximab_nonresponder_6hr_person19


title: Infliximab_responder_baseline_person20


title: Placebo_nonresponder_baseline_person22


title: Infliximab_nonresponder_2week_person26


title: Infliximab_nonresponder_2week_person19


title: Infliximab_nonresponder_24hr_person19


title: Infliximab_responder_24hr_person18


title: Infliximab_responder_6hr_person18


title: Infliximab_responder_2week_person17


title: Infliximab_nonresponder_baseline_person19


title: Placebo_nonresponder_24hr_person21


title: Placebo_nonresponder_24hr_person16


title: Infliximab_responder_6hr_person17


title: Placebo_nonresponder_2week_person16


title: Placebo_nonresponder_2week_person15


title: Infliximab_responder_baseline_person18


title: Placebo_nonresponder_6hr_person16


title: Infliximab_nonresponder_24hr_person14


title: Infliximab_responder_2week_person13


title: Infliximab_responder_24hr_person13


title: Infliximab_nonresponder_baseline_person14


title: Placebo_nonresponder_24hr_person15


title: Placebo_nonresponder_6hr_person15


title: Placebo_responder_2week_person12


title: Placebo_nonresponder_baseline_person15


title: Placebo_nonresponder_baseline_person16


title: Infliximab_responder_24hr_person11


title: Infliximab_responder_24hr_person17


title: Infliximab_responder_2week_person11


title: Placebo_responder_24hr_person12


title: Infliximab_responder_baseline_person13


title: Infliximab_nonresponder_6hr_person14


title: Placebo_responder_6hr_person12


title: Placebo_responder_baseline_person12


title: Infliximab_responder_baseline_person17


title: Infliximab_nonresponder_2week_person14


title: Infliximab_responder_6hr_person13


title: Infliximab_responder_6hr_person11


title: Infliximab_responder_baseline_person11


title: Placebo_nonresponder_2week_person10


title: Infliximab_responder_2week_person5


title: Placebo_nonresponder_baseline_person10


title: Infliximab_responder_24hr_person5


title: Infliximab_responder_baseline_person5


title: Placebo_nonresponder_2week_person9


title: Infliximab_responder_6hr_person5


title: Placebo_nonresponder_6hr_person9


title: Placebo_nonresponder_24hr_person9


title: Infliximab_responder_24hr_person8


title: Placebo_nonresponder_6hr_person10


title: Placebo_responder_24hr_person6


title: Placebo_responder_2week_person6


title: Placebo_nonresponder_baseline_person9


title: Placebo_nonresponder_24hr_person10


title: Infliximab_responder_baseline_person8


title: Infliximab_nonresponder_2week_person7


title: Infliximab_nonresponder_6hr_person7


title: Infliximab_nonresponder_24hr_person7


title: Placebo_responder_baseline_person6


title: Placebo_responder_6hr_person6


title: Infliximab_responder_2week_person8


title: Placebo_responder_2week_person4


title: Infliximab_responder_6hr_person8


title: Infliximab_nonresponder_baseline_person7


title: Placebo_responder_24hr_person4


title: Placebo_responder_6hr_person4


title: Placebo_responder_baseline_person4


title: Placebo_responder_2week_person3


title: foreskin-flutamide-biological rep3

city: Wilmington

first: Jack

last: Pike

address: 1600 Rockland Road

department: Urology Research

institute: AI duPont Hospital for Children

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit (Affymetrix)

scan_protocol: GeneChip Scanner 3000 (Affymetrix)

data_processing: R/Bioconductor -  AffylmGUI package with RMA normalization

label: Biotin

organism: Rattus norvegicus

source_name: foreskin-flutamide

label_protocol: Applause WT-Amp ST System (Nugen) using 50 ng total RNA, Encore Biotin Module

extract_protocol: Qiagen Rneasy RNA Extraction Kit

treatment_protocol: Pregnant Sprague Dawley rats were dosed daily with either corn oil or 5 mg/kg/day flutamide by oral gavage from gestational day 16-20.  Pups were euthanized on postnatal day 5 for tissue collection

tag: strain

value: Sprague Dawley

tag: treated with

value: 5 mg/kg/day flutamide

value: postnatal day 5

value: foreskin


title: foreskin-flutamide-biological rep5


title: Infliximab_nonresponder_2week_person34


title: foreskin-flutamide-biological rep4


title: foreskin-flutamide-biological rep6


title: foreskin-flutamide-biological rep2


title: foreskin-flutamide-biological rep7


title: Placebo_nonresponder_2week_person2

value: Placebo


title: foreskin-flutamide-biological rep1


title: Placebo_responder_24hr_person3

value: responder


title: foreskin-corn oil-biological rep7

source_name: foreskin-corn oil

value: Corn oil (control)


title: Placebo_responder_baseline_person3

value: Female

value: whole blood


title: foreskin-corn oil-biological rep3


title: Placebo_nonresponder_24hr_person2


title: Placebo_nonresponder_6hr_person2


title: foreskin-corn oil-biological rep6


title: foreskin-corn oil-biological rep5


title: Placebo_responder_6hr_person3


title: foreskin-corn oil-biological rep4


title: Infliximab_responder_2week_person1


title: foreskin-corn oil-biological rep1


title: Infliximab_responder_24hr_person1


title: Placebo_nonresponder_baseline_person2


title: foreskin-corn oil-biological rep2


title: Infliximab_responder_baseline_person1


title: MelJuSo cells 1 day post etoposide + aclarubicin

city: Palo Alto

first: Baoxu

last: Pang

state: CALIFORNIA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Beadlevel data was processed using the beadarray package, affy model background corrected, log2 transformed and RSN normalized using the lumi package. All packages are available in Bioconductor.

label_protocol: Standard Illumina protocol

growth_protocol: Cells were cultured in 10cm dishes and reached 80% confluency before treatment.

extract_protocol: Trizol extraction + RNeasy clean-up with DNase treatment (Qiagen)

treatment_protocol: Cells were treated with indicated drugs for 2 hours, followed by entensive washing to remove the drug.

tag: cell line

value: MelJuSo

tag: cell type

value: Human skin melanoma cell line

value: Etoposide 10uM 2 hours + Aclarubicin 10uM 2 hours

tag: time point

value: 1 day post drug removal


title: Infliximab_responder_6hr_person1

value: Infliximab

tag: group

tag: time

tag: subject


title: MelJuSo cells 1 day post doxorubicin

source_name: MelJuSo cells 1 day post doxorubicin

value: Doxorubicin 9uM 2 hours


title: MelJuSo cells 1 day post aclarubicin

source_name: MelJuSo cells 1 day post aclarubicin

value: Aclarubicin 10uM 2 hours


title: IFNc

city: Port St. Lucie

first: Xiaoyong

last: Sun

state: FL

address: 9801 SW Discovery Way

institute: VGTI, FL

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

source_name: Dermal fibroblasts, IFNbeta, 24 hr

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

growth_protocol: Fibroblasts were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Lonza, Basel, Switzerland), 50 µg/ml penicillin, and 50 µg/ml streptomycin in a humidified atmosphere of 5% CO2 at 37°C.

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

treatment_protocol: At confluence, serum-free media supplemented with 0.1% bovine serum albumin (BSA) were added to the cultures for 24 h prior to the treatment of Poly I:C for 2 hours or 24 hours (10 ug/ml), or IFN-β (100 U/ml) or other reagents for 24 hours, or infected with Ad-Egr-3 or Ad-GFP at 50 MOI for 48 hours.

value: neonatal foreskin

value: dermal fibroblasts

value: IFNbeta

value: 24 hr


title: HMG4

source_name: Dermal fibroblasts, HMGB1, 24 hr


title: HMG5


title: EGRa

source_name: Dermal fibroblasts, Ad-EGR3, 48 hr

value: 48 hr


title: GFPa

source_name: Dermal fibroblasts, Ad-GFP, 48 hr

value: Ad-GFP


title: MelJuSo cells un-treated

source_name: MelJuSo cells un-treated

value: Un-treated

value: control


title: HSP5

source_name: Dermal fibroblasts, HSP60, 24 hr


title: EGRb


title: CDD4

source_name: Dermal fibroblasts, CDDO, 24 hr

value: CDDO


title: HSP4


title: GFPb


title: CTRd

source_name: Dermal fibroblasts, Control


title: p24c

source_name: Dermal fibroblasts, PolyIC, 24 hr

value: PolyIC


title: CTRc


title: p2hc

source_name: Dermal fibroblasts, PolyIC, 2 hr

value: 2 hr


title: genomic DNA (remission sample) from pre-B ALL patient 819

city: Montreal

first: Stephan

last: Busche

state: Quebec

address: 740 Dr. Penfield Avenue

department: Human Genetics

institute: McGill University

description:
remission pre-B ALL sample
Individual_819

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: arrays were imaged using iScan Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio Software V2011.1

label: Cy3 and Cy5

source_name: remission sample from pre-B ALL patient 819

growth_protocol: primary cells isolated from patient's blood or bone marrow

extract_protocol: genomic DNA was isolated from frozen cell pellets using the genomic DNA purification kit (Gentra Systems), and 500 ng gDNA were used as input for bisulfite conversion employing the EZ DNA Methylation Kit (Zymo Research), all according to manufacturer’s protocol.

treatment_protocol: tumor samples: NA; remission samples: patients underwent treatment with uniform Dana-Farber Cancer Institute ALL Consortium protocols DFCI 95-01, 2000-01 or 2005-01.

value: male

tag: disease state

value: remission

tag: tumor subtype


title: genomic DNA (remission sample) from pre-B ALL patient 825

description:
remission pre-B ALL sample
Individual_825

source_name: remission sample from pre-B ALL patient 825

tag: gender

value: female


title: p2hb

tag: tissue


title: genomic DNA (remission sample) from pre-B ALL patient 817

description:
remission pre-B ALL sample
Individual_817

source_name: remission sample from pre-B ALL patient 817


title: p24b


title: CTRa


title: p2ha


title: genomic DNA (remission sample) from pre-B ALL patient 790

description:
remission pre-B ALL sample
Individual_790

source_name: remission sample from pre-B ALL patient 790


title: genomic DNA (remission sample) from pre-B ALL patient 820

description:
remission pre-B ALL sample
Individual_820

source_name: remission sample from pre-B ALL patient 820


title: p24a


title: genomic DNA (remission sample) from pre-B ALL patient 815

description:
remission pre-B ALL sample
Individual_815

source_name: remission sample from pre-B ALL patient 815


title: IFNa


title: CTRb


title: genomic DNA (remission sample) from pre-B ALL patient 801

description:
remission pre-B ALL sample
Individual_801

source_name: remission sample from pre-B ALL patient 801


title: genomic DNA (remission sample) from pre-B ALL patient 802

description:
remission pre-B ALL sample
Individual_802

source_name: remission sample from pre-B ALL patient 802


title: genomic DNA (remission sample) from pre-B ALL patient 775

description:
remission pre-B ALL sample
Individual_775

source_name: remission sample from pre-B ALL patient 775


title: genomic DNA (remission sample) from pre-B ALL patient 768

description:
remission pre-B ALL sample
Individual_768

source_name: remission sample from pre-B ALL patient 768


title: genomic DNA (remission sample) from pre-B ALL patient 794

description:
remission pre-B ALL sample
Individual_794

source_name: remission sample from pre-B ALL patient 794


title: genomic DNA (remission sample) from pre-B ALL patient 777

description:
remission pre-B ALL sample
Individual_777

source_name: remission sample from pre-B ALL patient 777


title: IFNb

source_name: Dermal fibroblasts, IFNbeta, 24 hr


title: genomic DNA (remission sample) from pre-B ALL patient 757

description:
remission pre-B ALL sample
Individual_757

source_name: remission sample from pre-B ALL patient 757


title: genomic DNA (remission sample) from pre-B ALL patient 752

description:
remission pre-B ALL sample
Individual_752

source_name: remission sample from pre-B ALL patient 752


title: genomic DNA (remission sample) from pre-B ALL patient 761

description:
remission pre-B ALL sample
Individual_761

source_name: remission sample from pre-B ALL patient 761


title: genomic DNA (remission sample) from pre-B ALL patient 767

description:
remission pre-B ALL sample
Individual_767

source_name: remission sample from pre-B ALL patient 767


title: genomic DNA (remission sample) from pre-B ALL patient 764

description:
remission pre-B ALL sample
Individual_764

source_name: remission sample from pre-B ALL patient 764


title: genomic DNA (remission sample) from pre-B ALL patient 753

description:
remission pre-B ALL sample
Individual_753

source_name: remission sample from pre-B ALL patient 753


title: Nr32_LFK5

city: Wuerzburg

first: Susanne

last: Kneitz

address: Am Hubland, Biocenter

department: Physiological Chemistry I

institute: University of Wuerzburg

description: enriched guard cell fraction of Arabidopsis thaliana

hyb_protocol: one-color microarray-based gene expression analysis protocol provided by Agilent including the one-color RNA spike-in kit (v5.0.1, 2006)

scan_protocol: Agilent Microarray Scanner,extended dynamic range (XDR) at high resolution (5 µm)

data_processing: The data were normalized using quantile-quantile as normalization method

source_name: Col-0 ; replicate 4

growth_protocol: Arapidopsis thaliana  plants were grown in soil and cultivated in a greenhouse under short-day conditions (8 h light/16 h darkness, 22°C/16°C) with illumination by 100 µmol m-2 sec-1 white light. Samples were collected after 4-5h of illumination.

extract_protocol: RNeasy Plant Mini Kit, according to the manufacturers protocol

treatment_protocol:
low humidity treatment: The soil surface of single potted 6-7 week old Arabidopsis thaliana plants was covered with foil to prevent excessive water evaporiation. The plants were subjected to an air stream of 20 ± 5 % rh in a climate chamber at 22 ± 2 °C and 100 µmol m-2 sec-1 white light. Controls were kept at >80% rh.
ABA-Spray treatment: Leaves were sprayed with 50 µM +/- abscisic acid solution, containing 25 µM biologically active ABA and 0.01% (v/v) Triton X-100.After 4 hours epidermal peels were harvested.

value: enriched guard cell

tag: ecotype

value: 4h >85% relative humidity


title: genomic DNA (remission sample) from pre-B ALL patient 762

description:
remission pre-B ALL sample
Individual_762

source_name: remission sample from pre-B ALL patient 762


title: genomic DNA (remission sample) from pre-B ALL patient 685

description:
remission pre-B ALL sample
Individual_685

source_name: remission sample from pre-B ALL patient 685


title: Nr31_LFK4

source_name: Col-0 ; replicate 3

label_protocol: one-color microarray-based gene expression analysis protocol provided by Agilent including the one-color RNA spike-in kit (v5.0.1, 2006)


title: genomic DNA (remission sample) from pre-B ALL patient 718

description:
remission pre-B ALL sample
Individual_718

source_name: remission sample from pre-B ALL patient 718


title: genomic DNA (remission sample) from pre-B ALL patient 663

description:
remission pre-B ALL sample
Sample_663

source_name: remission sample from pre-B ALL patient 663


title: genomic DNA (remission sample) from pre-B ALL patient 670

description:
remission pre-B ALL sample
Individual_670

source_name: remission sample from pre-B ALL patient 670


title: genomic DNA (remission sample) from pre-B ALL patient 614

description:
remission pre-B ALL sample
Individual_614

source_name: remission sample from pre-B ALL patient 614


title: genomic DNA (remission sample) from pre-B ALL patient 618

description:
remission pre-B ALL sample
Individual_618

source_name: remission sample from pre-B ALL patient 618


title: genomic DNA (remission sample) from pre-B ALL patient 657

description:
remission pre-B ALL sample
Individual_657

source_name: remission sample from pre-B ALL patient 657


title: genomic DNA (remission sample) from pre-B ALL patient 605

description:
remission pre-B ALL sample
Individual_605

source_name: remission sample from pre-B ALL patient 605


title: genomic DNA (remission sample) from pre-B ALL patient 595

description:
remission pre-B ALL sample
Individual_595

source_name: remission sample from pre-B ALL patient 595


title: Nr27_LF3

value: 4h 20% relative humidity


title: genomic DNA (remission sample) from pre-B ALL patient 579

description:
remission pre-B ALL sample
Individual_579

source_name: remission sample from pre-B ALL patient 579


title: Nr28_LF4


title: genomic DNA (remission sample) from pre-B ALL patient 580

description:
remission pre-B ALL sample
Individual_580

source_name: remission sample from pre-B ALL patient 580


title: genomic DNA (remission sample) from pre-B ALL patient 617

description:
remission pre-B ALL sample
Individual_617

source_name: remission sample from pre-B ALL patient 617


title: genomic DNA (remission sample) from pre-B ALL patient 424

description:
remission pre-B ALL sample
Individual_424

source_name: remission sample from pre-B ALL patient 424


title: Nr30_LFK3

source_name: Col-0 ; replicate 2


title: genomic DNA (remission sample) from pre-B ALL patient 443

description:
remission pre-B ALL sample
Individual_443

source_name: remission sample from pre-B ALL patient 443


title: Nr29_LFK2

source_name: Col-0 ; replicate 1


title: genomic DNA (remission sample) from pre-B ALL patient 411

description:
remission pre-B ALL sample
Individual_411

source_name: remission sample from pre-B ALL patient 411


title: genomic DNA (remission sample) from pre-B ALL patient 608

description:
remission pre-B ALL sample
Individual_608

source_name: remission sample from pre-B ALL patient 608


title: Nr25_LF1

description: enriched guard cell fraction of Arabidopsis thaliana


title: genomic DNA (remission sample) from pre-B ALL patient 390

description:
remission pre-B ALL sample
Individual_390

source_name: remission sample from pre-B ALL patient 390


title: genomic DNA (remission sample) from pre-B ALL patient 420

description:
remission pre-B ALL sample
Individual_420

source_name: remission sample from pre-B ALL patient 420


title: Nr26_LF2


title: genomic DNA (remission sample) from pre-B ALL patient 431

description:
remission pre-B ALL sample
Individual_431

source_name: remission sample from pre-B ALL patient 431


title: Nr24_gl11Kontr

source_name: gl1-1 ; replicate 4

value: 4h control-Spray


title: genomic DNA (remission sample) from pre-B ALL patient 392

description:
remission pre-B ALL sample
Individual_392

source_name: remission sample from pre-B ALL patient 392


title: genomic DNA (remission sample) from pre-B ALL patient 379

description:
remission pre-B ALL sample
Individual_379

source_name: remission sample from pre-B ALL patient 379


title: Nr23_gl11Kontr

source_name: gl1-1 ; replicate 3


title: Nr21_gl11Kontr

source_name: gl1-1 ; replicate 1


title: Nr22_gl11Kontr

source_name: gl1-1 ; replicate 2


title: genomic DNA (remission sample) from pre-B ALL patient 381

description:
remission pre-B ALL sample
Individual_381

source_name: remission sample from pre-B ALL patient 381


title: Nr19_gl11ABA

value: 4h ABA Spray


title: Nr20_gl11ABA


title: genomic DNA (remission sample) from pre-B ALL patient 372

description:
remission pre-B ALL sample
Individual_372

source_name: remission sample from pre-B ALL patient 372


title: genomic DNA (remission sample) from pre-B ALL patient 356

description:
remission pre-B ALL sample
Individual_356

source_name: remission sample from pre-B ALL patient 356


title: Nr15_BL22

description: leaf of Arabidopsis thaliana

source_name: Col-0 ; replicate 3

value: leaf

value: 5h light


title: Nr18_gl11ABA_v5


title: Nr15_gl11


title: Nr17_gl11ABA


title: Nr16_BL23

description: leaf of Arabidopsis thaliana

source_name: Col-0 ; replicate 4


title: genomic DNA (remission sample) from pre-B ALL patient 373

description:
remission pre-B ALL sample
Individual_373

source_name: remission sample from pre-B ALL patient 373


title: Nr14_BL21

description: leaf of Arabidopsis thaliana

source_name: Col-0 ; replicate 2


title: Nr13_BL20

description: leaf of Arabidopsis thaliana

source_name: Col-0 ; replicate 1


title: genomic DNA (tumor sample) from pre-B ALL patient 825

description:
tumor pre-B ALL sample
Individual_825

source_name: tumor sample from pre-B ALL patient 825

value: tumor


title: Nr12_slac15

source_name: slac1-3 ; replicate 3


title: genomic DNA (remission sample) from pre-B ALL patient 384

description:
remission pre-B ALL sample
Individual_384

source_name: remission sample from pre-B ALL patient 384


title: Nr11_slac15

source_name: slac1-3 ; replicate 2


title: Nr10_slac15

source_name: slac1-3 ; replicate 1


title: genomic DNA (tumor sample) from pre-B ALL patient 801

description:
tumor pre-B ALL sample
Individual_801

source_name: tumor sample from pre-B ALL patient 801

value: hyperdiploid


title: genomic DNA (tumor sample) from pre-B ALL patient 802

description:
tumor pre-B ALL sample
Individual_802

source_name: tumor sample from pre-B ALL patient 802

value: no abnormal finding


title: genomic DNA (tumor sample) from pre-B ALL patient 815

description:
tumor pre-B ALL sample
Individual_815

source_name: tumor sample from pre-B ALL patient 815


title: genomic DNA (tumor sample) from pre-B ALL patient 817

description:
tumor pre-B ALL sample
Individual_817

source_name: tumor sample from pre-B ALL patient 817


title: genomic DNA (tumor sample) from pre-B ALL patient 820

description:
tumor pre-B ALL sample
Individual_820

source_name: tumor sample from pre-B ALL patient 820


title: Nr13_gl11_v5

source_name: gl1-1 ; replicate 1


title: genomic DNA (tumor sample) from pre-B ALL patient 794

description:
tumor pre-B ALL sample
Individual_794

source_name: tumor sample from pre-B ALL patient 794


title: genomic DNA (remission sample) from pre-B ALL patient 375

description:
remission pre-B ALL sample
Individual_375

source_name: remission sample from pre-B ALL patient 375


title: genomic DNA (tumor sample) from pre-B ALL patient 790

description:
tumor pre-B ALL sample
Individual_790

source_name: tumor sample from pre-B ALL patient 790


title: Nr8_L24

source_name: Col-0 ; replicate 4


title: Nr7_L23

source_name: Col-0 ; replicate 3


title: genomic DNA (tumor sample) from pre-B ALL patient 768

description:
tumor pre-B ALL sample
Individual_768

source_name: tumor sample from pre-B ALL patient 768


title: Nr6_ler

source_name: ler ; replicate 2

value: ler


title: Nr7_ler

source_name: ler ; replicate 3


title: Nr14_gl11_v5

source_name: gl1-1 ; replicate 2


title: genomic DNA (tumor sample) from pre-B ALL patient 775

description:
tumor pre-B ALL sample
Individual_775

source_name: tumor sample from pre-B ALL patient 775


title: Nr6_L22

source_name: Col-0 ; replicate 2


title: Nr5_ler

source_name: ler ; replicate 1


title: genomic DNA (tumor sample) from pre-B ALL patient 777

description:
tumor pre-B ALL sample
Individual_777

source_name: tumor sample from pre-B ALL patient 777


title: genomic DNA (tumor sample) from pre-B ALL patient 764

description:
tumor pre-B ALL sample
Individual_764

source_name: tumor sample from pre-B ALL patient 764


title: genomic DNA (tumor sample) from pre-B ALL patient 761

description:
tumor pre-B ALL sample
Individual_761

source_name: tumor sample from pre-B ALL patient 761


title: genomic DNA (tumor sample) from pre-B ALL patient 762

description:
tumor pre-B ALL sample
Individual_762

source_name: tumor sample from pre-B ALL patient 762


title: genomic DNA (tumor sample) from pre-B ALL patient 767

description:
tumor pre-B ALL sample
Individual_767

source_name: tumor sample from pre-B ALL patient 767


title: Nr5_L21

source_name: Col-0 ; replicate 1


title: genomic DNA (tumor sample) from pre-B ALL patient 757

description:
tumor pre-B ALL sample
Individual_757

source_name: tumor sample from pre-B ALL patient 757


title: genomic DNA (tumor sample) from pre-B ALL patient 753

description:
tumor pre-B ALL sample
Individual_753

source_name: tumor sample from pre-B ALL patient 753


title: Nr4_ost12

source_name: ost1-2 ; replicate 2


title: GES-1, clopidogrel-1

city: Nanjing

first: wu

middle: hai

last: lu

address: 68 Changle Road

institute: nanjing first hospital

description: Gene expression after  GES-1 cells exposure to clopidogrel (1.5mmol/l)

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: GES-1 cells exposure to clopidogrel

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from cultured cells using the single-step Trizol RNA extraction kit, and its concentration and quality were determined by spectrophotometry and Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA) according to the manufacturer’s instructions, respectively. Only the samples that had no degradation were used to generate the labelled targets. Finally, total RNA was puriﬁed using an RNeasy mini kit (Qiagen).

treatment_protocol: Cell control group (treated with the medium containing 0.1% DMSO), and clopidogrel group (treated with the medium containing 1.5 mM of clopidogrel). Then the cells were cultured for 24 h.

value: gastric epithelial cells


title: genomic DNA (tumor sample) from pre-B ALL patient 752

description:
tumor pre-B ALL sample
Individual_752

source_name: tumor sample from pre-B ALL patient 752


title: genomic DNA (tumor sample) from pre-B ALL patient 819

description:
tumor pre-B ALL sample
Individual_819

source_name: tumor sample from pre-B ALL patient 819


title: genomic DNA (tumor sample) from pre-B ALL patient 718

description:
tumor pre-B ALL sample
Individual_718

source_name: tumor sample from pre-B ALL patient 718


title: genomic DNA (tumor sample) from pre-B ALL patient 670

description:
tumor pre-B ALL sample
Individual_670

source_name: tumor sample from pre-B ALL patient 670


title: genomic DNA (tumor sample) from pre-B ALL patient 657

description:
tumor pre-B ALL sample
Individual_657

source_name: tumor sample from pre-B ALL patient 657


title: GES-1, clopidogrel-3


title: Nr1_ost12

description: enriched guard cell fraction of Arabidopsis thaliana,

source_name: ost1-2 ; replicate 1


title: GES-1, clopidogrel-2


title: GES-1, control-3

description: Gene expression in normal GES-1 cells

source_name: normal GES-1 cells


title: genomic DNA (tumor sample) from pre-B ALL patient 685

description:
tumor pre-B ALL sample
Individual_685

source_name: tumor sample from pre-B ALL patient 685


title: genomic DNA (tumor sample) from pre-B ALL patient 663

description:
tumor pre-B ALL sample
Individual_663

source_name: tumor sample from pre-B ALL patient 663


title: GES-1, control-2

description: Gene expression in normal GES-1 cells


title: genomic DNA (tumor sample) from pre-B ALL patient 614

description:
tumor pre-B ALL sample
Individual_614

source_name: tumor sample from pre-B ALL patient 614


title: GES-1, control-1

description: Gene expression in normal GES-1 cells


title: Lung 6 days post etoposide rep 1

description: replicate 1

source_name: Lung 6 days post etoposide rep 1

treatment_protocol: Mice were injected iv with a single dose of 10 mg/kg doxorubicin or 35 mg/kg etoposide.

value: FVB nude

value: 10 weeks

value: lung

value: 35 mg/kg etoposide

value: 6 days post drug treatment


title: genomic DNA (tumor sample) from pre-B ALL patient 617

description:
tumor pre-B ALL sample
Individual_617

source_name: tumor sample from pre-B ALL patient 617

value: female


title: Lung 1 day post etoposide rep 2

description: replicate 2

source_name: Lung 1 day post etoposide rep 2

value: 1 day post drug treatment


title: Lung 6 days post doxorubicin rep 2

description: replicate 2

source_name: Lung 6 days post doxorubicin rep 2

value: 10 mg/kg doxorubicin


title: Lung 1 day post etoposide rep 1

description: replicate 1

source_name: Lung 1 day post etoposide rep 1


title: Lung 6 days post doxorubicin rep 1

description: replicate 1

source_name: Lung 6 days post doxorubicin rep 1


title: genomic DNA (tumor sample) from pre-B ALL patient 605

description:
tumor pre-B ALL sample
Individual_605

source_name: tumor sample from pre-B ALL patient 605

value: male

value: hypodiploidy


title: genomic DNA (tumor sample) from pre-B ALL patient 579

description:
tumor pre-B ALL sample
Individual_579

source_name: tumor sample from pre-B ALL patient 579


title: genomic DNA (tumor sample) from pre-B ALL patient 618

description:
tumor pre-B ALL sample
Individual_618

source_name: tumor sample from pre-B ALL patient 618


title: Lung 1 day post doxorubicin rep 1

description: replicate 1

source_name: Lung 1 day post doxorubicin rep 1


title: genomic DNA (tumor sample) from pre-B ALL patient 431

description:
tumor pre-B ALL sample
Individual_431

source_name: tumor sample from pre-B ALL patient 431


title: Lung 6 days post etoposide rep 2

description: replicate 2

source_name: Lung 6 days post etoposide rep 2


title: Lung 1 day post doxorubicin rep 2

description: replicate 2

source_name: Lung 1 day post doxorubicin rep 2


title: genomic DNA (tumor sample) from pre-B ALL patient 595

description:
tumor pre-B ALL sample
Individual_595

source_name: tumor sample from pre-B ALL patient 595

value: trisomy 5


title: genomic DNA (tumor sample) from pre-B ALL patient 580

description:
tumor pre-B ALL sample
Individual_580

source_name: tumor sample from pre-B ALL patient 580


title: genomic DNA (tumor sample) from pre-B ALL patient 411

description:
tumor pre-B ALL sample
Individual_411

source_name: tumor sample from pre-B ALL patient 411


title: Liver 6 days post etoposide rep 1

description: replicate 1

source_name: mouse liver

value: liver


title: genomic DNA (tumor sample) from pre-B ALL patient 443

description:
tumor pre-B ALL sample
Individual_443

source_name: tumor sample from pre-B ALL patient 443

value: tumor


title: genomic DNA (tumor sample) from pre-B ALL patient 424

description:
tumor pre-B ALL sample
Individual_424

source_name: tumor sample from pre-B ALL patient 424


title: Lung un-treated rep 2

description: replicate 2

source_name: Lung un-treated rep 2

value: un-treated

value: control


title: Lung un-treated rep 1

description: replicate 1

source_name: Lung un-treated rep 1


title: genomic DNA (tumor sample) from pre-B ALL patient 381

description:
tumor pre-B ALL sample
Individual_381

source_name: tumor sample from pre-B ALL patient 381

value: no abnormal finding


title: genomic DNA (tumor sample) from pre-B ALL patient 390

description:
tumor pre-B ALL sample
Individual_390

source_name: tumor sample from pre-B ALL patient 390

value: hyperdiploid


title: genomic DNA (tumor sample) from pre-B ALL patient 392

description:
tumor pre-B ALL sample
Individual_392

source_name: tumor sample from pre-B ALL patient 392


title: Liver 6 days post etoposide rep 2

description: replicate 2

value: FVB nude


title: Liver 1 day post doxorubicin rep 2

description: replicate 2

value: 10 weeks


title: genomic DNA (tumor sample) from pre-B ALL patient 420

description:
tumor pre-B ALL sample
Individual_420

source_name: tumor sample from pre-B ALL patient 420


title: Liver 1 day post doxorubicin rep 1

description: replicate 1


title: Liver un-treated rep 2

description: replicate 2


title: Liver 1 day post etoposide rep 2

description: replicate 2


title: genomic DNA (tumor sample) from pre-B ALL patient 379

description:
tumor pre-B ALL sample
Individual_379

source_name: tumor sample from pre-B ALL patient 379


title: Liver 1 day post etoposide rep 1

description: replicate 1


title: Heart 6 days post etoposide rep 2

description: replicate 2

source_name: mouse heart

value: heart


title: genomic DNA (tumor sample) from pre-B ALL patient 373

description:
tumor pre-B ALL sample
Individual_373

source_name: tumor sample from pre-B ALL patient 373


title: Liver 6 days post doxorubicin rep 2

description: replicate 2


title: Heart 6 days post etoposide rep 1

description: replicate 1

value: 35 mg/kg etoposide


title: Liver un-treated rep 1

description: replicate 1


title: genomic DNA (tumor sample) from pre-B ALL patient 384

description:
tumor pre-B ALL sample
Individual_384

source_name: tumor sample from pre-B ALL patient 384


title: genomic DNA (tumor sample) from pre-B ALL patient 375

description:
tumor pre-B ALL sample
Individual_375

source_name: tumor sample from pre-B ALL patient 375


title: Heart 6 days post doxorubicin rep 2

description: replicate 2

value: 6 days post drug treatment


title: genomic DNA (tumor sample) from pre-B ALL patient 372

description:
tumor pre-B ALL sample
Individual_372

source_name: tumor sample from pre-B ALL patient 372


title: Heart 6 days post doxorubicin rep 1

description: replicate 1


title: Heart 1 day post etoposide rep 2

description: replicate 2


title: Heart 1 day post doxorubicin rep 1

description: replicate 1


title: genomic DNA (tumor sample) from pre-B ALL patient 608

description:
tumor pre-B ALL sample
Individual_608

source_name: tumor sample from pre-B ALL patient 608


title: Heart 1 day post etoposide rep 1

description: replicate 1


title: Heart un-treated rep 1

description: replicate 1


title: Heart 1 day post doxorubicin rep 2

description: replicate 2


title: Heart un-treated rep 2

description: replicate 2


title: genomic DNA (tumor sample) from pre-B ALL patient 356

description:
tumor pre-B ALL sample
Individual_356

source_name: tumor sample from pre-B ALL patient 356


title: 34-43wk DTG rep1 tech rep2

city: Omaha

first: Patrick

last: Swanson

state: NE

address: 2500 California Plaza

institute: Creighton University

description:
Gene expression data from splenic CD19+CD5+ lymphocytes
DTG (M53) #2 CD19+CD5+

hyb_protocol: cDNA was hybridized overnight to Mouse Gene 1.0 ST Arrays according  manufacturer’s instructions.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 3000 7G

data_processing: Expression ws normalized using RMA on the Affymetrix Expression Console software.

source_name: CD19+CD5+ splenic lymphocytes

label_protocol: Biotin-end labeled cDNA was prepared from total RNA (100-200ng) using whole transcript labeling kits from either Affymetrix or Ambion per manufacturer’s suggestions.

extract_protocol: Total RNA by Trizol method using Ambion Ribopure Kit according to manufacturer’s instructions.

value: 34-43 weeks

tag: genotype/variation

value: DTG

value: CD19+CD5+ splenic lymphocytes


title: 34-43wk Eµ-TCL1 rep1

description:
Gene expression data from splenic CD19+CD5+ lymphocytes
Eµ-TCL1 (M52) CD19+CD5+


title: 34-43wk DTG rep2

description:
Gene expression data from splenic CD19+CD5+ lymphocytes
DTG (F57) CD19+CD5+


title: Liver 6 days post doxorubicin rep 1

description: replicate 1

source_name: mouse liver

tag: treatment

value: 10 mg/kg doxorubicin


title: 34-43wk dnRAG1 rep3

description:
Gene expression data from splenic CD19+CD5+ lymphocytes
dnRAG1 (M63) CD19+CD5+


title: 34-43wk DTG rep1 tech rep1

description:
Gene expression data from splenic CD19+CD5+ lymphocytes
DTG (M53) #1 CD19+CD5+


title: 34-43wk dnRAG1 rep2

description:
Gene expression data from splenic CD19+CD5+ lymphocytes
dnRAG1 (M62) CD19+CD5+


title: 34-43wk dnRAG1 rep1

description:
Gene expression data from splenic CD19+CD5+ lymphocytes
dnRAG1 (M51) CD19+CD5+


title: 34-43wk WT rep2

description:
Gene expression data from splenic CD19+B220hiCD5- lymphocytes
WT (F58) CD19+B220hiCD5-

source_name: CD19+B220hiCD5- splenic lymphocytes

value: WT

value: CD19+B220hiCD5- splenic lymphocytes


title: 34-43wk WT rep1

description:
Gene expression data from splenic CD19+B220hiCD5- lymphocytes
WT (F8) CD19+B220hiCD5-


title: 12wk DTG rep2

description:
Gene expression data from splenic CD19+CD5+ lymphocytes
DTG (M187) CD19+CD5+

value: 12 weeks


title: 12wk Eµ-TCL1 rep1

description:
Gene expression data from splenic CD19+CD5+ lymphocytes
Eµ-TCL1 (M167) CD19+CD5+


title: 12wk DTG rep3

description:
Gene expression data from splenic CD19+CD5+ lymphocytes
DTG (M199) CD19+CD5+


title: 12wk dnRAG1 rep2

description:
Gene expression data from splenic CD19+CD5+ lymphocytes
dnRAG1 (M194) CD19+CD5+


title: 12wk Eµ-TCL1 rep2

description:
Gene expression data from splenic CD19+CD5+ lymphocytes
Eµ-TCL1 (M173) CD19+CD5+


title: 12wk dnRAG1 rep1

description:
Gene expression data from splenic CD19+CD5+ lymphocytes
dnRAG1 (M175) CD19+CD5+


title: 12wk WT rep2

description:
Gene expression data from splenic CD19+B220hiCD5- lymphocytes
WT (M188) CD19+B220hiCD5-


title: 12wk WT rep1

description:
Gene expression data from splenic CD19+B220hiCD5- lymphocytes
WT (M183) CD19+B220hiCD5-


title: 12wk DTG rep1

description:
Gene expression data from splenic CD19+CD5+ lymphocytes
DTG (M176) CD19+CD5+


title: Control-type-QQ-time-72-rep-2

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: 3464_WAP_1_mouse_06_Ctl-QQ-72-Q-16-m-D11-4085_01_7447

hyb_protocol: All cDNAs were hybridized to the commercial Affymetrix mouse 1.0 ST GeneChip

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

data_processing: The data were analyzed with EC 1.2 using Affymetrix default analysis for this chip design. Affymetrix-algorithm-name = rma-gene-default  (v.1.0), program-name = Expression Console (v. 1.1.2800.28061).

label_protocol: Fragmented ds cDNAs were then end-labeled with biotin using terminal transferase (Nugen Inc.)

growth_protocol: Prior to injection trophozoites were grown to log-phase

extract_protocol: Both RNA and genomic DNA were extracted using AllPrep DNA/RNA® 96 kit (Qiagen) following the manufacturer’s recommendations, except that RNA samples received an additional on-column DNase I treatment during extraction

treatment_protocol: 2x10^6 parasites were suspended in 150μl and injected intracecally

tag: strain background

value: containing the humanized LEPR Q allele at codon 223

tag: sample group

value: not infected (control)

value: cecal tissues


title: Control-type-QQ-time-72-rep-1

description: 3462_WAP_1_mouse_04_Ctl-QQ-72-Q-11-f-G03-4099_01_8018


title: Primary tumour region 7 RMH8

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

country: France

institute: Cancer Research Centre of Lyon

description: clear cell Renal Cell Carinoma, region 7

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
B Allele Frequencies and logRs were obtained using the aroma R package.
B Allele Frequencies: estimated ratio of allele B against allele A;  logR: logarithmic ratio of DNA content against expectations.

source_name: kidney

label_protocol: standard Affymetrix protocol

extract_protocol: Fresh frozen

treatment_protocol: Patients P5, P6 and P7 underwent 6 weeks of Everolimus pre-treatment before a week wash-out followed by nephrectomy. All 5 other patients were untreated.

value: Primary tumour

tag: tissue section

value: region 7

value: clear cell Renal Cell Carinoma

tag: batch


title: Control-type-QQ-time-12-rep-3

description: 3461_WAP_1_mouse_03_Ctl-QQ-12-Q-1-m-D03-4053_01_8072


title: Primary tumour region 10 RMH3

description: clear cell Renal Cell Carinoma, region 8

value: region 10


title: Primary tumour region 6 RMH3

description: clear cell Renal Cell Carinoma, region 6

value: region 6


title: Primary tumour region 8 RMH3

value: region 8


title: Primary tumour region 8 RMH8


title: Primary tumour region 5 RMH8

value: region 5


title: Primary tumour region 4 RMH8

description: clear cell Renal Cell Carinoma, region 4

value: region 4


title: Primary tumour region 6 RMH8


title: Primary tumour region 2 RMH8

description: clear cell Renal Cell Carinoma, region 2

value: region 2


title: Control-type-QQ-time-12-rep-2

description: 3460_WAP_1_mouse_02_Ctl-QQ-12-Q-21-f-E07-4061_01_7353


title: L914F TIE2-transfected HUVECs, biological replicate 3

city: Brussels

first: Miikka

last: Vikkula

address: 74(+5) Avenue Hippocrate

country: Belgium

institute: de Duve Institute, Université catholique de Louvain

description: HUVEC - retroviral infection for L914F TIE2 overexpression.

hyb_protocol: 5 µg of fragmented, biotinylated target were hybridized to the Affymetrix GeneChip® Human Exon 1.0 ST Array at 45°C for 16-18 hours. Microarrays were washed and stained on the GeneChip® Fluidics Station 450 using the GeneChip® Hybridization Wash and Stain Kit.

scan_protocol: GeneChip® Scanner 3000 7G.

data_processing:
Statistical analysis and visualization of the microarray data was carried out using GeneSpring 12.5 GX software (Agilent Technologies, Santa Clara, CA, USA). Data were quantile-normalized, summarized using robust multichip analysis (RMA), adjusted for probe sequence. A log2 conversion and a baseline transformation to the median of all samples were carried out. The lowest 20th percentile of raw intensity values were filtered out, while retaining entities for which all 3 samples in any one condition had values above the cut-off.
Core exons are included in the analysis. Transcript assignments are based on human genome build hg19.
GeneSpring.GeneLevel.Affymetrix_ExonExprChip_HuEx-1_0-st-v2_na31_hg19_2010-08-27_1353666145
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.na31.hg19.core.csv

source_name: L914F TIE2-expressing HUVEC, retroviral infection

label_protocol: cDNA was fragmented with UDG (uracil DNA glycosylase) and APE 1 (apurinic/apyrimidic endonuclease 1) and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip® WT Terminal Labeling Kit.

growth_protocol: Non-transfected (NT) and retrovirally transfected HUVEC-lines were maintained in endothelial cell growth medium (endothelial cell basal medium and growth supplement, Cell Applications, San Diego, CA, USA), supplemented with 10% FBS.

extract_protocol: Total RNA was extracted from frozen cell pellets using TriPure (Roche Diagnostics, Mannheim, Germany).

treatment_protocol: Full-length WT-TIE2 (WT), R849W-TIE2 (R849W) or L914F-TIE2 (L914F) were cloned into pMXs vector (gift from T. Kitamura, University of Tokyo, Japan) and packaging cell line 293-GPG VSV-G was transfected for retrovirus production with Fugene 6 (Roche).

value: human umbilical vein endothelial cell (HUVEC)

tag: tie2 type


title: Normal blood RMH8

description: blood

value: blood

value: normal


title: Primary tumour region 10 RK29


title: Primary tumour region 4 RMH3


title: Normal blood RMH3

description: blood


title: L914F TIE2-transfected HUVECs, biological replicate 1

tag: cell type


title: Control-type-QQ-time-12-rep-1

description: 3459_WAP_1_mouse_01_Ctl-QQ-12-Q-6-f-E05-4060_01_7321


title: C57BL/6, Control, male, biological rep3

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

description: C57 Ctr M_3

hyb_protocol: The samples were hybridized to Mouse Gene ST1.0 microarrays according to standardized protocols and reagents from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed in Expression Console software (Affymetrix) employing the probe logarithmic intensity error algorithm (parameters - PM-GCBG background subtraction, quantile normalization, iterPLIER summarization) and the constant 16 was added to all the data points.

label_protocol: The samples were labelled according to standardized protocols and reagents from Affymetrix.

growth_protocol: Peripheral lung tissue was obtained from mice aged 2 weeks after in utero exposure to arsenic.

extract_protocol: Lung tissue was excised from mice, stabilized in RNALater and disrupted in TRIzol with a rotor stator homogenizer. RNA was extracted with TRIzol followed by RNeasy.

treatment_protocol: Pregnant mice were exposed to 0 (control) or 100μg/L arsenic via drinking water from day 8 of gestation until the birth of their offspring. Gene expression was profiled in peripheral lung of the offspring at two weeks postnatal age.

tag: strain

value: male

tag: age

value: 2 weeks

value: Peripheral lung

tag: treatment group

value: No treatment (Control)


title: R849W TIE2-transfected HUVECs, biological replicate 3

description: HUVEC - retroviral infection for R849W TIE2 overexpression.

source_name: R849W TIE2-expressing HUVEC, retroviral infection


title: Primary tumour region 9 RK29

value: region 9

tag: subject


title: C57BL/6, Control, male, biological rep1

description: C57 Ctr M_1


title: Primary tumour region 1 RMH3

description: clear cell Renal Cell Carinoma, region 1

value: Primary tumour

value: region 1

tag: disease state


title: Primary tumour region 3 RMH3

description: clear cell Renal Cell Carinoma, region 3

value: region 3

value: clear cell Renal Cell Carinoma


title: Primary tumour region 3 RMH8


title: R849W TIE2-transfected HUVECs, biological replicate 1


title: R849W TIE2-transfected HUVECs, biological replicate 2


title: C57BL/6, Control, female, biological rep3

description: C57 Ctr F_3

value: female


title: Primary tumour region 8 RK29

value: region 8


title: Primary tumour region 7 RK29

value: region 7


title: C57BL/6, Arsenic, male, biological rep3

description: C57 Ars M_3

value: In utero exposure to Arsenic


title: L914F TIE2-transfected HUVECs, biological replicate 2


title: Primary tumour region 11 RK29

value: region 11


title: C57BL/6, Arsenic, male, biological rep2

description: C57 Ars M_2


title: C57BL/6, Control, female, biological rep1

description: C57 Ctr F_1


title: Wild-type TIE2-transfected HUVECs, biological replicate 3

description: HUVEC - retroviral infection for wild-type TIE2 overexpression.

source_name: Wild-type TIE2-expressing HUVEC, retroviral infection

value: human umbilical vein endothelial cell (HUVEC)

value: wild-type


title: C57BL/6, Arsenic, male, biological rep1

description: C57 Ars M_1


title: Primary tumour region 2 RMH3

value: region 2


title: C57BL/6, Arsenic, female, biological rep3

description: C57 Ars F_3


title: Primary tumour region 5 RK29

description: clear cell Renal Cell Carinoma, region 5

value: region 5


title: Primary tumour region 1 RMH8


title: C57BL/6, Arsenic, female, biological rep2

description: C57 Ars F_2

value: 2 weeks


title: Non-transfected HUVECs, biological replicate 3

description: HUVEC - no retroviral infection.

source_name: Non-transfected HUVEC, uninfected

value: endogeneous


title: Non-transfected HUVECs, biological replicate 1

description: HUVEC - no retroviral infection.


title: C57BL/6, Arsenic, female, biological rep1

description: C57 Ars F_1

value: Peripheral lung


title: Non-transfected HUVECs, biological replicate 2

description: HUVEC - no retroviral infection.


title: Primary tumour region 3 RK29


title: Primary tumour region 4 RK29

value: region 4


title: Wild-type TIE2-transfected HUVECs, biological replicate 2


title: Primary tumour region 13 RK29

value: Primary tumour

value: region 13


title: C3H/HeARC, Control, male, biological rep2

description: C3H Ctr M_2

value: male

value: No treatment (Control)


title: sample ID 18=KEIO ID T469: noncancerous laryngeal tissue next to cancer A

city: Hachioji

first: Kaho

last: Minoura

state: Tokyo

institute: Agilent Technologies Japan Ltd

description:
KEIOID_T469:Larynx_6
noncancerous laryngeal tissue next to cancer A

hyb_protocol: Agilent miRNA Microarray protocol version 1.5 (December 2007). We used the Human miRNA Microarray Kit V2 (Agilent Technologies, Santa Clara, CA), which contains 20-40 features targeting each of 723 human miRNAs (Agilent design ID 019118) as annotated in the Sanger miRBase, release 10.1. The entire labeling reaction was hybridized to each array for 20 hours at 55°C.

data_processing:
TotalGeneSignal calculated with FeatureExtraction ver 9.5.3.1 followed Agilent GeneSpring GX7.3 analysis. Signal intensity less than 0.01 were set to 0.01. No global normalization was applied for 2 reasons: 1. the input amount of totalRNA was strictly controlled as 100 ng per sample, and 2. entire labeled molecules were hybridized to each array.
Normal controls and cancer samples were compared using Welch's t-test (p<0.05) and differentially expressed miRNAs with at least a 2-fold change in expression were considered to be potential biomarkers.

label_protocol: Agilent miRNA Microarray protocol version 1.5 (December 2007). One hundred ng of total RNA was used as an input into the labeling reaction.

extract_protocol: Total RNA including low molecular weight RNA from tissue samples was isolated using the mirVanaTM miRNA Isolation Kit (Ambion) according to the manufacturer's instructions. The quality of the RNA samples was assessed using an Agilent 2100 Bioanalyzer, and only the samples meeting the criteria of 28S/18S > 1 and RNA Integrity Number (RIN) ≥ 7.5 were used for all analyses.

value: noncancerous laryngeal tissue


title: sample ID 19=KEIO ID T479: noncancerous laryngeal tissue next to cancer B

description:
KEIOID_T479:Larynx_7
noncancerous laryngeal tissue next to cancer B

scan_protocol: Agilent miRNA Microarray protocol version 1.5 (December 2007).


title: Primary tumour region 2 RK29

value: clear cell Renal Cell Carinoma


title: Wild-type TIE2-transfected HUVECs, biological replicate 1


title: sample ID 14=KEIO ID T478: laryngeal cancer B

description:
KEIOID_T478:Larynx_2
laryngeal cancer B

source_name: laryngeal cancer

value: laryngeal cancer


title: C3H/HeARC, Control, female, biological rep3

description: C3H Ctr F_3

value: female


title: C3H/HeARC, Control, female, biological rep2

description: C3H Ctr F_2


title: C3H/HeARC, Control, female, biological rep1

description: C3H Ctr F_1


title: C3H/HeARC, Control, male, biological rep1

description: C3H Ctr M_1


title: C3H/HeARC, Control, male, biological rep3

description: C3H Ctr M_3


title: C3H/HeARC, Arsenic, male, biological rep2

description: C3H Ars M_2

value: In utero exposure to Arsenic


title: Primary tumour region 1 RK29

value: region 1


title: Primary tumour region 3 RK23

value: region 3


title: Primary tumour region 6 RK29

value: region 6


title: sample ID 13=KEIO ID T468: laryngeal cancer A

description:
KEIOID_T468:Larynx_1
laryngeal cancer A


title: C3H/HeARC, Arsenic, male, biological rep3

description: C3H Ars M_3


title: C3H/HeARC, Arsenic, male, biological rep1

description: C3H Ars M_1


title: Normal blood RK29

description: blood

value: blood

value: normal


title: C3H/HeARC, Arsenic, female, biological rep2

description: C3H Ars F_2

value: 2 weeks


title: Balb/c, Control, male, biological rep2

description: Balb Ctr M_2

value: Balb/c

value: Peripheral lung


title: C3H/HeARC, Arsenic, female, biological rep1

description: C3H Ars F_1


title: Primary tumour region 2 RK23

value: Primary tumour

value: region 2


title: C3H/HeARC, Arsenic, female, biological rep3

description: C3H Ars F_3


title: Balb/c, Control, male, biological rep3

description: Balb Ctr M_3

value: male


title: Normal blood RK23

description: blood


title: sample ID 15=KEIO ID T485: laryngeal cancer C

description:
KEIOID_T485:Larynx_3
laryngeal cancer C


title: Balb/c, Control, female, biological rep3

description: Balb Ctr F_3

value: No treatment (Control)


title: Balb/c, Control, male, biological rep1

description: Balb Ctr M_1


title: Primary tumour region 2 RK21


title: Primary tumour region 1 RK23


title: Primary tumour region 4 RK23

value: region 4


title: Primary tumour region 5 RK21

value: region 5

value: clear cell Renal Cell Carinoma


title: Primary tumour region 3 RK21


title: Balb/c, Control, female, biological rep1

description: Balb Ctr F_1

value: female


title: SW620 cells 6 days post doxorubicin

source_name: SW620 cells 6 days post doxorubicin

tag: cell line

value: Human  colon adenocarcinoma

value: Doxorubicin 9uM 2 hours

tag: time point

value: 6 days post drug removal


title: Primary tumour region 12 RK29

tag: tissue

value: region 12


title: SW620 cells 6 days post etoposide

source_name: SW620 cells 6 days post etoposide

value: Etoposide 60uM 2 hours


title: Balb/c, Control, female, biological rep2

description: Balb Ctr F_2

tag: gender


title: Balb/c, Arsenic, male, biological rep2

description: Balb Ars M_2

value: In utero exposure to Arsenic


title: Primary tumour region 4 RK21


title: SW620 cells 1 day post etoposide

source_name: SW620 cells 1 day post etoposide

value: 1 day post drug removal


title: SW620 cells 1 day post doxorubicin

source_name: SW620 cells 1 day post doxorubicin


title: Balb/c, Arsenic, male, biological rep3

description: Balb Ars M_3

value: Balb/c

value: 2 weeks


title: Primary tumour region 7 P7

value: Primary tumour

value: region 7


title: Balb/c, Arsenic, male, biological rep1

description: Balb Ars M_1

value: male

value: Peripheral lung


title: Primary tumour region 1 RK21

value: region 1


title: Primary tumour region 6 P7

value: region 6


title: Normal blood RK21

description: blood

value: blood

value: normal


title: thp1-del-2-b

city: Utrecht

last: Kemmeren

state: Utrecht

address: Universiteitsweg 100

department: Department of Molecular Cancer Research

institute: UMC Utrecht

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing:
genes, no bg corr, dye corr
limma

organism: Saccharomyces cerevisiae

label_protocol: robot amplification and labeling v1.0

growth_protocol: Yeast growth for expression profiling in Tecan platereader v1.0

extract_protocol: yeast HTP RNA isolation for robot v2.0

tag: genotype

source_name: refpool

growth_protocol: yeast-deleteome[grow]

extract_protocol: yeast RNA isolation for robotic amplification v1.0

value: wild type


title: Primary tumour region 3 P7

value: region 3

value: clear cell Renal Cell Carinoma


title: Primary tumour region 5 P7

value: region 5


title: SW620 cells un-treated

source_name: SW620 cells un-treated

value: Human  colon adenocarcinoma

tag: treatment

value: Un-treated

value: control


title: Primary tumour region 15 P7

value: region 15


title: Primary tumour region 9 P7

value: region 9


title: Balb/c, Arsenic, female, biological rep1

description: Balb Ars F_1

value: Balb/c

value: female

value: 2 weeks

value: In utero exposure to Arsenic


title: Balb/c, Arsenic, female, biological rep3

description: Balb Ars F_3

value: Peripheral lung


title: Balb/c, Arsenic, female, biological rep2

description: Balb Ars F_2


title: sem1-del-1-b


title: sem1-del-1-a


title: Primary tumour region 2 P7

value: Primary tumour

value: region 2


title: MelJuSo cells 6 days post doxorubicin

source_name: MelJuSo cells 6 days post doxorubicin

value: MelJuSo

value: Human skin melanoma cell line

value: Doxorubicin 9uM 2 hours

value: 6 days post drug removal


title: MelJuSo cells 6 days post etoposide

source_name: MelJuSo cells 6 days post etoposide

value: Etoposide 60uM 2 hours


title: Primary tumour region 13 P6

value: region 13

value: clear cell Renal Cell Carinoma


title: LNCaP-vector-DHT-3

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

hyb_protocol: 2.5ug of ST cDNA were hybridized for 18h at 45 degrees on theAffymetrix Gene ChIP Human gene 1.0 ST Array

scan_protocol: Arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000 with Command Console Software.

data_processing: Raw intensity files from the Affymetrix Human Gene 1.0 ST GeneChip arrays were processed using Affymetrix Expression Console version 1.1.   Gene-level expression measurements were computed using the iterPLIER algorithm on the “core” probesets and exported with annotation release 30, dated November 9th, 2009.

source_name: LNCaP-vector-DHT

label_protocol: Biotinylated cDNA were prepared according to standard NuGEN protocol from 50ug total RNA.

growth_protocol: LNCaP cells  were cultured in 5% FBS supplemented IMEM. They were seeded at 1.6x106 cells on poly-l-lysine coated plates and transfected with either 7ug of either pcDNA3.1 FLAG  or pcDNA3.1-BAF57-FLAG and 1ug each of H2B-GFP overnight in serum free medium.   Fresh 5% charcoal dextran treated (CDT) IMEM was replenished for 24h before treatment .

extract_protocol: Trizol extraction of RNA was performed as per manufacturer's instructions and purified using Qiagen RNAeasy Mini kit

treatment_protocol: Cells were treated for 12h with either 0.1% ethanol(vehicle control) or 1nM DHT

value: LNCaP

tag: transfection

value: pcDNA3.1 vector

value: DHT


title: MelJuSo cells 2 days post etoposide

source_name: MelJuSo cells 2 days post etoposide

value: 2 days post drug removal


title: MelJuSo cells 2 days post doxorubicin

source_name: MelJuSo cells 2 days post doxorubicin


title: thp1-del-2-a

value: wild type


title: Primary tumour region 15 P6

source_name: kidney

value: region 15


title: sac3-del-1-a


title: Primary tumour region 8 P6

value: region 8


title: LNCaP-BAF57-EtOH-3

value: EtOH


title: MelJuSo cells 1 day post etoposide rep 2

description: replicate 2

value: 1 day post drug removal


title: Normal kidney P7

description: normal adult kidney

value: Normal kidney

value: normal


title: Primary tumour region 11 P6

value: Primary tumour

value: region 11


title: sac3-del-1-b


title: Cumulus cells from oocyte at MI stage , biological rep1

description: Gene expression data from cumulus cells isolated from oocyte at MI stage

source_name: Cumulus cells isolated from oocyte at stage metaphase I (MI) of PCOS patients

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

value: Cumulus cells

tag: cell cyle

value: metaphase I

value: Polycystic ovary syndrome


title: Primary tumour region 10 P6

description: clear cell Renal Cell Carinoma, region 7

tag: tissue section

value: region 10

value: clear cell Renal Cell Carinoma


title: LNCaP-vector-DHT-2

value: LNCaP

value: pcDNA3.1 vector


title: Primary tumour region 12 P6

value: region 12

tag: batch


title: Cumulus cells from oocyte at MII stage , biological rep3

description: Gene expression data from cumulus cells isolated from oocyte at MII stage

source_name: Cumulus cells isolated from oocyte at stage metaphase II (MII) of PCOS patients

value: metaphase II


title: LNCaP-BAF57-EtOH-2


title: Cumulus cells from oocyte at MII stage , biological rep2


title: Primary tumour region 6 P6

value: region 6


title: LNCaP-vector-EtOH-1

source_name: LNCaP-vector-EtOH


title: Primary tumour region 5 P6

value: region 5


title: MelJuSo cells 1 day post doxorubicin rep 2

description: replicate 2

value: MelJuSo

value: Human skin melanoma cell line

value: Doxorubicin 9uM 2 hours


title: Primary tumour region 4 P6

value: region 4


title: 3D MDCK, biological rep6

status: Public on Jun 03 2013

city: New Haven

first: Erika

middle: Krystal

last: Wells

state: CT

address: 333 Cedar Street SHM B117/119

department: Cellular and Molecular Physiology

institute: Yale University

description: Gene expression data from multicellular MDCK cysts derived from 3D collagen type I culture

hyb_protocol: Fragments of 35-200 bases were hybridized to Affymetrix Canine Genome 2.0 Array at 45oC for 16 hours. Genechips were washed and stained with an Affymetrix fluidics station, stained with streptavidin-phycoerythrin and scanned with an Affymetrix GeneChip Scanner 3000.

scan_protocol: GeneChips were analyzed with Affymetrix GeneChip Operating Software (GCOS).

data_processing: The data were analyzed using Guanine and Cysteine-Robust Multiarray Analysis (GC-RMA).

organism: Canis lupus familiaris

source_name: MDCK cells grown in 3-dimensional collagen culture for 8 days

label_protocol: 5 ug of pooled total RNA was used to obtain biotinylated cRNA following the standard Affymetrix protocol

growth_protocol: MDCK II tet-off cells were grown in DMEM (Invitrogen) supplemented with 10% FBS, 1% penicillin/streptomycin, 1% L-glutamine and G418 (Gibco). Cells were maintained at 37oC with 5% CO2 atmosphere in a humidified incubator.

extract_protocol: Type I collagen gels were digested with 5 mls of a 0.01% collagenase mixture containing RNase OUT in PBS at 4oC for approximately 1 hour on a rotator. Following two low speed (500 rpm) spins and PBS washes 1ml TRIZol reagent was added to each individual sample. Total RNA was isolated following the manufacturer's instructions. Total RNA was purified using the Qiagen RNeasy Kit according to the manufacturer's instructions. Due to limitations in yield, 4 separate RNA samples were pooled for application to each individual array.

treatment_protocol: Fresh media was applied on the initial day of growth (day 0) and subsequently changed on days 3 and 6 of growth.  All cultures were grown until day 8.

tag: final morphology

value: Cysts

value: Madin-Darby Canine Kidney

tag: growth condition


title: MelJuSo cells un-treated

source_name: MelJuSo cells un-treated

tag: cell type

value: Un-treated

value: control


title: 3D MDCK, biological rep1


title: 3D MDCK, biological rep2


title: 3D MDCK, biological rep4


title: Cumulus cells from oocyte at MII stage , biological rep1

city: Yan tai

last: Huang

institute: Yuhuangding hospital of Yantai

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

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 to analyze the hybridization data.

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 arbitrarily set to 100.

value: Cumulus cells

value: Polycystic ovary syndrome


title: 3D MDCK, biological rep5


title: 3D MDCK, biological rep3


title: LNCaP-vector-EtOH-3

value: EtOH


title: MelJuSo cells 1 day post doxorubicin rep 1

description: replicate 1

value: 1 day post drug removal


title: Primary tumour region 3 P6

value: Primary tumour

value: region 3

value: clear cell Renal Cell Carinoma


title: 2D MDCK, biological rep6

description: Gene expression data from flat sheets of MDCK cells derived from 2D collagen type I culture

source_name: MDCK cells grown in 2-dimensional collagen culture for 8 days

value: Flat sheet


title: 2D MDCK, biological rep4


title: 2D MDCK, biological rep5


title: MelJuSo cells 1 day post etoposide rep 1

description: replicate 1

value: Etoposide 60uM 2 hours