title: GM11870-0hr

description:
Baseline, GM11870

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12390-0hr

status: Public on Aug 04 2011

type: RNA

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

country: USA

institute: Perelman School of Medicine at the University of Pennsylvania

description:
Baseline, GM12390

Gene expression data from lymphoblastoid cells prior to irradiation.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16-18 hr at 45C on Affymetrix GeneChip Human U133A 2.0 Chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Expression Console software using the MAS5 probe summary method and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lymphoblastoid cell line, 0hr

label_protocol: Biotinylated cRNA was prepared using the MessageAmp II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion/Applied Biosystems) from 1 microg of total RNA following manufacturer's instructions.

growth_protocol: The cells were grown at a density of 500,000 cells/ml in RPMI 1640 with 15% FBS, 1% penicillin-streptomycin, 2mM L-glutamine at 37°C in a humidified 5% CO2 chamber.

extract_protocol: RNA was extracted using the RNeasy Mini-Kit (Qiagen) as per the manufacturer's instructions.

treatment_protocol: 10 Gy of ionizing radiation (IR) in a 137Cs irradiator.

tag: coriell cell line

tag: cell type

value: lymphoblastoid cells

tag: ceph id

tag: relationship

value: daughter

tag: treatment

tag: treatment time


title: GM11875-0hr

description:
Baseline, GM11875

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12092-0hr

description:
Baseline, GM12092

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12396-0hr

description:
Baseline, GM12396

Gene expression data from lymphoblastoid cells prior to irradiation.

value: son


title: GM12464-0hr

description:
Baseline, GM12464

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12392-0hr

description:
Baseline, GM12392

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12463-0hr

description:
Baseline, GM12463

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12460-0hr

description:
Baseline, GM12460

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12459-0hr

description:
Baseline, GM12459

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12389-0hr

description:
Baseline, GM12389

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12457-0hr

description:
Baseline, GM12457

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12477-0hr

description:
Baseline, GM12477

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM13131-0hr

description:
Baseline, GM13131

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12476-0hr

description:
Baseline, GM12476

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12478-0hr

description:
Baseline, GM12478

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12458-0hr

description:
Baseline, GM12458

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12462-0hr

description:
Baseline, GM12462

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12393-0hr

description:
Baseline, GM12393

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12709-0hr

description:
Baseline, GM12709

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12461-0hr

description:
Baseline, GM12461

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12719-0hr

description:
Baseline, GM12719

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12710-0hr

description:
Baseline, GM12710

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12475-0hr

description:
Baseline, GM12475

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12712-0hr

description:
Baseline, GM12712

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12472-0hr

description:
Baseline, GM12472

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12711-0hr

description:
Baseline, GM12711

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12473-0hr

description:
Baseline, GM12473

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12108-0hr

description:
Baseline, GM12108

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12713-0hr

description:
Baseline, GM12713

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12715-0hr

description:
Baseline, GM12715

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12714-0hr

description:
Baseline, GM12714

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12105-0hr

description:
Baseline, GM12105

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12101-0hr

description:
Baseline, GM12101

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12102-0hr

description:
Baseline, GM12102

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12103-0hr

description:
Baseline, GM12103

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12104-0hr

description:
Baseline, GM12104

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12271-0hr

description:
Baseline, GM12271

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12106-0hr

description:
Baseline, GM12106

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12265-0hr

description:
Baseline, GM12265

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12267-0hr

description:
Baseline, GM12267

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12826-0hr

description:
Baseline, GM12826

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12270-0hr

description:
Baseline, GM12270

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12268-0hr

description:
Baseline, GM12268

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12822-0hr

description:
Baseline, GM12822

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12819-0hr

description:
Baseline, GM12819

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12328-0hr

description:
Baseline, GM12328

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12820-0hr

description:
Baseline, GM12820

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12107-0hr

description:
Baseline, GM12107

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12825-0hr

description:
Baseline, GM12825

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12838-0hr

description:
Baseline, GM12838

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12266-0hr

description:
Baseline, GM12266

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12824-0hr

description:
Baseline, GM12824

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12823-0hr

description:
Baseline, GM12823

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12835-0hr

description:
Baseline, GM12835

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12880-0hr

description:
Baseline, GM12880

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12833-0hr

description:
Baseline, GM12833

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12834-0hr

description:
Baseline, GM12834

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12836-0hr

description:
Baseline, GM12836

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12886-0hr

description:
Baseline, GM12886

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12879-0hr

description:
Baseline, GM12879

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12844-0hr

description:
Baseline, GM12844

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12837-0hr

description:
Baseline, GM12837

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12882-0hr

description:
Baseline, GM12882

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12900-0hr

description:
Baseline, GM12900

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12881-0hr

description:
Baseline, GM12881

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12474-0hr

description:
Baseline, GM12474

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12884-0hr

description:
Baseline, GM12884

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12883-0hr

description:
Baseline, GM12883

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12821-0hr

description:
Baseline, GM12821

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12885-0hr

description:
Baseline, GM12885

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12901-0hr

description:
Baseline, GM12901

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM11872-6hr

description:
6hr Post IR, GM11872

Gene expression data from lymphoblastoid cells following 10 Gy irradiation in a 137Cs irradiator.

source_name: Lymphoblastoid cell line, 6hr

value: ionizing radiation (IR)


title: GM12906-0hr

description:
Baseline, GM12906

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM11842-0hr

description:
Baseline, GM11842

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM11839-6hr

description:
6hr Post IR, GM11839

Gene expression data from lymphoblastoid cells following 10 Gy irradiation in a 137Cs irradiator.

value: maternal grandfather


title: Line B chicken intestine challenged 1 with Lesion Score 2

status: Public on Jul 01 2011

city: Blacksburg

first: Huifeng

last: Li

state: VA

address: 3570 Litton Reaves Hall

department: Animal and Poultry Sciences

institute: Virginia Tech

description:
Chicken intestine B-LS2-13
Gene expression data from intestine of line B chicken challenged with 1x 10^4 E. maxima oocysts.

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

scan_protocol: GeneChips were scanned using Affymetrix GeneChip(R) Scanner (GCS) 3000.

data_processing: The data were analyzed with ArrayAssist using GC-RMA.

organism: Gallus gallus

source_name: small intestine, line B, challenged with E. maxima oocysts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: Chickens were fed with commerical diet ad libitum and had free access to water.

extract_protocol: Total RNA was isolated for the microarray study. Chick intestinal samples were ground in mortar and pestle under liquid nitrogen individually. Total RNA from each intestinal sample was isolated using the RNeasy Mini Kit (Qiagen). One chick's sample was used for one microarray hybridization, no RNA pool was used.

treatment_protocol: Sixty-five male and 65 female line A and line B chicks were housed in batteries at 5-6 chicks per cage. Cages that housed 5 chicks contained either 2 males and 3 females or 3 males and 2 females.  Cages that housed 6 chicks had 3 females and 3 males.  Each battery contained an equal number of line A and line B chicks.  At 2 weeks of age, chicks were individually weighed and orally gavaged with low (1 x 10^4), medium (1.5 x 10^4), or high (2 x 10^4)  of E. maxima oocysts (USDA, Beltsville, MD) in 0.5 ml of water.  Control (non-challenged) chicks were placed in the top cages of the batteries to prevent cross-contamination.  Chicks challenged with the low, medium or high doses of E. maxima were randomly distributed in the other three levels of the batteries.  There were 6 replicate cages per treatment per line. In total, sixteen chicks were selected for the microarray experiment, including 4 control chicks and 4 low-dose treatment chicks from line A, and 4 control chicks and 4 low-dose treament chicks from line B.

tag: chicken line

value: B

tag: tissue

value: jejunum

tag: challenge

value: 1x10^4 Eimeria maxima oocysts

tag: lesion score


title: Line A chicken intestine challenged 3 with Lesion Score 3

description:
Chicken intestine A-LS3-7
Gene expression data from intestine of line A chicken challenged with 1x 10^4 E. maxima oocysts.

source_name: small intestine, line A, challenged with E. maxima oocysts

value: A


title: Line B chicken intestine challenged 3 with Lesion Score 4

description:
Chicken intestine B-LS3-15
Gene expression data from intestine of line B chicken challenged with 1x 10^4 E. maxima oocysts.


title: Line B chicken intestine challenged 4 with Lesion Score 4

description:
Chicken intestine B-LS4-16
Gene expression data from intestine of line B chicken challenged with 1x 10^4 E. maxima oocysts.


title: GM12899-0hr

description:
Baseline, GM12899

Gene expression data from lymphoblastoid cells prior to irradiation.


title: GM12839-0hr

description:
Baseline, GM12839

Gene expression data from lymphoblastoid cells prior to irradiation.


title: Line A chicken intestine challenged 4 with Lesion Score 4

description:
Chicken intestine A-LS4-8
Gene expression data from intestine of line A chicken challenged with 1x 10^4 E. maxima oocysts.


title: GM11831-6hr

description:
6hr Post IR, GM11831

Gene expression data from lymphoblastoid cells following 10 Gy irradiation in a 137Cs irradiator.


title: Line B chicken intestine challenged 2 with Lesion Score 3

description:
Chicken intestine B-LS2-14
Gene expression data from intestine of line B chicken challenged with 1x 10^4 E. maxima oocysts.


title: Line B chicken intestine control 2 with Lesion Score 0

description:
Chicken intestine B-C-LS0-10
Gene expression data from intestine of non-challenged line B chicken.

source_name: small intestine, line B, non-challenged


title: Line A chicken intestine challenged 2 with Lesion Score 1

description:
Chicken intestine A-LS1-6
Gene expression data from intestine of line A chicken challenged with 1x 10^4 E. maxima oocysts.


title: Line B chicken intestine control 3 with Lesion Score 0

description:
Chicken intestine B-C-LS0-11
Gene expression data from intestine of non-challenged line B chicken.


title: Line A chicken intestine challenged 1 with Lesion Score 1

description:
Chicken intestine A-LS1-5
Gene expression data from intestine of line A chicken challenged with 1x 10^4 E. maxima oocysts.


title: TMD8 shIRF4_3'UTR 24h - mAdbID:99965

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

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

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 99965

hyb_protocol: Agilent Hybridization Protocol Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 10.1.1.1). Spot values were normalized using the default linear-lowess normalization.

source_name: TMD8 shControl - 24 hr

label_protocol:
Cy3 Labeling Protocol
Other: A 1 ug of total RNA was labeled with Cy3.

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 24 hours.

value: blood

tag: cell line

tag: disease state

value: B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: TMD8 shIRF4_3'UTR - 24 hr

label_protocol:
Cy5 Labeling Protocol
Other: A 1 ug of total RNA was labeled with Cy5.

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shIRF4_3'UTR. shRNA expression was induced with doxycycline for 24 hours.


title: TMD8 shIRF4_3'UTR 48h - mAdbID:99966

description: mAdb experiment ID: 99966

source_name: TMD8 shControl - 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 48 hours.

source_name: TMD8 shIRF4_3'UTR - 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shIRF4_3'UTR. shRNA expression was induced with doxycycline for 48 hours.


title: Line B chicken intestine control 1 with Lesion Score 0

description:
Chicken intestine B-C-LS0-9
Gene expression data from intestine of non-challenged line B chicken.


title: OCILY3 shIRF4_3'UTR 96h - mAdbID:99897

description: mAdb experiment ID: 99897

source_name: OCILY3 shControl - 96 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 96 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 96 hours.

source_name: OCILY3 shIRF4_3'UTR - 96 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 96 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shIRF4_3'UTR. shRNA expression was induced with doxycycline for 96 hours.


title: TMD8 shIRF4_3'UTR 72h - mAdbID:99967

description: mAdb experiment ID: 99967

source_name: TMD8 shControl - 72 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 72 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 72 hours.

source_name: TMD8 shIRF4_3'UTR - 72 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 72 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shIRF4_3'UTR. shRNA expression was induced with doxycycline for 72 hours.


title: Line A chicken intestine control 1 with Lesion Score 0

description:
Chicken intestine A-C-LS0-1
Gene expression data from intestine of non-challenged line A chicken.

source_name: small intestine, line A, non-challenged


title: Line A chicken intestine control 4 with Lesion Score 1

description:
Chicken intestine A-C-LS1-4
Gene expression data from intestine of non-challenged line A chicken.


title: Line B chicken intestine control 4 with Lesion Score 1

description:
Chicken intestine B-C-LS1-12
Gene expression data from intestine of non-challenged line B chicken.


title: Line A chicken intestine control 3 with Lesion Score 0

description:
Chicken intestine A-C-LS0-3
Gene expression data from intestine of non-challenged line A chicken.


title: TMD8 shIRF4_3'UTR 96h - mAdbID:99968

description: mAdb experiment ID: 99968

source_name: TMD8 shControl - 96 hr

source_name: TMD8 shIRF4_3'UTR - 96 hr


title: OCILY3 shIRF4_3'UTR 72h - mAdbID:99896

description: mAdb experiment ID: 99896

source_name: OCILY3 shControl - 72 hr

source_name: OCILY3 shIRF4_3'UTR - 72 hr


title: Line A chicken intestine control 2 with Lesion Score 0

description:
Chicken intestine A-C-LS0-2
Gene expression data from intestine of non-challenged line A chicken.


title: KMS12 shIRF4_3'UTR 48h - repeat 1 - mAdbID:87190

description: mAdb experiment ID: 87190

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.5.1.1). Spot values were normalized using the default linear-lowess normalization.

source_name: KMS12 shi_2046 Untreated

label_protocol:
Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
Trizol Total RNA
Extraction method: Trizol
Other: Total RNA was extracted using Trizol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).

value: myeloma

tag: genotype/variation

value: shirf4_2046 (shIRFb)

source_name: KMS12 shi_2046 day2

label_protocol:
Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

treatment_protocol:
Treatment type: compound
Agent: doxycycline
Treatment dose: 20 ng/ml
Treatment time: 2 days
Treatment temperature: 37c


title: HBL-1 shIRF4_3'UTR 24h - mAdbID:99872

description: mAdb experiment ID: 99872

source_name: HBL-1 shControl - 24 hr

source_name: HBL-1 shIRF4_3'UTR - 24 hr


title: OCILY3 shIRF4_3'UTR 24h - mAdbID:99894

description: mAdb experiment ID: 99894

source_name: OCILY3 shControl - 24 hr

source_name: OCILY3 shIRF4_3'UTR - 24 hr


title: HBL-1 shIRF4_cds 48h - mAdbID:99877

description: mAdb experiment ID: 99877

source_name: HBL-1 shControl - 48 hr

source_name: HBL-1 shIRF4_cds - 48 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 48 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shIRF4_cds. shRNA expression was induced with doxycycline for 48 hours.


title: KMS12 shIRF4_3'UTR 144h - repeat 1 - mAdbID:87193

description: mAdb experiment ID: 87193

source_name: KMS12 shi_2046 day6

treatment_protocol:
Treatment type: compound
Agent: doxycycline
Treatment dose: 20 ng/ml
Treatment time: 6 days
Treatment temperature: 37c


title: HBL-1 shIRF4_cds 24h - mAdbID:99876

description: mAdb experiment ID: 99876

source_name: HBL-1 shIRF4_cds - 24 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 24 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shIRF4_cds. shRNA expression was induced with doxycycline for 24 hours.


title: HBL-1 shIRF4_cds 72h - mAdbID:99878

description: mAdb experiment ID: 99878

source_name: HBL-1 shControl - 72 hr

source_name: HBL-1 shIRF4_cds - 72 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 72 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shIRF4_cds. shRNA expression was induced with doxycycline for 72 hours.


title: HBL-1 shIRF4_3'UTR 72h - mAdbID:99874

description: mAdb experiment ID: 99874

source_name: HBL-1 shIRF4_3'UTR - 72 hr


title: KMS12 shIRF4_3'UTR 96h - repeat 1 - mAdbID:87191

description: mAdb experiment ID: 87191

source_name: KMS12 shi_2046 day4

treatment_protocol:
Treatment type: compound
Agent: doxycycline
Treatment dose: 20 ng/ml
Treatment time: 4 days
Treatment temperature: 37c


title: KMS12 shIRF4_3'UTR 96h - repeat 2 - mAdbID:87192

description: mAdb experiment ID: 87192


title: OCILY3 shIRF4_3'UTR 48h - mAdbID:99895

description: mAdb experiment ID: 99895

source_name: OCILY3 shControl - 48 hr

source_name: OCILY3 shIRF4_3'UTR - 48 hr


title: HBL-1 shIRF4_cds 96h - mAdbID:99879

description: mAdb experiment ID: 99879

source_name: HBL-1 shControl - 96 hr

source_name: HBL-1 shIRF4_cds - 96 hr

treatment_protocol:
Treatment type: shRNA transduction
Treatment time: 96 hours
In-vitro treatment: Cells were transduced with retroviral vectors expressing shIRF4_cds. shRNA expression was induced with doxycycline for 96 hours.


title: HBL-1 shIRF4_3'UTR 96h - mAdbID:99875

description: mAdb experiment ID: 99875

source_name: HBL-1 shIRF4_3'UTR - 96 hr


title: HBL-1 shIRF4_3'UTR 48h - mAdbID:99873

description: mAdb experiment ID: 99873

source_name: HBL-1 shIRF4_3'UTR - 48 hr


title: NA18980_2 genotyping at HMS (NimbleGen 2.1M)

status: Public on Jun 30 2011

type: genomic

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

hyb_protocol: Hybridizations were performed according to manufacture's instructions, carried out on the Maui Hybridization System (BioMicro Systems Inc).

scan_protocol: Arrays were scanned on a DNA Microarray Scanner with Surescan High-Resolution Technology (G2464CA, Agilent Technologies)

data_processing:
Normalization was performed using the segMNT algorithm at a 1X window averaging a minimum segment difference score of 0.3)
The Nexus rank segmentation software was used for CNV discovery

molecule: genomic DNA

source_name: Input DNA from Coriell Cell Repositories

label_protocol: 1 ug reactions of each sample were labeled in quadruplicate according to manufacture's instructions using cy3 and cy5-random nonamers

extract_protocol: DNA was obtained from Coriell Cell Repositories, extracted from lymphoblastoid cell lines.


title: NA18980_3 genotyping at HMS (NimbleGen 2.1M)


title: NA12239_3 genotyping at HMS (NimbleGen 2.1M)


title: NA18576_3 genotyping at HMS (NimbleGen 2.1M)


title: NA18576_1 genotyping at HMS (NimbleGen 2.1M)


title: NA12239_2 genotyping at HMS (NimbleGen 2.1M)


title: NA18576_3 genotyping at WTSI (NimbleGen 2.1M)


title: NA18517_3 genotyping at HMS (NimbleGen 2.1M)


title: NA18980_3 genotyping at WTSI (NimbleGen 2.1M)


title: NA12239_3 genotyping at WTSI (NimbleGen 2.1M)


title: NA10851_3 genotyping at HMS (NimbleGen 2.1M)


title: NA18517_1 genotyping at WTSI (NimbleGen 2.1M)


title: NA18576_2 genotyping at HMS (NimbleGen 2.1M)


title: NA12239_1 genotyping at WTSI (NimbleGen 2.1M)


title: NA18517_2 genotyping at WTSI (NimbleGen 2.1M)


title: NA18517_3 genotyping at WTSI (NimbleGen 2.1M)


title: NA18980B genotyping at WTSI (WGTS)

hyb_protocol: Microarray hybridizations were performed as previously described (Fiegler, H et al, Nature 444, 444-454 2006)

scan_protocol: Array images were acquired using a 5-um resolution Agilent Technologies G2505A laser scanner. Fluorescence intensities and log2 ration values were extracted using BlueFuse software.

data_processing:
After image quantification, log2 ratio calulation and block median normalization, a G+C correction was introduced, consisting of normalizing the log 2 ratios of each clone using the G+C percent of that clone
Copy number variable segments were detected using to CNVfinder algorithm.

label_protocol: The first two replicates were run with the test labeled with Cy5 and reference with Cy3; the third replicate consisted of the dye swap.

value: lymphoblastoid cell lines

tag: batch number

tag: genotyping center

value: WTSI


title: NA18576_2 genotyping at WTSI (NimbleGen 2.1M)


title: NA10851_1 genotyping at HMS (NimbleGen 2.1M)


title: NA18576_1 genotyping at WTSI (NimbleGen 2.1M)


title: NA15510_3 genotyping at WTSI (NimbleGen 2.1M)


title: NA18980_1 genotyping at HMS (NimbleGen 2.1M)


title: NA15510_1 genotyping at WTSI (NimbleGen 2.1M)


title: NA15510_3 genotyping at HMS (NimbleGen 2.1M)


title: NA15510_2 genotyping at HMS (NimbleGen 2.1M)


title: NA18980A genotyping at WTSI (WGTS)


title: NA15510_2 genotyping at WTSI (NimbleGen 2.1M)


title: NA18980C genotyping at WTSI (WGTS)


title: NA18517_1 genotyping at HMS (NimbleGen 2.1M)


title: NA18980_1 genotyping at WTSI (NimbleGen 2.1M)


title: NA18980_2 genotyping at WTSI (NimbleGen 2.1M)


title: NA15510B genotyping at WTSI (WGTS)


title: NA18517B genotyping at WTSI (WGTS)


title: NA15510C genotyping at WTSI (WGTS)


title: NA10851_2 genotyping at HMS (NimbleGen 2.1M)


title: NA10851C genotyping at WTSI (WGTS)


title: NA12239B genotyping at WTSI (WGTS)


title: NA12239_2 genotyping at WTSI (NimbleGen 2.1M)


title: NA10851A genotyping at WTSI (WGTS)


title: NA10851B genotyping at WTSI (WGTS)


title: NA18576B genotyping at WTSI (WGTS)


title: NA18517C genotyping at WTSI (WGTS)


title: NA12239A genotyping at WTSI (WGTS)


title: NA18576C genotyping at WTSI (WGTS)


title: NA15510A genotyping at WTSI (WGTS)


title: NA12239C genotyping at WTSI (WGTS)


title: NA18517_3 genotyping at WTSI 2 (G4423B 018898)

hyb_protocol: On each slide, a total combined 55ug of DNA was hybridized according to the 40-hour manual protocol described by manufacturer.

scan_protocol: Arrays were scanned at 5 micron resolution in an Agilent Scanner

data_processing: Images were processed with Agilent Feature Extraction v9.5.1.1, and were required to show derivative Log Ratio spread (DLRS) values < 0.3. CNV detection was performed using Agilent's ADM-2 and also with the Nexus rank segmentation software.

label_protocol: Invitrogen BioPrime CGH labeling kit was used (cat. No. 18094011), according to the manufactures protocol.

tag: batch

tag: site


title: NA18980_1 genotyping at WTSI 2 (G4423B 018898)


title: NA18576_2 genotyping at WTSI 2 (G4423B 018898)


title: NA18576A genotyping at WTSI (WGTS)


title: NA18980_3 genotyping at WTSI 2 (G4423B 018898)


title: NA18576_1 genotyping at WTSI 2 (G4423B 018898)


title: NA18980_2 genotyping at WTSI 2 (G4423B 018898)


title: NA10851_3 genotyping at WTSI 2 (G4423B 018898)

label: c5; self_self


title: NA15510_3 genotyping at WTSI 2 (G4423B 018898)


title: NA12239_3 genotyping at WTSI 2 (G4423B 018898)


title: NA18517_2 genotyping at WTSI 2 (G4423B 018898)


title: NA10851_2 genotyping at WTSI 2 (G4423B 018898)


title: NA10851_3 genotyping at WTSI (NimbleGen 2.1M)


title: NA10851_1 genotyping at WTSI 2 (G4423B 018898)


title: NA15510_1 genotyping at WTSI 2 (G4423B 018898)


title: NA18980_3 genotyping at WTSI 1 (G4423B 018898)


title: NA12239_2 genotyping at WTSI 2 (G4423B 018898)


title: NA15510_2 genotyping at WTSI 2 (G4423B 018898)


title: NA18576_3 genotyping at WTSI 1 (G4423B 018898)


title: NA18980_1 genotyping at WTSI 1 (G4423B 018898)


title: NA18517_3 genotyping at WTSI 1 (G4423B 018898)


title: NA18517A genotyping at WTSI (WGTS)


title: NA18980_2 genotyping at WTSI 1 (G4423B 018898)


title: NA18517_2 genotyping at WTSI 1 (G4423B 018898)


title: NA18576_3 genotyping at WTSI 2 (G4423B 018898)


title: NA15510_2 genotyping at WTSI 1 (G4423B 018898)


title: NA12239_1 genotyping at WTSI 2 (G4423B 018898)


title: NA18576_2 genotyping at WTSI 1 (G4423B 018898)


title: NA10851_1 genotyping at WTSI (NimbleGen 2.1M)


title: NA18576_1 genotyping at WTSI 1 (G4423B 018898)


title: NA12239_2 genotyping at WTSI 1 (G4423B 018898)


title: NA15510_1 genotyping at WTSI 1 (G4423B 018898)


title: NA18517_1 genotyping at WTSI 2 (G4423B 018898)


title: NA15510_3 genotyping at WTSI 1 (G4423B 018898)


title: NA18517_1 genotyping at WTSI 1 (G4423B 018898)


title: NA10851_2 genotyping at WTSI (NimbleGen 2.1M)


title: NA12239_1 genotyping at WTSI 1 (G4423B 018898)


title: NA12239_3 genotyping at WTSI 1 (G4423B 018898)


title: NA18980_1 genotyping at TCAG (G4423B 018898)

value: TCAG


title: NA10851_3 genotyping at WTSI 1 (G4423B 018898)


title: NA18576_1 genotyping at TCAG (G4423B 018898)


title: NA18980_3 genotyping at TCAG (G4423B 018898)


title: NA10851_2 genotyping at WTSI 1 (G4423B 018898)


title: NA15510_2 genotyping at TCAG (G4423B 018898)


title: NA18517_3 genotyping at TCAG (G4423B 018898)


title: NA18576_2 genotyping at TCAG (G4423B 018898)


title: NA18517_2 genotyping at TCAG (G4423B 018898)


title: NA18517_1 genotyping at TCAG (G4423B 018898)


title: NA10851_3 genotyping at TCAG (G4423B 018898)

label: c3; self_self


title: NA15510_3 genotyping at TCAG (G4423B 018898)


title: NA10851_2 genotyping at TCAG (G4423B 018898)


title: NA10851_2 genotyping at TCAG (G4423B 018897)


title: NA10851_1 genotyping at WTSI 1 (G4423B 018898)


title: NA15510_1 genotyping at TCAG (G4423B 018898)


title: NA12239_3 genotyping at TCAG (G4423B 018898)


title: NA10851_1 genotyping at TCAG (G4423B 018898)


title: NA12239_2 genotyping at TCAG (G4423B 018898)


title: NA18980_1 genotyping at TCAG (G4423B 018897)


title: NA12239_1 genotyping at TCAG (G4423B 018898)


title: NA10851_3 genotyping at TCAG (G4423B 018897)


title: NA18980_2 genotyping at TCAG (G4423B 018897)


title: NA18980_3 genotyping at TCAG (G4423B 018897)


title: NA18576_3 genotyping at TCAG (G4423B 018898)


title: NA18576_2 genotyping at TCAG (G4423B 018897)


title: NA10851_1 genotyping at TCAG (G4423B 018897)


title: NA18980_2 genotyping at TCAG (G4423B 018898)


title: NA18517_2 genotyping at TCAG (G4423B 018897)


title: NA18576_3 genotyping at TCAG (G4423B 018897)


title: NA18517_3 genotyping at TCAG (G4423B 018897)


title: NA18517_1 genotyping at TCAG (G4423B 018897)


title: NA15510_2 genotyping at TCAG (G4423B 018897)


title: NA15510_3 genotyping at TCAG (G4423B 018897)


title: NA12239_3 genotyping at TCAG (G4423B 018897)


title: NA12239_3 genotyping at WTSI (NimbleGen 720K)


title: NA18576_1 genotyping at TCAG (G4423B 018897)


title: NA12239_2 genotyping at TCAG (G4423B 018897)


title: NA18517_3 genotyping at WTSI (NimbleGen 720K)


title: pediatric T-ALL patient #96 reanalysis

status: Public on Apr 11 2011

city: Utrecht

first: Jules

last: Meijerink

address: Uppsalalaan 8

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267382

hyb_protocol: Hybridization of Humane Genome U133 plus2.0 oligonucleotide microarrays (Affymetrix, Santa-Clara, USA) and washing steps were performed according to the manufacturers’ protocol.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip scanner 3000

data_processing:
Probeset intensities were extracted in R (R2.10.1).
Probeset intensities have been RMA-solo, RMA or VSN normalized

source_name: pediatric T-ALL patient #96

label_protocol: Copy-DNA and ccRNA syntheses from total RNA, hybridization of Humane Genome U133 plus2.0 oligonucleotide microarrays (Affymetrix, Santa-Clara, USA) and washing steps were performed according to the manufacturers’ protocol.

extract_protocol: Genomic DNA and total cellular RNA were isolated using Trizol (Invitrogen) according to the manufacturers’ protocol, with minor modifications. An additional phenol-chloroform extraction was performed and the RNA was precipitated with isopropanol along with 1 mL (20 mg/mL) glycogen (Roche, Almere, The Netherlands). After precipitation, RNA pellets were dissolved in 20 mL RNAse-free TE-buffer (10 mM Tris-HCl, 1 mM EDTA, pH=8.0). The RNA concentration was quantified spectrophotometrically. Integrity of total RNA was checked using the Agilent 2100 Bio-analyzer (Agilent, Santa-Clara, USA).

treatment_protocol: Leukemic cells were isolated and enriched from these samples. Within 24 hours after sampling, mononuclear cells were isolated by density gradient centrifugation using Lymphoprep (density 1.077 g/mL; Nycomed Pharma, Oslo, Norway), and centrifuged at 480g for 15 minutes at room temperature. The collected mononuclear cells were washed twice and kept in culture medium consisting of RPMI 1640 medium (Dutch modification without L-glutamine; Gibco BRL, Life Technologies, Breda, The Netherlands), 20% fetal calf serum (FCS; Integro, Zaandam, The Netherlands), 2 mM L-glutamine (Gibco BRL, Life Technologies) 5 µg/mL insulin, 5 µg/mL transferrin, 5 ng/mL sodium selenite (ITS media supplement; Sigma, St Louis, MO), 100 IU/mL penicillin, 100 µg/mL streptomycin, 0.125 µg/mL fungizone (Gibco BRL, Life Technologies), and 0.2 mg/mL gentamycin (Gibco BRL, Life Technologies). Contaminating nonleukemic cells were removed by immunomagnetic beads. as described by Kaspers et al (1994). All resulting samples contained 90% leukemic cells, as determined morphologically by May-Grünwald-Giemsa-stained cytospins (Merck, Darmstadt, Germany). Viably frozen T-ALL cells were used for DNA and RNA extraction, and a minimum of 5 million leukemic cells were lysed in Trizol reagent (Invitrogen, Life Technologies, Breda, The Netherlands) and stored at -80°C.

value: pediatric T-ALL cells

tag: cytogenetics


title: NA15510_1 genotyping at TCAG (G4423B 018897)


title: pediatric T-ALL patient #98 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267384

source_name: pediatric T-ALL patient #98

tag: cell type


title: NA18576_3 genotyping at WTSI (NimbleGen 720K)


title: pediatric T-ALL patient #94 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267380

data_processing:
Probeset intensities were extracted in R versions 2.8.0 and 2.10.0.
Probeset intensities were normalized using RMA.

source_name: pediatric T-ALL patient #94


title: pediatric T-ALL patient #97 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267383

source_name: pediatric T-ALL patient #97


title: NA18980_3 genotyping at WTSI (NimbleGen 720K)


title: NA12239_1 genotyping at TCAG (G4423B 018897)


title: pediatric T-ALL patient #99 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267385

source_name: pediatric T-ALL patient #99


title: NA10851_3 genotyping at WTSI (NimbleGen 720K)


title: pediatric T-ALL patient #89 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267375

source_name: pediatric T-ALL patient #89


title: NA18980_2 genotyping at WTSI (NimbleGen 720K)


title: pediatric T-ALL patient #85 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267371

source_name: pediatric T-ALL patient #85


title: pediatric T-ALL patient #90 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267376

source_name: pediatric T-ALL patient #90


title: pediatric T-ALL patient #87 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267373

source_name: pediatric T-ALL patient #87


title: NA18517_1 genotyping at WTSI (NimbleGen 720K)


title: pediatric T-ALL patient #88 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267374

source_name: pediatric T-ALL patient #88


title: pediatric T-ALL patient #86 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267372

source_name: pediatric T-ALL patient #86


title: pediatric T-ALL patient #84 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267370

source_name: pediatric T-ALL patient #84


title: pediatric T-ALL patient #81 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267367

source_name: pediatric T-ALL patient #81


title: pediatric T-ALL patient #83 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267369

source_name: pediatric T-ALL patient #83


title: pediatric T-ALL patient #95 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267381

source_name: pediatric T-ALL patient #95


title: pediatric T-ALL patient #82 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267368

source_name: pediatric T-ALL patient #82


title: NA12239_2 genotyping at WTSI (NimbleGen 720K)

source_name: Input DNA from Coriell Cell Repositories


title: NA18517_2 genotyping at WTSI (NimbleGen 720K)


title: pediatric T-ALL patient #80 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267366

source_name: pediatric T-ALL patient #80


title: NA15510_3 genotyping at WTSI (NimbleGen 720K)


title: NA10851_2 genotyping at WTSI (NimbleGen 720K)


title: NA18576_2 genotyping at WTSI (NimbleGen 720K)


title: NA15510_2 genotyping at WTSI (NimbleGen 720K)


title: pediatric T-ALL patient #92 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267378

source_name: pediatric T-ALL patient #92


title: NA10851_1 genotyping at WTSI (NimbleGen 720K)


title: NA18576_1 genotyping at WTSI (NimbleGen 720K)


title: NA15510_1 genotyping at WTSI (NimbleGen 720K)


title: pediatric T-ALL patient #77 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267363

source_name: pediatric T-ALL patient #77


title: NA18980_1 genotyping at WTSI (NimbleGen 720K)


title: pediatric T-ALL patient #93 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267379

source_name: pediatric T-ALL patient #93


title: pediatric T-ALL patient #138

source_name: pediatric T-ALL patient #140

value: unknown


title: NA12239_1 genotyping at WTSI (NimbleGen 720K)


title: pediatric T-ALL patient #74 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267360

source_name: pediatric T-ALL patient #74


title: pediatric T-ALL patient #79 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267365

source_name: pediatric T-ALL patient #79


title: pediatric T-ALL patient #143


title: pediatric T-ALL patient #136 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267410

source_name: pediatric T-ALL patient #136


title: pediatric T-ALL patient #131 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267406

source_name: pediatric T-ALL patient #131


title: pediatric T-ALL patient #140 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267412


title: pediatric T-ALL patient #142


title: pediatric T-ALL patient #133 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267408

source_name: pediatric T-ALL patient #133


title: pediatric T-ALL patient #91 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267377

source_name: pediatric T-ALL patient #91


title: pediatric T-ALL patient #137 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267411

source_name: pediatric T-ALL patient #137


title: pediatric T-ALL patient #132 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267407

source_name: pediatric T-ALL patient #132


title: pediatric T-ALL patient #129 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267404

source_name: pediatric T-ALL patient #129


title: pediatric T-ALL patient #128 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267403

source_name: pediatric T-ALL patient #128


title: pediatric T-ALL patient #75 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267361

source_name: pediatric T-ALL patient #75


title: pediatric T-ALL patient #127 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267402

source_name: pediatric T-ALL patient #127


title: pediatric T-ALL patient #73 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267359

source_name: pediatric T-ALL patient #73


title: pediatric T-ALL patient #141


title: pediatric T-ALL patient #78 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267364

source_name: pediatric T-ALL patient #78


title: pediatric T-ALL patient #124 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267399

source_name: pediatric T-ALL patient #124

value: HOXA


title: pediatric T-ALL patient #119


title: pediatric T-ALL patient #126 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267401

source_name: pediatric T-ALL patient #126


title: pediatric T-ALL patient #116

source_name: pediatric T-ALL patient #140


title: pediatric T-ALL patient #130 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267405

source_name: pediatric T-ALL patient #130


title: pediatric T-ALL patient #145


title: pediatric T-ALL patient #125 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267400

source_name: pediatric T-ALL patient #125


title: pediatric T-ALL patient #135 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267409

source_name: pediatric T-ALL patient #135


title: pediatric T-ALL patient #120 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267395

source_name: pediatric T-ALL patient #120


title: pediatric T-ALL patient #121 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267396

source_name: pediatric T-ALL patient #121


title: pediatric T-ALL patient #123 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267398

source_name: pediatric T-ALL patient #123


title: pediatric T-ALL patient #118


title: pediatric T-ALL patient #122 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267397

source_name: pediatric T-ALL patient #122


title: pediatric T-ALL patient #76 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267362

source_name: pediatric T-ALL patient #76


title: HeLa_Scaffold_rep134_ENCODE1.0F

status: Public on Mar 23 2011

city: Charlottesville

first: Mignon

middle: A

last: Keaton

address: 1340 Jefferson Park Ave, Rm 1232

department: Biochemistry and Molecular Genetics

institute: University of Virginia

description: Three biological Replicates of nuclear scaffold DNA (scaffold_1, scaffold_3, and scaffold_4), two biological replicates of genomic DNA (genomic_1, genomic_3) and one technical replicate of genomic DNA (genomic_2) hybridized to ENCODE 1.0F tiling array.

hyb_protocol: 5 ug of labeled DNA was hybridization to the arrays according to manufacturer’s protocol

scan_protocol: Each microarray was scanned and analyzed for signal intensities using a GeneChIP Scanner 3000 and GeneChIP Operating Software (GCOS; Affymetrix).

data_processing:
Hybridization data was analysed using Model-based analysis tool (MAT) for tiling arrays (Johnson et al., 2006) and genomic positions (using the hg17 build (May 2004) of the Human genome assembly) with BbandWidth=500 MaxGap=500 and Pvalue cuttoff =1.00e-03 to generate the bar file of MAT score (MAT_rep134_p3.encode_ncbiv35.bpmap_matscore.bar) and bed file of nuclear scaffold attachment sites (MAT_rep134_p3.bed).
Nuclear scaffold attachment regions were remapped to the hg18 build of the genome using the UCSC Genome Browser liftover tool (http://genome.ucsc.edu), trimmed to the ENCODE pilot region cooridinates (hg18), and any intervals that were less than 2501 bp apart were joined to account for potential gaps in the data due to repetitive sequences that were not spotted on the microarray to generate MAT_rep134_p3.hg18.bed.trim.join2500bp.bed file.

The bar and bed files are linked as supplementary files on the Series record.

source_name: Nuclear Scaffold DNA purified from HeLa cells

label_protocol: Samples were fragmented to 50-100bp size by DNaseI treatment and the fragmented DNA was labeled  with biotin-ddATP using terminal tranferase.

growth_protocol: Adherant HeLa (ATCC CCL-2) cells were maintained in DMEM/high glucose (Hyclone, Thermo Scientific) in the presence of 10% DCS and 1X penicillin/streptomycin at in 5% CO2 37 degrees.

extract_protocol: Sample DNA was recovered by proteinase K treatment, phenol:chlorofom:isoamyl extraction, and ethanol precipitation from either fractionated nuclear scaffolds (scaffold samples) or total cell lysate (genomic samples). Genomic DNA was further purifed by phenol:chlorofom:isoamyl extraction and ethanol precipitation following digestion with restriction enzymes.

value: HeLa

tag: sample type

value: fractionated nuclear scaffold

source_name: HeLa genomic DNA digested with EcoRI and HindIIII

extract_protocol: Sample DNA was recovered by proteinase K treatment, phenol:chlorofom:isoamyl extraction, and ethanol precipitation from either fractionated nuclear scaffold (scaffold samples) or total cell lysate (genomic samples). Genomic DNA was further purifed by phenol:chlorofom:isoamyl extraction and ethanol precipitation following digestion with restriction enzymes.

value: total cell lysate


title: pediatric T-ALL patient #113


title: pediatric T-ALL patient #111


title: roots Rm1021 at 21d

status: Public on Mar 26 2011

city: Stanford

first: Adriana

middle: Parra

last: Rightmyer

state: CA

address: 371 Serra Mall

department: Biology

institute: Stanford University

description:
A17_Rm1021_21d
Gene expression data from roots harvested 21 day after Rm 1021 treatment.

hyb_protocol: Hybridization was performed as described in the Affymetrix technical manual, at the Stanford Protein and Nucleic Acid Facility (Stanford, CA).

scan_protocol: Scanning were performed as described in the Affymetrix technical manual.

data_processing: Pixel values were extracted from scan files by using Affymetrix MAS 5.0 software, and .CEL files were analyzed by using DCHIP 1.3. Probe sets specifying bacterial genes were masked before analysis. Expression analysis was performed as described in Mitra et al., 2004 (PMID 15220482). The data from the independent biological replicates for each condition were combined.

organism: Medicago truncatula

source_name: roots harvested 21 days after Rm1021 treatment

label_protocol: Biotin-labeled cRNA was synthesized using the BioArray high yield RNA transcription labeling kit (Enzo diagnostics).

growth_protocol: Twenty M. truncatula plants were grown per Petri plate (240835, Nunc, Rochester, NY, USA) containing buffered nodulation medium (BNM; Ehrhardt et al., 1992), pH6.5 with 1 mM α-aminoisobutyric acid (AIB). Three plates were performed at this time point and treatment.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was used for double-stranded cDNA synthesis.

treatment_protocol: Plants were inoculated 6 d after planting with either 1 μl of a suspension of Rm1021 (optical density at 600 nm [OD600]=0.05) or 1 μl of 0.5X BNM as a mock control.

tag: cultivar

value: Jemalong A17

tag: genotype

value: wild-type

value: roots

tag: growth condition

value: BNM containing 2.5% (w/v) agar

value: Sinorhizobium meliloti Rm1021

tag: time after treatment

value: 21 days

tag: amount of total rna

value: 40 µg


title: pediatric T-ALL patient #114


title: pediatric T-ALL patient #104 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267390

source_name: pediatric T-ALL patient #104


title: pediatric T-ALL patient #107 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267393

source_name: pediatric T-ALL patient #107


title: pediatric T-ALL patient #117


title: pediatric T-ALL patient #103 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267389

source_name: pediatric T-ALL patient #103


title: pediatric T-ALL patient #110


title: pediatric T-ALL patient #115


title: pediatric T-ALL patient #112


title: pediatric T-ALL patient #101 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267387

source_name: pediatric T-ALL patient #101


title: YDFR.C, rep2

status: Public on Mar 17 2011

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

description:
YDFR-sub-cutan variant, replicate 2
Gene expression of YDFR, cutaneous variant

hyb_protocol: according to the instruction manual, as described in the Affymetrix website

data_processing:
Onlyl gene-level analyses was performed. RMA normalization, summarization by mean and batch effect removal, all were done by Partek Genomics suite (version 6.5) Copyright © 2010).
Log2 signal intensities after normalization, summarization and batch effect removal, as implicated in the "data processing" raw. Only 17881 probes remain after sumarization.

source_name: YDFR, cutaneous variant

growth_protocol: Cells were grown in RPMI-1640 medium supplemented with 10% heat-inactivated fetal calf serum (FCS), 2 mmol/ml L-glutamine, 0.01 M HEPES buffered saline, 100 units/ml penicillin, 0.1 mg/ml streptomycin, and 12.5 units/ml nystatin. All cells were routinely cultured in humidified air with 5% CO2 at 37°C. The cells were routinely tested for the presence of mycoplasma.

extract_protocol: total RNA was isolated using the Qiagen Rneasy Mini Kit (Qiagen, Valencia, CA). Samples were treated for DNase using DNase Set (Qiagen). RNA concentrations were determined by the absorbance at 260 nm and quality control standards were A260/A280 = 1.8 – 2.0.

value: melanoma cells

tag: malignancy stage

value: primary tumor


title: pediatric T-ALL patient #102 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267388

source_name: pediatric T-ALL patient #102


title: pediatric T-ALL patient #105 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267391

source_name: pediatric T-ALL patient #105


title: YDFR.CB2, rep1

description:
YDFR-second cycle of intrcardiac inoculation, brain metastasis variant, replicate 1
Gene expression of YDFR, brain metastasis variant

scan_protocol: according to the instruction manual, as described in the Affymetrix website

source_name: YDFR, brain metastasis variant

value: brain metastasis


title: roots Rm1021 at 14d

description:
A17_Rm1021_14d
Gene expression data from roots harvested 14 day after Rm 1021 treatment.

source_name: roots harvested 14 days after Rm1021 treatment

tag: tissue

tag: treatment

value: 14 days


title: RALL.CB1, rep1

description:
RALL-first cycle of intrcardiac inoculation, brain metastasis variant, replicate 1
Gene expression of RALL, brain metastasis variant

source_name: RALL, brain metastasis variant

label_protocol: according to the instruction manual, as described in the Affymetrix website


title: RALL.C, rep1

description:
RALL-sub_cutan variant, replicate 1
Gene expression of RALL, cutaneous variant

source_name: RALL, cutaneous variant


title: RKTJ.C, rep1

description:
RKTJ-sub-cutan variant, rep1
Gene expression of RKTJ, cutaneous variant

source_name: RKTJ, cutaneous variant


title: roots Rm1021 at 7d

description:
A17_Rm1021_7d
Gene expression data from roots harvested 7 day after Rm 1021 treatment.

source_name: roots harvested 7 days after Rm1021 treatment

value: 7 days


title: YDFR.C, rep1

description:
YDFR-sub-cutan variant, replicate 1
Gene expression of YDFR, cutaneous variant


title: 10^-6M BPA treatment, replicate1 (methylation)

status: Public on Mar 10 2011

first: Yong

last: Huang

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit and Protocol.

scan_protocol: GeneChip Scanner 3000.

data_processing: RMA normalization and peak signal detection using CisGenome software.

source_name: Normal breast epithelium, 10^-6M BPA

label_protocol: One round of linear amplification was performed, followed by 14 cycles of PCR using universal primers and direct incorporation of dUTP. Double-stranded DNA terminal labeling using terminal Deoxynucleotidyl, Transferase, DLR (biotin-labeled).

growth_protocol: Standard conditions (37°C and 5% CO2 until confluent).

extract_protocol:
Genomic DNA were extracted using a DNA extraction kit (Qiagen).

The DNA was fragmented (150-500bp) by sonication. The methylated DNA was immunoprecipitated with a monoclonal antibody against 5-methylcytidine (Eurogentec, San Diego, CA; Cat# BI-MECY-0100; Lot# 080808).

treatment_protocol: 10^-6M BPA continuously for two weeks.

tag: cell line

value: normal breast epithelial

value: bisphenol A (BPA)

tag: treatment dosage

tag: treatment duration

value: 2 weeks


title: RKTJ.CB1, rep1

description:
RKTJ-first cycle of intrcardiac inoculation, brain metastasis variant, replicate 1
Gene expression of RKTJ, brain metastasis variant

source_name: RKTJ, brain metastasis variant


title: 10^-5M BPA treatment, replicate2 (methylation)

source_name: Normal breast epithelium, 10^-5M BPA

treatment_protocol: 10^-5M BPA continuously for two weeks.


title: 10^-5M BPA treatment, replicate1 (methylation)


title: pediatric T-ALL patient #100 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267386

source_name: pediatric T-ALL patient #100

value: pediatric T-ALL cells

value: HOXA


title: DMSO Control (methylation)

description: Control

source_name: Normal breast epithelium, control

treatment_protocol: DMSO

value: DMSO


title: pediatric T-ALL patient #109 reanalysis

description:
This Sample represents a reanalysis of the CEL file initially submitted as:
GSM267394

source_name: pediatric T-ALL patient #109


title: prolactin pituitary tumours_agressive-invasive_5

status: Public on Mar 16 2011

city: BRON

first: Joël

last: LACHUER

address: 16 avenue du Doyen Lépine

country: France

institute: INSERM

hyb_protocol: Ten micrograms of biotin-labeled aRNA was fragmented using 5 μl of fragmentation buffer in a final volume of 20 µl then was mixed with 240 µl of Amersham hybridization solution (GE  Healthcare Europe GmbH, Freiburg, Germany) and injected onto CodeLink Uniset Human Whole Genome bioarrays (GE Healthcare Europe GmbH, Freiburg, Germany). Arrays were hybridized overnight at 37°C at 300 rpm in an incubator. The slides were washed in stringent TNT buffer at 46°C for 1 hour, then a streptavidin-cy5 (GE Healthcare) detection step was performed. Each slide was incubated for 30 min in 3.4 ml of streptavidin-cy5 solution as described previously (Fevre-Montange et al 2006), then was washed 4 times in 240 ml of TNT buffer, rinsed twice in 240 ml of water containing 0.2%Triton X-100, and dried by centrifugation at 600 rpm.

scan_protocol: The slides were scanned using a GenePix 4000B scanner (Axon, Union City, USA) and GenePix 3.0 software, with the laser set at 635 mm, the laser power at 100%, and the photomultiplier tube voltage at 60%.

data_processing: The relative intensity of the raw hybridization signal on arrays varies in different experiments. CodeLink Expression Analysis v4.0 software was therefore used to normalize the raw hybridization signal on each array to the median of the array (median intensity is 1 after normalization) for better cross-array comparison. The threshold of detection was calculated using the normalized signal intensity of the 100 negative control probes in the array; spots with signal intensities below this threshold are referred to as “absent”.

source_name: agressive-invasive prolactin pituitary tumour

label_protocol: Total RNA (2 µg) was amplified and biotin-labelled by a round of in vitro transcription (IVT) with a Message Amp aRNA kit (Ambion, Austin, Texas, USA) following the manufacturer’s protocol.

extract_protocol: Total RNA was extracted from the human pituitary tumours using Trizol (Invitrogen, Carlsbad, California, USA), according to the manufacturer’s protocol.

value: prolactin pituitary tumour

tag: tumor stage

value: agressive-invasive

tag: gender

value: female


title: 10^-6M BPA treatment, replicate2 (methylation)


title: 10^-5M BPA treatment, replicate3 (methylation)


title: YDFR.CB1, rep 1

description:
YDFR-first cycle of intrcardiac inoculation, brain metastasis variant, replicate 1
Gene expression of YDFR, brain metastasis variant


title: prolactin pituitary tumours_non-invasive_9

source_name: non-invasive prolactin pituitary tumour

value: non-invasive

value: male


title: prolactin pituitary tumours_non-invasive_13


title: prolactin pituitary tumours_invasive_7

source_name: invasive prolactin pituitary tumour

value: invasive


title: prolactin pituitary tumours_agressive-invasive_3


title: prolactin pituitary tumours_agressive-invasive_2


title: prolactin pituitary tumours_agressive-invasive_1


title: prolactin pituitary tumours_non-invasive_10


title: prolactin pituitary tumours_invasive_8


title: prolactin pituitary tumours_non-invasive_11


title: prolactin pituitary tumours_agressive-invasive_4


title: prolactin pituitary tumours_agressive-invasive_6


title: prolactin pituitary tumours_non-invasive_12


title: Third biological repeat 50°C

status: Public on Mar 02 2011

city: Edmonton

last: Gänzle

address: 4-10 Ag/For Centre

department: AFNS

institute: University of Alberta

description:
Analysis used GGG10 RNA as control samples for comparison to the AW1.7 RNA samples at 50°C heatshock.

This Sample represents two dye-swap samples.

hyb_protocol: Labeled cDNA was hybridized to 3x6 K E. coli Microarray Slides (Dept. of Biological Science, University of Alberta, Canada). The microarray slides contain 5,978 70mer probes printed in triplicate, which represent open reading frames in the genomes of E. coli strains K12, O157:H7 EDL933, and O157:H7 Sakai. Three independent biological repeats were analyzed, and technical repeats (dye-swap) were performed for two of three biological repeats.

scan_protocol: Arrays were scanned with GenePix 4000B (Molecular Devices, Sunnyvale, USA).

data_processing:
Raw data were normalized and log2 transformed with the Acuity 4.0 software package, and data with low fluorescence intensities were eliminated. Genes were considered to be differentially expressed if the absolute values of log2 mean expression ratios were ≥ 1.

The data did not undergo normalization across samples.

organism: Escherichia coli

source_name: AW1.7, steady-state continuous cultured experimental samples at 37°C and then 15 minutes heatshock at 50 °C

label_protocol: The cDNA was labeled with the Array 900MPX Expression Array Detection Kit (Genisphere) according to the instructions of the supplier.

growth_protocol: Cultures were inoculated from a single colony, incubated overnight, sub-cultured with a 1% inoculum, and grown to the late exponential growth phase, corresponding to an OD600 nm of 0.6 – 0.7.

extract_protocol: For RNA isolation, 0.5 mL of the cultures were mixed with 1 mL RNA protect (Qiagen, Ontario, Canada) and RNA was isolated using the RNeasy Mini kit (Qiagen). RNA was quantified with a Nanodrop Spectrophotometer (Thermo scientific, Wilmington, USA) and RNA quality was determined with a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). RNA samples (approximately 30 µg) were treated with 1U RNase free DNase I (Ambion, Ontario, Canada) at 37°C for 30 min and 1U RNase inhibitor (Ambion) was added prior to storage at 4°C. RNA was reverse-transcribed using the Array 900MPX Expression Array Detection Kit (Genisphere, Hatfield, USA) according to the instructions of the manufacturer. The cDNA was purified using the MinElute PCR Purification Kit (Quiagen), and the purified DNA was used for microarray and qPCR experiments.

treatment_protocol: RNA was isolated from late exponential cultures, or from late exponential cells heat-shocked by exposure to 50°C for 15 min.

tag: strain

tag: heat sensitivity

value: resistant

value: 50°C heatshock

source_name: GGG10, steady-state continuous cultured experimental samples at 37°C and then 15 minutes heatshock at 50 °C

value: sensitive


title: Second biological repeat 50°C


title: Control, rep2

status: Public on Feb 01 2011

city: La Jolla

first: Roy

middle: M

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

description:
5448533031_F
Replicate 2 of 2.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization in GeneSpring GX11.

organism: Mus musculus

source_name: MC38 cells, control

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

growth_protocol: MC38 cells were grown in normal growth medium.

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

tag: cell type

value: colon carcinoma

tag: background strain

tag: media

value: normal


title: First biological repeat 37°C

description: Analysis used GGG10 RNA as control samples for comparison to the AW1.7 RNA samples at 37°C.

source_name: AW1.7, steady-state continuous cultured experimental samples at 37°C

source_name: GGG10, steady-state continuous cultured experimental samples at 37°C


title: First biological repeat 50°C

description: Analysis used GGG10 RNA as control samples for comparison to the AW1.7 RNA samples at 50°C heatshock.


title: Third biological repeat 37°C

description:
Analysis used GGG10 RNA as control samples for comparison to the AW1.7 RNA samples at 37°C.

This Sample represents two dye-swap samples.


title: AG174_HPUra_DnaD_rep2

status: Public on Dec 07 2010

city: Cambridge

first: Alan

middle: D.

last: Grossman

email: clee2@mit.edu, adg@mit.edu

state: MA

address: 31 Ames Street, 68-530

institute: MIT

hyb_protocol: Samples were hybridized as described in Auchtung et al. 2005 PNAS 102:12554-9 [PMID 16105942].

scan_protocol: Arrays were scanned and analyzed with GenePix Pro 3.0 (Axon Instruments).

data_processing: GPR files were loaded and processed in Prep+07 (BMC Bioinformatics 2009, 10:16 [PMID 19134227; doi:10.1186/1471-2105-10-16). Lowess normalization was performed and spots for which signal was 90% within 2SD above background were removed. Results from the Prep+07 analysis were manually curated in Microsoft Excel for spots that had <2 datapoints with quality data for downstream analysis.

organism: Bacillus subtilis

source_name: AG174, HPUra treated, 30 minutes, DnaD IP

label_protocol: Samples were prepared for microarray analysis by labelling aliquots of the resuspended immunoprecipitated DNA or total control DNA with aminoallyl-dUTP using 13 U Sequenase (USB) and 5 μg random nonamer. The labelled samples were purified, conjugated to Cy3 or Cy5, and hybridized to microarrays.

growth_protocol: Cells were grown in minimal 1% glucose medium until OD600 reached approximately 0.6. At this point, cells were treated with HPUra or not, and growth was continued for another 30 minutes before harvesting.

extract_protocol:
Chromatin immunoprecipitation (ChIP) of DNA bound to native proteins was done essentially as described (1998, Lin and Grossman, Cell, 92:675-685 [PMID 9506522]; 2007, Breier and Grossman, Molecular Microbiology, 64:703-718 [PMID 17462018]).

Anti-DnaB/C/D were custom antibodies (sera), and were obtained from Covance (CRP, Inc); they do not have a catalog number. Anti-DnaB, anti-DnaC and anti-DnaD were raised in rabbits after purification of tagged proteins in the Grossman lab. For the experiments, the following bleeds were used:
DnaB: rabbit HM654, exsanguination
DnaC: rabbit HM6351, test bleed 2
DnaD: rabbit HM6354, production bleed 3
The IP requires a second antibody: AffiniPure Donkey Anti-Chicken IgY from Jackson ImmunoResearch Laboratories Inc. Catalog #703-005-155.

treatment_protocol: To induce replication stress by arresting the replicative polymerase PolC, the inhibitor HPUra was added at a final concentration of 38 ug/mL to exponentially growing cells for 30 minutes.

tag: growth phase

value: exponential

tag: isolation

value: anti-DnaD IP-associated DNA

tag: antibody

value: anti-DnaD

value: 30 minutes HPUra

source_name: AG174, HPUra treated, 30 minutes, total DNA

value: total chromosomal DNA


title: Hoxa9-ER on day 3, rep 3

city: Ann Arbor

first: Jay

last: Hess

state: MI

address: 1301 Catherine

department: Pathology

institute: University of Michigan

description: Gene expression data from murine cell line transduced with epitope tagged forms of Hoxa9 day 3

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing: The data were analyzed with robust multi-array average (RMA) normalization using default background adjustment and quantile normalization settings.

source_name: Murine bone marrow transduced with epitope tagged forms of Hoxa9 on day 3

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

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

value: Hoxa9-ER cells

tag: age

value: 6-8 week old

value: murine bone marrow transduced with epitope tagged forms of Hoxa9

tag: time point

value: day 3


title: Control, rep1

description:
5448533031_E
Replicate 1 of 2.


title: Hoxa9-ER on day 4, rep 3

description: Gene expression data from murine cell line transduced with epitope tagged forms of Hoxa9 day 4

source_name: Murine bone marrow transduced with epitope tagged forms of Hoxa9 on day 4

value: female

value: day 4


title: Stimulated, rep1

description:
5448533031_C
Replicate 1 of 2.

source_name: MC38 cells, stimulated

treatment_protocol: Subconfluent cultures of MC38 cells were serum-starved for 16 hrs and activated with 10ug/mL S100A8/A9 for 6 hrs.

value: reduced serum


title: Hoxa9-ER on day 5, rep 3

description: Gene expression data from murine cell line transduced with epitope tagged forms of Hoxa9 day 5

source_name: Murine bone marrow transduced with epitope tagged forms of Hoxa9 on day 5

value: day 5


title: Hoxa9-ER on day 0, rep 2

description: Gene expression data from murine cell line transduced with epitope tagged forms of Hoxa9 day 0

source_name: Murine bone marrow transduced with epitope tagged forms of Hoxa9 on day 0

value: day 0


title: Hoxa9-ER on day 0, rep 3


title: Genomic DNA of HBT1

status: Public on Dec 31 2010

city: Bangalore

first: Kaustuv

last: Sanyal

state: Karnataka

address: Jakkur

department: Molecular Biology and Genetics Unit

country: India

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

hyb_protocol: 5 micrograms of cy3 labeled samples were hybridized.  Hybridizations were done using the aCGH Hybridization kit of Agilent (Part Number: 5190-0404). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 40 hours

scan_protocol: The hybridized slides were washed using Agilent aCGH wash buffers (Part No: 5188-5221/22) and scanned using the Agilent Microarray Scanner G2505C

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1) and obtained background subtracted and spatially detrended Processed Signal intensities.

organism: Candida albicans x Candida dubliniensis

label_protocol: The samples for Comparative Genomic DNA Hybridization were labeled using Agilent Genomic DNA labeling Kit (Part Number: 5190-0453). 1 Micrograms of each sample was digested using Alu1 and Rsa1. This restricted DNA was then labeled with Cy3  dUTP using random primer labeling method. The labeled DNA was then concentrated and quality assessed for yields and specific activity.

growth_protocol: All the four yeast strains were taken from asynchronously grown cultures in YPD(U).

extract_protocol: Total genomic DNAs of J118, CdUM4b, the ptCaCd strain, HBT1 and the pdCaCd strain, HBP1 were recovered by organic extraction following digestion of the cell wall with 20 µg/ml Lyticase (SIGMA ALDRICH) and Proteinase K treatment (Roche Diagnostics) as described by Kaiser et al. (1994)

treatment_protocol: No special treatment was performed on the cells.

value: ptCaCd Pseudotetraploid hybrid


title: Hoxa9-ER on day 5, rep 2


title: AG174_HPUra_DnaD_rep3

extract_protocol: Chromatin immunoprecipitation (ChIP) of DNA bound to native proteins was done essentially as described (1998, Lin and Grossman, Cell, 92:675-685 [PMID 9506522]; 2007, Breier and Grossman, Molecular Microbiology, 64:703-718 [PMID 17462018]).


title: AG174_HPUra_DnaD_rep1


title: Hoxa9-ER on day 4, rep 2


title: Hoxa9-ER on day 3, rep 2


title: Hoxa9-ER on day 4, rep 1


title: Hoxa9-ER on day 5, rep 1


title: Unstimulated, rep2

description:
5448533031_B
Replicate 2 of 2.

source_name: MC38 cells, unstimulated

treatment_protocol: Subconfluent cultures of MC38 cells were serum-starved for 16 hrs and not activated with 10ug/mL S100A8/A9 for 6 hrs.

value: colon carcinoma


title: Unstimulated, rep1

description:
5448533031_A
Replicate 1 of 2.


title: AG174_expo_DnaD_rep2

source_name: AG174, non-treated, DnaD IP

source_name: AG174, non-treated, total DNA


title: Genomic DNA of J118

organism: Candida albicans

value: Candida albicans(Ca)


title: Genomic DNA of CdUM4b

organism: Candida dubliniensis

value: Candida dubliniensis (Cd)


title: Hoxa9-ER on day 3, rep 1


title: Genomic DNA of HBP1

value: pdCaCd Pseudodiploid progeny hybrid


title: AG174_expo_DnaD_rep1

value: exponential

value: anti-DnaD IP-associated DNA

value: anti-DnaD


title: AG174_expo_DnaD_rep3

value: total chromosomal DNA


title: AG174_expo_DnaC_rep1

source_name: AG174, non-treated, DnaC IP

value: anti-DnaC IP-associated DNA

value: anti-DnaC


title: AG174_HPUra_DnaB_rep3

source_name: AG174, HPUra treated, 30 minutes, DnaB IP

value: anti-DnaB IP-associated DNA

value: anti-DnaB

value: 30 minutes HPUra


title: AG174_HPUra_DnaC_rep3

source_name: AG174, HPUra treated, 30 minutes, DnaC IP


title: AG174_expo_DnaC_rep2


title: AG174_HPUra_DnaB_rep1


title: AG174_HPUra_DnaB_rep2


title: AG174_expo_DnaC_rep3


title: AG174_expo_DnaB_rep3

source_name: AG174, non-treated, DnaB IP


title: AG174_expo_DnaB_rep1


title: AG174_HPUra_DnaC_rep2


title: AG174_expo_DnaA_rep3

source_name: AG174, non-treated, DnaA IP

extract_protocol:
Chromatin immunoprecipitation (ChIP) of DNA bound to native proteins was done essentially as described (1998, Lin and Grossman, Cell, 92:675-685 [PMID 9506522]; 2007, Breier and Grossman, Molecular Microbiology, 64:703-718 [PMID 17462018]).

Anti-DnaA was raised in chicken and comes from W. F. Burkholder (Stanford). The use of these antibodies is described in Goranov 2005 Proc Nat Acad Sci USA and Breier 2009 J. Bacteriol. Anti-DnaA serum came from chicken #1316. The IP requires a second antibody: AffiniPure Donkey Anti-Chicken IgY from Jackson ImmunoResearch Laboratories Inc. Catalog #703-005-155.

value: anti-DnaA IP-associated DNA

value: anti-DnaA


title: AG174_expo_DnaA_rep1


title: AG174_HPUra_DnaA_rep2

source_name: AG174, HPUra treated, 30 minutes, DnaA IP


title: Hoxa9-ER on day 0, rep 1

value: Hoxa9-ER cells

value: female

value: 6-8 week old

value: murine bone marrow transduced with epitope tagged forms of Hoxa9

value: day 0


title: AG174_expo_DnaB_rep2


title: AG174_HPUra_DnaA_rep3


title: AG174_HPUra_DnaA_rep1


title: AG174_expo_DnaA_rep2


title: Mxcre;E2F1-/-2-/-3f/f (experimental), rep4

status: Public on Dec 03 2010

city: Columbus

first: Prashant

last: Trikha

state: OH

address: 460 W 12 Avenue

department: HCG

institute: Ohio State University

description:
H10
Gene expression data from Cd11B + myeloid cells.

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430.2 GeneChip Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Gene Chips were scanned using the Affy GeneChip Scanner 3000.

data_processing: The data were analyzed with RMAExpress (version 1.0 beta 4) and normalized using Quantile Normalization. Robust multi-array analysis (RMA) was performed with default parameter settings and the output was log transformed.

label: Biotin

source_name: Cd11b +  myeloid cells, experimental

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA.

treatment_protocol: Eight-week-old mice received five injections of 250ug of polyinosine-polycytidine (pIpC) every alternate day and mice were sacrificed 24 hrs after the last injection.

value: mixed (FVB+ C57BL6)

tag: genotype

value: 8 weeks

tag: tissue

value: bone marrow

value: Cd11b + myeloid cells


title: Mxcre;E2F1-/-2-/-3f/f (experimental), rep2

description:
3b
Gene expression data from Cd11B + myeloid cells.


title: Mxcre;E2F1-/-2-/-3f/f (experimental), rep1

description:
3a
Gene expression data from Cd11B + myeloid cells.


title: Mxcre;E2F1-/-2-/-3f/f (experimental), rep3

description:
F4
Gene expression data from Cd11B + myeloid cells.


title: CaSki HPV(+), MeDIP-ChIP, array B

status: Public on Dec 01 2010

first: Jung

last: Kim

address: 1420 Washington Heights

description:
CaSki HPV(+)
Methylated DNA, which is immunoprecipitated using an antibody against 5-methyl-cytosine, is compared against input DNA.
The input DNA sample is a mixture of the mock-immunoprecipitated DNA from the four cell lines.

hyb_protocol: Hybridization mixes were prepared using the Affymetrix GeneChip Hybridization Wash and Stain Kit (Part 900720). Hybridization was at 45oC for 16-18 hours in an Affymetrix GeneChip Hybridization Oven.

scan_protocol: Scanning was performed with GenPathway (San Diego, CA) using the GeneChIP Scanner 3000 7G.

data_processing:
The Affymetrix Human Tiling 2.0R Array Set is a set of 7 tiling arrays divided by chromosome, and consisting of a total of more than 40 million 25-mer oligos. Raw data were read into R using the AffyTiling package and were quantile normalized. Oligos were annotated to CpG islands and genes using the UCSC CpG islands and known genes tracks, respectively. Testing for methylated and differentially methylated regions was performed using an empirical Bayes approach with moderated variance in ANOVA.  This method takes into account the dependency of variance on intensity level, with variance tending to decrease with increasing intensity.  The estimates of fold change over input and between HPV(+) and HPV(-) cells were smoothed using a moving window average of 175 bp length.

The BED and input DNA CEL files are linked to the Series GSE24090 record as supplementary files.

source_name: MeDIP-ChIP DNA from CaSki, HPV(+)

label_protocol: Methylated DNA IP-on-Chip was performed with GenPathway (San Diego, CA) using the GeneChip Human Tiling 2.0R Array Set (Affymetrix, Santa Clara, CA). Following preclearing with protein G agarose beads (Invitrogen), DNA was denatured and immunoprecipitated using an anti-5-methyl-cytosine antibody (Capralogics, P00704, Lot# P704020607), and incubated overnight at 4C, with protein G agarose beads. An aliquot of each precipitated sample was used for QPCR to confirm the enrichment of methylated regions, using a GenPathway proprietary method. Immunoprecipitated and input DNAs (mock-IP'ed SCC4, SCC47, SCC74A, and CaSki cell lines) were amplified, and QPCR again verified enrichment of methylated regions in IP'ed DNA. Amplified immunoprecipitated and input DNAs were labeled according to Affymetrix procedures.

growth_protocol: HPV(+) and HPV(-) SCC cell lines were cultured to near confluence in ventilated 75cm2 cell culture flasks in DMEM (Gibco) supplemented with 20% fetal bovine serum (FBS) and prophylactic antibiotics. At 90-95% confluence, the cells were photographed through a 20x objective lens, and then harvested with Trypsin/EDTA. Total cell counts for each flask were obtained using a Coulter Particle Counter (Beckman Coulter). Trypsin was neutralized with culture media containing 2% FBS, and cell pellets were washed with sterile phosphate-buffered saline (PBS), pH 7.4, prior to digestion for nucleic acid isolation.

extract_protocol: DNA was isolated using a modified protocol for the QiaAmp DNA Mini Kit for Blood and Body Fluids (Qiagen, Valencia, CA). In brief, ≤5 million cells were suspended in 200uL of PBS to which 20uL of Proteinase K (Qiagen) was added. A 5mm stainless steel bead was added to each tube and cells were simultaneously disrupted and homogenized with 2 bursts at 15Hz, 20 seconds each, in a TissueLyser II (Qiagen). Following homogenization, 20uL of RNase A (Qiagen) was added to each tube. After the addition of RNase A, DNA isolation was carried out as per manufacturer’s instructions for processing blood and body fluids with spin column technology. Genomic DNA was eluted in 100uL final volume of nuclease-free water, pre-warmed to 40°C. Four 25uL elutions were performed, each of which were incubated on the spin column membrane for 5 minutes before eluting.

tag: cell line

value: CaSki

value: female genital squamous cell carcinoma

tag: hpv status

value: positive

tag: tissue derivation

value: cervix

tag: antibody vendor

value: Capralogics

tag: antibody catalog #

tag: antibody lot #

source_name: Input DNA, mock IP

value: UM-SCC-4, UM-SCC-47, UM-SCC-74A, and CaSki


title: E2F1-/-2+/+3f/f (control), rep2

description:
1b
Gene expression data from Cd11B + myeloid cells.

source_name: Cd11b +  myeloid cells, control


title: E2F1-/-2+/+3f/f (control), rep4

description:
H11
Gene expression data from Cd11B + myeloid cells.


title: SCC4 HPV(-), MeDIP-ChIP, array A

description:
SCC4 HPV(-)
Methylated DNA, which is immunoprecipitated using an antibody against 5-methyl-cytosine, is compared against input DNA.
The input DNA sample is a mixture of the mock-immunoprecipitated DNA from the four cell lines.

source_name: MeDIP-ChIP DNA from SCC4, HPV(-)

value: head and neck squamous cell carcinoma (HNSCC)

value: negative

value: tongue

tag: gender


title: SCC4 HPV(-), MeDIP-ChIP, array B

tag: cell type

value: female


title: CaSki HPV(+), MeDIP-ChIP, array G


title: E2F1-/-2+/+3f/f (control), rep3

description:
i1
Gene expression data from Cd11B + myeloid cells.

tag: background strain


title: SCC47 HPV(+), MeDIP-ChIP, array A

description:
SCC47 HPV(+)
Methylated DNA, which is immunoprecipitated using an antibody against 5-methyl-cytosine, is compared against input DNA.
The input DNA sample is a mixture of the mock-immunoprecipitated DNA from the four cell lines.

source_name: MeDIP-ChIP DNA from SCC47, HPV(+)

value: male


title: SCC74A HPV(-), MeDIP-ChIP, array B

description:
SCC74A HPV(-)
Methylated DNA, which is immunoprecipitated using an antibody against 5-methyl-cytosine, is compared against input DNA.
The input DNA sample is a mixture of the mock-immunoprecipitated DNA from the four cell lines.

source_name: MeDIP-ChIP DNA from SCC74A, HPV(-)


title: CaSki HPV(+), MeDIP-ChIP, array A


title: SCC74A HPV(-), MeDIP-ChIP, array G


title: SCC74A HPV(-), MeDIP-ChIP, array A


title: SCC47 HPV(+), MeDIP-ChIP, array B


title: SCC47 HPV(+), MeDIP-ChIP, array G


title: SCC4 HPV(-), MeDIP-ChIP, array G


title: SCC74A HPV(-), MeDIP-ChIP, array E


title: CaSki HPV(+), MeDIP-ChIP, array E


title: CaSki HPV(+), MeDIP-ChIP, array D


title: SCC4 HPV(-), MeDIP-ChIP, array E


title: SCC47 HPV(+), MeDIP-ChIP, array E


title: SCC47 HPV(+), MeDIP-ChIP, array D


title: SCC4 HPV(-), MeDIP-ChIP, array D


title: SCC47 HPV(+), MeDIP-ChIP, array C


title: SCC74A HPV(-), MeDIP-ChIP, array C


title: CaSki HPV(+), MeDIP-ChIP, array C


title: E2F1-/-2+/+3f/f (control), rep1

description:
1a
Gene expression data from Cd11B + myeloid cells.


title: SCC4 HPV(-), MeDIP-ChIP, array C


title: CaSki HPV(+), MeDIP-ChIP, array F


title: SCC47 HPV(+), MeDIP-ChIP, array F


title: SCC74A HPV(-), MeDIP-ChIP, array F


title: SCC4 HPV(-), MeDIP-ChIP, array F


title: Stimulated, rep2

description:
5448533031_D
Replicate 2 of 2.

source_name: MC38 cells, stimulated

value: colon carcinoma

tag: media

value: reduced serum

tag: treatment


title: SCC74A HPV(-), MeDIP-ChIP, array D


title: OC18_Aza

status: Public on Nov 17 2010

city: Durham

first: Susan

middle: K.

last: Murphy

state: NC

address: B226 LSRC B Wing, Research Drive, Box 91012

department: Obstetrics and Gynecology

institute: Duke University Medical Center

scan_protocol: Standard Affymetrix protocol.

data_processing: RMA normalization with RMAExpress software (http://rmaexpress.bmbolstad.com) using background adjustment, quantile normalization and median polish summarization.

source_name: serous epithelial ovarian cancer cells, treated with 5-AzaC

label_protocol: Affymetrix one cycle IVT.

growth_protocol: Cells were grown in a 1:1 mixture of Medium 199 and MCDB 105 medium with 15% FBS in a humidifed incubator maintained at 37 degrees Celsius with 5% CO2 until confluent.

extract_protocol: RNA Stat-60.

treatment_protocol: When confluent, cells underwent selective trypsinization to remove fibroblasts and were divided into two dishes and grown until ~70% confluent, at which time they were mock treated or treated with 5 µM 5-azacytidine (5-azaC) for 72 hours.  Normal OSE (NO) cells were similarly treated, but due to small numbers of cells, we pooled specimens from five individuals to use for each of the arrays. All specimen cultures were analyzed by immunocytochemical staining using anti-cytokeratin antibodies; only cultures with >90% epithelial content were used for the microarrays.

value: ovary

value: serous epithelial ovarian cancer cells

value: 5-azacytidine (5-AzaC)


title: OC16_Aza


title: Second biological repeat 37°C

first: Michael

description:
Analysis used GGG10 RNA as control samples for comparison to the AW1.7 RNA samples at 37°C.

This Sample represents two dye-swap samples.

source_name: AW1.7, steady-state continuous cultured experimental samples at 37°C

tag: strain

tag: heat sensitivity

value: resistant

source_name: GGG10, steady-state continuous cultured experimental samples at 37°C

value: sensitive


title: OC26_Aza


title: OC6_Aza


title: OC10_Mock

source_name: serous epithelial ovarian cancer cells, mock treated

value: mock


title: OC16_Mock


title: OC14_Mock


title: OC22_Mock


title: OC14_Aza


title: OC15_Aza


title: OC18_Mock


title: OC22_Aza


title: BorOC28_Aza

source_name: serous borderline ovarian cells, treated with 5-AzaC

value: serous borderline ovarian cells


title: OC15_Mock


title: OC7_Aza

source_name: endometrioid ovarian cancer cells, treated with 5-AzaC

value: endometrioid ovarian cancer cells


title: BorOC2_Aza


title: OC10_Aza


title: OC26_Mock


title: NO2_Aza

source_name: normal ovarian surface epithelium, pooled from five individuals, treated with 5-AzaC

value: normal ovarian surface epithelium


title: NO1_Aza


title: OC6_Mock


title: OC7_Mock

source_name: endometrioid ovarian cancer cells, mock treated


title: OC1_Aza


title: OC20_Mock


title: OC27_Aza


title: OC5_Aza


title: OC27_Mock


title: OC20_Aza


title: AG174_HPUra_DnaC_rep1

source_name: AG174, HPUra treated, 30 minutes, DnaC IP

tag: growth phase

value: exponential

tag: isolation

value: anti-DnaC IP-associated DNA

tag: antibody

value: anti-DnaC

value: 30 minutes HPUra

source_name: AG174, HPUra treated, 30 minutes, total DNA

value: total chromosomal DNA


title: OC1_Mock

tag: tissue

value: female


title: PEO1(CD133-)-Decitabine treated

description:
9950_PEO1(CD133-)-D
Experiment 2.

source_name: ovarian cancer cells treated with 5 µM decitabine for 72 hours

growth_protocol: All cells, including sorted CD133+ and CD133- A2780 and PEO1 cells, were grown in RPMI1640 media with 10% FBS in a humidifed incubator maintained at 37 degrees Celsius with 5% CO2 until ~70% confluent.

treatment_protocol: At ~70% confluence, cells were either mock treated with tissue culture media (Mock) or with 5 µM 5-aza-2'-deoxxycytidine (Decitabine) for 72 hours.

tag: cell line

value: ovarian cancer cells

tag: cell population

value: decitabine


title: HEYA8-Decitabine treated, rep2

description:
9862_HEYA8-D_replicate
Experiment 1.


title: OC5_Mock

value: ovary


title: PEO1(CD133-)-Mock treated

description:
9949_PEO1(CD133-)
Experiment 2.

source_name: ovarian cancer cells, mock treated


title: A2780(CD133+)-Decitabine treated

description:
9944_A2780(CD133+)-D
Experiment 2.


title: PEO1(CD133+)-Decitabine treated

description:
9948_PEO1(CD133+)-D
Experiment 2.


title: BorOC28_Mock

source_name: serous borderline ovarian cells, mock treated


title: NO2_Mock

source_name: normal ovarian surface epithelium, pooled from five individuals, mock treated


title: A2780(CD133-)-Mock treated

description:
9945_A2780(CD133-)
Experiment 2.


title: A2780(CD133+)-Mock treated

description:
9943_A2780(CD133+)
Experiment 2.


title: BorOC2_Mock


title: A2780(CD133-)-Decitabine treated

description:
9946_A2780(CD133-)-D
Experiment 2.


title: 41M-Decitabine treated

description:
9936_41M-D
Experiment 1.


title: ME-180A-Decitabine treated

description:
9934_ME-180A-D
Experiment 1.

source_name: cervical cancer cells treated with 5 µM decitabine for 72 hours

value: cervical cancer cells


title: IGROV1-Decitabine treated

description:
9932_IGROV1-D
Experiment 1.


title: NO1_Mock


title: ME-180-Decitabine treated

description:
9930_ME-180-D
Experiment 1.


title: MCAS-Decitabine treated

description:
9942_MCAS-D
Experiment 1.

value: MCAS


title: PEO1(CD133+)-Mock treated

description:
9947_PEO1(CD133+)
Experiment 2.


title: ME-180C-Decitabine treated

description:
9940_ME-180-D
Experiment 1.


title: A2780-Decitabine treated

description:
9922_A2780-D
Experiment 1.


title: FUOV1-Decitabine treated

description:
9926_FUOV1-D
Experiment 1.


title: Tyk-nu-Decitabine treated

description:
9918_Tyk-nu-D
Experiment 1.

value: Tyk-nu


title: Tyk-nu-cisR-Decitabine treated

description:
9920_Tyk-nu-cisR-D
Experiment 1.

value: Tyk-nu-cisR


title: A2780-cisR-Decitabine treated

description:
9924_A2780-cisR-D
Experiment 1.


title: TOV-112D-Decitabine treated

description:
9916_TOV-112D-D
Experiment 1.


title: TOV-21G-Decitabine treated

description:
9938_TOV-21G-D
Experiment 1.


title: DOV13-Decitabine treated

description:
9906_DOV13-D
Experiment 1.


title: CAOV-2-Decitabine treated

description:
9908_CAOV-2-D
Experiment 1.


title: CH1-cisR-Decitabine treated

description:
9914_CH1-cisR-D
Experiment 1.


title: CH1-Decitabine treated

description:
9912_CH1-D
Experiment 1.


title: DOV13B-Decitabine treated

description:
9904_DOV13B-D
Experiment 1.


title: DOV13A-Decitabine treated

description:
9902_DOV13A-D
Experiment 1.


title: OVCA429-Decitabine treated

description:
9892_OVCA429-D
Experiment 1.


title: OV90-Decitabine treated

description:
9928_OV90-D
Experiment 1.


title: OVCA432-Decitabine treated

description:
9894_OVCA432-D
Experiment 1.


title: OVCA433-Decitabine treated

description:
9896_OVCA433-D
Experiment 1.


title: CAOV-3-Decitabine treated

description:
9910_CAOV-3-D
Experiment 1.


title: SKOV-4-Decitabine treated

description:
9884_SKOV-4-D
Experiment 1.


title: OVARY1847-Decitabine treated

description:
9898_OVARY1847-D
Experiment 1.


title: SKOV-3-Decitabine treated

description:
9882_SKOV-3-D
Experiment 1.


title: SKOV-8-Decitabine treated

description:
9888_SKOV-8-D
Experiment 1.


title: OVCAR-8-Decitabine treated

description:
9878_OVCAR-8-D
Experiment 1.


title: OVCAR-10-Decitabine treated

description:
9880_OVCAR-10-D
Experiment 1.


title: OVCAR-5-Decitabine treated

description:
9876_OVCAR-5-D
Experiment 1.


title: OVCA420-Decitabine treated

description:
9890_OVCA420-D
Experiment 1.


title: SKOV-6-Decitabine treated

description:
9886_SKOV-6-D
Experiment 1.


title: HEYC2-Decitabine treated

description:
9864_HEYC2-D
Experiment 1.


title: PEO4-Decitabine treated

description:
9868_PEO4-D
Experiment 1.


title: HEYA8-Decitabine treated, rep1

description:
9862_HEYA8-D
Experiment 1.


title: OVCAR-3-Decitabine treated

description:
9874_OVCAR-3-D
Experiment 1.


title: PEO1-Decitabine treated

description:
9866_PEO1-D
Experiment 1.


title: OVCAR-2-Decitabine treated

description:
9872_OVCAR-2-D
Experiment 1.


title: HEY-Decitabine treated

description:
9860_HEY-D
Experiment 1.

value: HEY


title: PA-1-Decitabine treated

description:
9900_PA1-D
Experiment 1.


title: IGROV1-Mock treated

description:
9931_IGROV1
Experiment 1.

value: mock


title: MCF7-Decitabine treated

description:
9870_MCF7-D
Experiment 1.

source_name: breast cancer cells treated with 5 µM decitabine for 72 hours

value: breast cancer cells


title: ME-180A-Mock treated

description:
9933_ME-180A
Experiment 1.

source_name: cervical cancer cells, mock treated


title: A2780-Mock treated

description:
9921_A2780
Experiment 1.


title: 41M-cisR-Decitabine treated

description:
10064_41M-cisR-D
Experiment 1.


title: MCAS-Mock treated

description:
9941_MCAS
Experiment 1.


title: FUOV1-Mock treated

description:
9925_FUOV1
Experiment 1.


title: TOV-112D-Mock treated

description:
9915_TOV-112D
Experiment 1.


title: Tyk-nu-cisR-Mock treated

description:
9919_Tyk-nu-cisR
Experiment 1.


title: Tyk-nu-Mock treated

description:
9917_Tyk-nu
Experiment 1.


title: CH1-Mock treated

description:
9911_CH1
Experiment 1.


title: CAOV-2-Mock treated

description:
9907_CAOV-2
Experiment 1.


title: DOV13-Mock treated

description:
9905_DOV13
Experiment 1.


title: DOV13B-Mock treated

description:
9903_DOV13B
Experiment 1.


title: CAOV-3-Mock treated

description:
9909_CAOV-3
Experiment 1.


title: PA-1-Mock treated

description:
9899_PA-1
Experiment 1.


title: DOV13A-Mock treated

description:
9901_DOV13A
Experiment 1.


title: OVCA433-Mock treated

description:
9895_OVCA433
Experiment 1.


title: ME-180C-Mock treated

description:
9939_ME-180C
Experiment 1.


title: OVCA432-Mock treated

description:
9893_OVCA432
Experiment 1.


title: OVARY1847-Mock treated

description:
9897_OVARY1847
Experiment 1.


title: ME-180-Mock treated

description:
9929_ME-180
Experiment 1.


title: OVCA420-Mock treated

description:
9889_OVCA420
Experiment 1.


title: 41M-Mock treated

description:
9935_41M
Experiment 1.


title: SKOV-8-Mock treated

description:
9887_SKOV-8
Experiment 1.


title: OV90-Mock treated

description:
9927_OV90
Experiment 1.


title: OVCAR-10-Mock treated

description:
9879_OVCAR-10
Experiment 1.


title: SKOV-6-Mock treated

description:
9885_SKOV-6
Experiment 1.


title: TOV-21G-Mock treated

description:
9937_TOV-21G
Experiment 1.


title: SKOV-3-Mock treated

description:
9881_SKOV-3
Experiment 1.


title: PEO4-Mock treated

description:
9867_PEO4
Experiment 1.


title: CH1-cisR-Mock treated

description:
9913_CH1-cisR
Experiment 1.


title: OVCAR-2-Mock treated

description:
9871_OVCAR-2
Experiment 1.


title: OVCAR-3-Mock treated

description:
9873_OVCAR-3
Experiment 1.


title: OVCAR-5-Mock treated

description:
9875_OVCAR-5
Experiment 1.


title: SKOV-4-Mock treated

description:
9883_SKOV-4
Experiment 1.


title: MCF7-Mock treated

description:
9869_MCF7
Experiment 1.

source_name: breast cancer cells, mock treated


title: OVCAR-8-Mock treated

description:
9877_OVCAR-8
Experiment 1.


title: A2780-cisR-Mock treated

description:
9923_A2780-cisR
Experiment 1.


title: OVCA429-Mock treated

description:
9891_OVCA429
Experiment 1.


title: HEYA8-Mock treated

description:
9861_HEYA8
Experiment 1.


title: HEYC2-Mock treated

description:
9863_HEYC2
Experiment 1.


title: 41M-cisR-Mock treated

description:
10063_41M-cisR
Experiment 1.


title: HEY-Mock treated

description:
9859_HEY
Experiment 1.