title: dobbi-00100: NCI_U133A_NC 112T

value: Adrenal Cortical Adenoma

value: Adrenal Gland


title: cho-00156: CHTN-OS-134

status: Public on May 07 2015

type: RNA

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Ovary

tag: Sex

value: F

tag: disease state

value: Ovary cancer

tag: disease location

value: Ovary

tag: organism part

tag: histology

value: serous

tag: disease stage

tag: tumor grading


title: cho-00156: CHTN-OS-115

scan_protocol: See mage-tab files linked to series entry for additional details

value: U


title: Amoxicillin rep1

city: Buffalo

first: Jiho

last: Sohn

state: New York

address: 3435 Main Street, 644 Biomedical Research Building

department: Oral Biology

institute: SUNY Buffalo

hyb_protocol: standard procedures recommended by Affymetrix was used

data_processing: The raw microarray data was normalized by the Robust Multi-Array (RMA) method using Affy package in Bioconductor

organism: Mus musculus

source_name: liver

growth_protocol: C57BL/6J mice received three antibiotic courses: at days 10-15, 28-31, and 37-40 of life, amoxicillin or tylosin.Livers were collected at age 22 weeks, RNA was extracted, and transcriptional differences were measured by microarray analysis.

extract_protocol: RNeasy Mini Kit (Qiagen, Valencia CA)

treatment_protocol: Tylosin tartrate and amoxicillin trihydrate (Sigma Aldrich, St. Louis MO) were dissolved in distilled deionized water at concentrations of 0.333 and 0.167 mg/mL, respectively, to provide mice with 50 mg of tylosin or 25 mg of amoxicillin per kg body mass/day, based on an estimated daily water consumption of 150 mL/kg body mass.

tag: age

value: 24 week

tag: gender

value: Female

tag: strain

tag: tissue

value: liver


title: cho-00156: CHTN-OS-107

data_processing: See mage-tab files linked to series entry for additional details

value: serous/endometrioid


title: Tylosin rep1

scan_protocol: standard procedures recommended by Affymetrix was used


title: ICAR _SUI_2

city: Auckland

first: Caroline

middle: Gwendolyn

last: Walker

state: Outside the US or Canada

address: 3A symonds st

department: University of Auckland

country: New Zealand

institute: DairyNZ Ltd

description: En3 12

hyb_protocol: Eight hundred and twenty five nanograms of Cy3- and Cy5-labeled cRNA were added to Agilent-023647 4x44k 60-mer oligonucleotide microarrays (G2519F 023647) and hybridized overnight at 65°C (17 hours). Slides were then washed with Agilent Gene Expression Wash Buffers 1 and 2 according to the manufacturer's instructions, inserted into a slide cover with ozone barrier, and scanned on an Agilent C scanner at 5µm.

scan_protocol: Slides were scanned on an Agilent C scanner at 5µm.

data_processing: Agilent Feature Extraction software version 10.7.3.1 was used to analyze the scanned Agilent microarray. The 24 scanned microarray image files were uploaded to the Feature Extraction software. Using a design file (023647), the Feature Extraction software locates features and converts the extracted data from each feature into a quantitative log2ratio. This software removes pixel outliers, performs statistical tests on the non-outlier pixels, subtracts background from features and flags any outlier features. The software was then used to perform LOWESS (locally weighted linear regression analysis) dye normalization and to calculate a p-value for each feature.

organism: Bos taurus

source_name: Intercaruncular, SUI

label_protocol: One hundred and fifty nanograms of RNA were amplified using the Agilent Low Input Quick Amp Labeling Kit, two color (Agilent, G2519F) to generate fluorescent complimentary RNA (cRNA) according to the manufacturer's instructions. cRNA quantity was measured by spectrophotometry using a ND-1000 (Nanodrop Technologies, Wilmington, DE).

extract_protocol: Endometrial tissue was homogenised in Qiagen buffer RLT (QIAGEN GmbH, QIAGEN, Hilden, Germany) using a TissueLyser II (Qiagen). Approximately 30 mg of tissue was homogenized for 2 minutes with three ball bearings of 1/8 inch diameter (Farrell Bearings, Hamilton, NZ) in a tube containing RLT lysis buffer (Qiagen). Total RNA was extracted using a Qiagen RNeasy kit (QIAGEN). All samples were DNase treated using the Ambion DNA-free kit (Ambion, Austin, TX) according to the manufacturer's instructions. RNA quantity was determined by spectrophotometry in a Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE). RNA integrity was checked using the Agilent 2100 Bioanalyzer with a RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA).

tag: breed

value: Holstein Friesian

value: intercaruncular endometrium

value: subclinical endometritis

tag: pmn%

tag: progesterone concentration (ng/ml)

tag: bacteriology score

tag: animal identifier

source_name: Pooled reference

value: caruncular and intercaruncular endometrium

value: subclinical endometritis and control

tag: sample type

value: reference


title: cho-00156: CHTN-OS-091

label_protocol: See mage-tab files linked to series entry for additional details

tag: Sex


title: dobbi-00100: NCI_U133A_NC 114

source_name: Sloan Kettering Institute for Cancer Research

extract_protocol: See mage-tab files linked to series entry for additional details

tag: cell line

tag: disease state

value: Stage IA

value: Lung

value: male

value: Lung Adenocarcinoma


title: cho-00156: CHTN-OS-093

value: F

value: Ovary cancer

tag: disease location

value: Ovary

tag: organism part


title: dobbi-00100: NCI_U133A_NC 109C

tag: disease stage

tag: histology


title: Control rep2

label_protocol: standard procedures recommended by Affymetrix was used

tag: age

value: 24 week


title: dobbi-00100: NCI_U133A_NC 116

tag: tumor grading

value: Stage IIIB

value: female


title: Control rep1

tag: gender

value: Female

tag: strain

value: liver


title: TSEC FFA767- biological rep3

city: Aurora

first: Michael

last: Edwards

state: CO

address: 12700 East 19th Avenue, Box C272

department: Pulmonary

institute: UC Denver

hyb_protocol: Following fragmentation, 3.5mg of fragmented and labeled ss-DNA were hybridized for 16h at 45C with 60rpm rotation on GeneChip® Mouse Gene 2.0 ST Array per protocol (GeneChip WT PLUS Reagent Kit User Manual, 2013, Affymetrix).   GeneChips were washed and stained in the Affymetrix Fluidics Station 450 per protocol (GeneChip WT PLUS Reagent Kit User Manual, 2013, Affymetrix).

scan_protocol: GeneChips were scanned using Affymetrix® GeneChip® Scanner 3000

data_processing: Partek Genomics Suite v6.6 was used to import and process these data using quantile normalization and RMA background correction adjusting for GC content.  Only those probes with log2 expression greater than 4.5 in at least one sample (26,084 out of 41,353 total) were used for subsequent statistical analysis.

source_name: Murine Liver Sinusoidal Endothelial Cell Line (TSEC)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip WT PLUS Reagent Kit User Manual, 2013, Affymetrix)

growth_protocol: TSECs were plated at 1,000,000 cells per well in a 24 well plate.

extract_protocol: Extraction of RNA was performed using QIAgen RNeasy Kit according to manufacturers protocol

treatment_protocol: Cells were treated 0.66mM Oleic Acid and 0.33mM Palmitic Acid  and/or 30uM INT-767 for 8 hours.

tag: treatment

tag: cell type


title: dobbi-00100: NCI_U133A_NC 106C


title: Control rep3

tag: tissue


title: dobbi-00100: NCI_U133A_NC 108C


title: cho-00156: CHTN-OS-077B

value: serous


title: TSEC 767- biological rep3

value: Murine Liver Sinusoidal Endothelial Cell Line


title: TSEC FFA767- biological rep2


title: cho-00156: CHTN-OS-089


title: cho-00156: CHTN-OS-063


title: cho-00156: CHTN-OS-066


title: TSEC FFA- biological rep1

value: FFA


title: TSEC FFA- biological rep3


title: dobbi-00100: CL2003092403AA

source_name: Dana Farber Cancer Institute


title: TSEC FFA- biological rep2


title: TSEC FFA767- biological rep1


title: carpt-00469: RA50AT

type: genomic

molecule: genomic DNA

source_name: Prostate Cancer

value: Prostate Cancer

value: Adrenal

tag: pathological stage

value: metastatic tumor

source_name: Promega Female Genomic DNA


title: TSEC 767- biological rep1


title: dobbi-00100: CL2003092405AA

value: Malignant G1 Stromal Tumor

value: Stomach


title: TSEC Media- biological rep1

value: Media


title: cho-00156: CHTN-OS-085

value: F


title: dobbi-00100: CL2003092402AA

value: Squamous Cell Carcinoma

value: Lung


title: dobbi-00100: CL2003092401AA


title: TSEC 767- biological rep2


title: cho-00156: CHTN-OS-055

value: Ovary cancer

value: Ovary


title: cho-00156: CHTN-OS-048


title: dobbi-00100: CL2003092327AA

value: Stage IB

value: male

value: Lung Adenocarcinoma


title: dobbi-00100: NCI_U133A_NC 165T

value: melanoma

value: Skin

value: carcinoma


title: Human naive B-cell-rep 20

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from human naive B-cell, rep 20.

hyb_protocol: Samples were hybridized onto Affymetrix Human GeneChip 2.0 ST arrays according to manufacturer's recommendations.

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

data_processing: The data were analyzed with Expression Console 1.3 using Affymetrix default analysis.

source_name: Human naive B-cell

label_protocol: cDNA was generated from 5ng of total RNA using WT-Ovation™ Pico system (version 1) RNA Amplification System followed by double-stranded cDNA synthesis using WT-Ovation™ Exon Module.

growth_protocol: PBMCs were washed in PBS with 4% heat-inactivated FBS and incubated for 30 min at 4 °C with mouse monoclonal fluorescently labelled antibodies specific for surface molecules.

extract_protocol: The singlet lymphocytes were then gated using CD19+ CD20+ followed by a CD10- gate to identify mature B cells. Further discrimination using CD21 and CD27 allowed gating on atypical MBCs (CD10- CD19+ CD20+ CD21- CD27-), classical MBCs (CD10- CD19+ CD20+ CD21+ CD27+) and naïve B cells (CD10- CD19+ CD20+ CD21+ CD27-) that were sorted using a FACSAria (BD Biosciences).

treatment_protocol: B cells were isolated with the negative selection Human B Cell Enrichment Kit (STEMCELL Technologies) according to the manufacturer's instructions.

value: naive B-cell (CD10- CD19+ CD20+ CD21+ CD27-)


title: C6 Stat3 S2_NimbleGen

city: Uppsala

first: Marcin

last: Kruczyk

address: Husargatan 3

country: Sweden

institute: Uppsala University

description: Chip-ChIP C6 cells Stat3

hyb_protocol: the immunoprecipitated chromatin was hybridized to Rat ChIP 3x720K RefSeq promoter oligonucleotide chips (Roche NimbleGen, Waldkraiburg, Germany); two-color competitive hybridization was performed with a labeled input as a reference.

scan_protocol: The arrays were scanned using a NimbleGen MS 200 Microarray Scanner (Roche) according to the manufacturer's instructions.

data_processing: The chromosomal locations of the binding peaks P-Stat3 were identified with the program NimbleScan (version 2.5) using the default parameters. The chromosomal locations of the peaks were imported into a relational database and mapped to the nearest gene with Ensembl (version 60) after providing the software with the Nimblegen range (-5000 to 1000) from the transcription start site of the gene. P-Stat3 peaks were mapped to genes using the procedure built into the Nencki Genomics Database (www.nencki-genomics.org) (Krystkowiak et al., submitted), with the additional condition that each peak is mapped only to its nearest gene at the distance range covered by the Nimblegene chips (-5000, +1000 from the transcription start site). From the metioned software we obtained a .csv file containing information about the peaks (among others chormosome, peak start, peak stop and peak score). We prepared a python script to copy the data from these fields to a new text file following .bed file format.

organism: Rattus norvegicus

source_name: Stat3 ChIP DNA from C6

label_protocol: Prior labeling, the immunoprecipitated DNA was amplified with a whole genome amplification WGA3 kit (Sigma-Aldrich, St. Louis, MO) according to the manufacturer’s protocol. Samples were independently labeled samples using a NimbleGen Dual-Color DNA Labeling Kit (Roche) according to the manufacturer's instructions.

growth_protocol: The rat C6 glioma cells purchased from ATCC were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Sigma) and antibiotics (50 U/ml penicillin, 50 μg/ml streptomycin). Cells were grown in 6-cm diameter culture plates (Corning) in a humidified atmosphere of CO2/air (5%/95%) at 37°C.

extract_protocol: For ChIP-chip experiments, 5 x 107 C6 glioma cells were cultured to 90% confluence. Cells were treated with 1% formaldehyde, and the cross-linked chromatin was sonicated (average size, 300 bp). Immunoprecipitation were performed with components of the ChIP IT kit according to the manufacturer’s instructions (Active Motif, Carlsbad, CA). Each sample was immunoprecipitated with 1 µg of anti-P-Stat3 antibody (sc-7993X, Santa Cruz, CA). The amount and quality of immunoprecipitated DNA were determined by capillary electrophoresis with a Bioanalyzer 2100 and a High Sensitivity DNA LabChip kit from Agilent Technologies (Santa Clara, CA).

value: C6 glioma cells

tag: chip antibody

value: anti-P-Stat3 antibody (sc-7993X, Santa Cruz)

source_name: C6 Input DNA

value: none (input)


title: TSEC Media- biological rep2

value: Murine Liver Sinusoidal Endothelial Cell Line


title: Human naive B-cell-rep 19

description: Gene expression data from human naive B-cell, rep 19.


title: TSEC Media- biological rep3

value: Media


title: cho-00156: CHTN-OS-047

value: F

value: serous


title: C6 Stat3 S1_NimbleGen

description: Chip-ChIP C6 cells Stat3


title: cho-00156: CHTN-OS-044


title: cho-00156: CHTN-OS-043


title: dobbi-00100: CL2003092326AA

value: Lung


title: cho-00156: CHTN-OS-041

value: Ovary cancer


title: Human naive B-cell-rep 18

description: Gene expression data from human naive B-cell, rep 18.


title: Human naive B-cell-rep 15

description: Gene expression data from human naive B-cell, rep 15.


title: Human naive B-cell-rep 14

description: Gene expression data from human naive B-cell, rep 14.


title: cho-00156: CHTN-OS-029

value: Ovary


title: cho-00156: CHTN-OS-031


title: cho-00156: CHTN-OS-013


title: dobbi-00100: CL2003092322AA

value: Stomach Adenocarcinoma

value: Stomach


title: dobbi-00100: CL2003092320AA


title: dobbi-00100: CL2003092321AA

value: Adrenal Cortical Adenoma

value: Adrenal Gland


title: Human naive B-cell-rep 7

description: Gene expression data from human naive B-cell, rep 7.


title: Human naive B-cell-rep 4

description: Gene expression data from human naive B-cell, rep 4.


title: dobbi-00100: CL2003092323AA

value: Non neoplastic liver with cirrosis

value: Liver


title: Human naive B-cell-rep 8

description: Gene expression data from human naive B-cell, rep 8.

value: naive B-cell (CD10- CD19+ CD20+ CD21+ CD27-)


title: Human naive B-cell-rep 6

description: Gene expression data from human naive B-cell, rep 6.


title: Human naive B-cell-rep 17

description: Gene expression data from human naive B-cell, rep 17.


title: Human naive B-cell-rep 9

description: Gene expression data from human naive B-cell, rep 9.


title: Human naive B-cell-rep 5

description: Gene expression data from human naive B-cell, rep 5.


title: dobbi-00100: CL2003092324AA


title: Human naive B-cell-rep 10

description: Gene expression data from human naive B-cell, rep 10.


title: Human naive B-cell-rep 13

description: Gene expression data from human naive B-cell, rep 13.


title: Human naive B-cell-rep 11

description: Gene expression data from human naive B-cell, rep 11.


title: dobbi-00100: CL2003092325AA

value: Leiomyoma

value: Uterus


title: cho-00156: CHTN-OS-011


title: cho-00156: CHTN-OS-010


title: cho-00156: CHTN-OS-002


title: Human naive B-cell-rep 1

description: Gene expression data from human naive B-cell, rep 1.


title: Human classical B-cell-rep 19

description: Gene expression data from human classical B-cell, rep 19.

source_name: Human classical B-cell

value: classical B-cell (CD10- CD19+ CD20+ CD21+ CD27+)


title: cho-00156: CHTN-OM-038

value: mucinous


title: Human naive B-cell-rep 2

description: Gene expression data from human naive B-cell, rep 2.


title: dobbi-00100: CL2003092318AA


title: Human naive B-cell-rep 3

description: Gene expression data from human naive B-cell, rep 3.


title: cho-00156: CHTN-OM-037

value: serous/mucinous


title: Human classical B-cell-rep 16

description: Gene expression data from human classical B-cell, rep 16.


title: Human classical B-cell-rep 20

description: Gene expression data from human classical B-cell, rep 20.


title: Human classical B-cell-rep 17

description: Gene expression data from human classical B-cell, rep 17.


title: Human classical B-cell-rep 18

description: Gene expression data from human classical B-cell, rep 18.


title: Human classical B-cell-rep 15

description: Gene expression data from human classical B-cell, rep 15.


title: dobbi-00100: CL2003092317AA

value: Stage IB

value: female


title: cho-00156: CHTN-OM-036

value: F


title: dobbi-00100: CL2003092315AA

value: Stage IA

value: Lung

value: male

value: Adenocartcinoma of Lung


title: dobbi-00100: CL2003092316AA

value: Stage IIIB


title: Human classical B-cell-rep 14

description: Gene expression data from human classical B-cell, rep 14.


title: Human classical B-cell-rep 13

description: Gene expression data from human classical B-cell, rep 13.


title: Human classical B-cell-rep 12

description: Gene expression data from human classical B-cell, rep 12.


title: Human classical B-cell-rep 10

description: Gene expression data from human classical B-cell, rep 10.


title: dobbi-00100: CL2003092314AA

value: Large Cell Lymphoma

value: Lymphoid tissue


title: Human classical B-cell-rep 9

description: Gene expression data from human classical B-cell, rep 9.


title: Human classical B-cell-rep 11

description: Gene expression data from human classical B-cell, rep 11.


title: dobbi-00100: CL2003092313AA

value: Metastatic Renal Cell Carcinoma

value: Kidney

value: Metastatic Renal Cell Carcinoma, clear cell type


title: cho-00156: CHTN-OM-007

value: Ovary cancer

value: Ovary


title: dobbi-00100: CL2003092312AA

value: Ovarian Adenocarcinoma

value: Papillary Serous Adenocarcinoma


title: Human naive B-cell-rep 12

description: Gene expression data from human naive B-cell, rep 12.

value: naive B-cell (CD10- CD19+ CD20+ CD21+ CD27-)


title: Human classical B-cell-rep 7

description: Gene expression data from human classical B-cell, rep 7.

value: classical B-cell (CD10- CD19+ CD20+ CD21+ CD27+)


title: Human classical B-cell-rep 8

description: Gene expression data from human classical B-cell, rep 8.


title: cho-00156: CHTN-OE-092

value: F

value: endometrioid


title: cho-00156: CHTN-OM-023

value: mucinous


title: dobbi-00100: CL2003092311AA

value: Leiomyoma

value: Uterus


title: cho-00156: CHTN-OM-017


title: dobbi-00100: CL2003092310AA

value: Stomach

value: Malignant G1 stromal tumor


title: dobbi-00100: CL2003092308AA

value: Non neoplastic liver with cirrosis

value: Liver


title: Human classical B-cell-rep 5

description: Gene expression data from human classical B-cell, rep 5.


title: Human classical B-cell-rep 2

description: Gene expression data from human classical B-cell, rep 2.


title: Human classical B-cell-rep 4

description: Gene expression data from human classical B-cell, rep 4.


title: Human atypical B-cell-rep 19

description: Gene expression data from human atypical B-cell, rep 19.

source_name: Human atypical B-cell

value: atypical B-cell (CD10- CD19+ CD20+ CD21- CD27-)


title: Human classical B-cell-rep 6

description: Gene expression data from human classical B-cell, rep 6.


title: cho-00156: CHTN-OE-082

value: endometrioid/serous


title: Human classical B-cell-rep 1

description: Gene expression data from human classical B-cell, rep 1.


title: Human atypical B-cell-rep 20

description: Gene expression data from human atypical B-cell, rep 20.


title: cho-00156: CHTN-OE-087

value: Ovary cancer


title: Human atypical B-cell-rep 17

description: Gene expression data from human atypical B-cell, rep 17.


title: cho-00156: CHTN-OM-035

value: Ovary


title: dobbi-00100: CL2003092404AA


title: dobbi-00100: CL2003092307AA

value: Stomach Adenocarcinoma


title: Human atypical B-cell-rep 16

description: Gene expression data from human atypical B-cell, rep 16.


title: cho-00156: CHTN-OE-077


title: cho-00156: CHTN-OE-076


title: Human atypical B-cell-rep 18

description: Gene expression data from human atypical B-cell, rep 18.


title: dobbi-00100: CL2003092306AA

value: Adrenal Cortical Adenoma

value: Adrenal Gland


title: Human atypical B-cell-rep 15

description: Gene expression data from human atypical B-cell, rep 15.


title: Human atypical B-cell-rep 13

description: Gene expression data from human atypical B-cell, rep 13.


title: dobbi-00100: CL2003092305AA


title: cho-00156: CHTN-OE-059


title: dobbi-00100: CL2003092304AA


title: Human atypical B-cell-rep 10

description: Gene expression data from human atypical B-cell, rep 10.


title: Human atypical B-cell-rep 12

description: Gene expression data from human atypical B-cell, rep 12.


title: dobbi-00100: CL2003092303AA


title: dobbi-00100: CL2003092319AA


title: cho-00156: CHTN-OE-061


title: cho-00156: CHTN-OE-056


title: dobbi-00100: CL2003092301AA


title: Human atypical B-cell-rep 11

description: Gene expression data from human atypical B-cell, rep 11.


title: Human atypical B-cell-rep 14

description: Gene expression data from human atypical B-cell, rep 14.


title: Human atypical B-cell-rep 7

description: Gene expression data from human atypical B-cell, rep 7.


title: cho-00156: CHTN-OE-060


title: Human atypical B-cell-rep 8

description: Gene expression data from human atypical B-cell, rep 8.


title: Human atypical B-cell-rep 5

description: Gene expression data from human atypical B-cell, rep 5.


title: Human atypical B-cell-rep 9

description: Gene expression data from human atypical B-cell, rep 9.


title: Human atypical B-cell-rep 4

description: Gene expression data from human atypical B-cell, rep 4.


title: dobbi-00100: CL2003092302AA


title: dobbi-00100: NCI_control4

source_name: U. Michigan Medical School


title: cho-00156: CHTN-OE-053


title: dobbi-00100: NCI_control3


title: Human atypical B-cell-rep 6

description: Gene expression data from human atypical B-cell, rep 6.


title: cho-00156: CHTN-OE-047


title: cho-00156: CHTN-OE-065


title: cho-00156: CHTN-OE-042


title: dobbi-00100: NCI_C2_U133A


title: Human atypical B-cell-rep 2

description: Gene expression data from human atypical B-cell, rep 2.


title: cho-00156: CHTN-OE-038


title: dobbi-00100: NCI_93


title: Human atypical B-cell-rep 1

description: Gene expression data from human atypical B-cell, rep 1.


title: dobbi-00100: NCI_85_U133A


title: Human atypical B-cell-rep 3

description: Gene expression data from human atypical B-cell, rep 3.


title: p23t

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description:
Sample name: ext0714
patient 23 organoids

hyb_protocol: 100 ng of labeled cRNA was hybridized to Hugene2.0  according to manufacturer’s protocol (Affymetrix).

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

data_processing: Expression data (cel files) were normalized with the rma_sketch algorithm using Affy Powertools  (Affymetrix)

source_name: colon carcinoma organoids

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

growth_protocol: healthy and tumor organoids were harvested from Matrigel and trypsinized. After trypsinization, cells were resuspended in Matrigel. After allowing the Matrigel to solidify, Human Intestinal Stem Cell medium (HISC) was added and crypts were incubated at 37 oC.  The composition of HISC is: Basal culture medium with 50% Wnt conditioned medium, 20% R-Spondin conditioned medium, 10% Noggin conditioned medium,  1 x B27, 1,25 mM n-Acetyl Cysteine, 10 mM Nicotinamide, 50 ng/ml human EGF, 10 nM Gastrin, 500 nM A83-01, 3 uM SB202190, 10 nM Prostaglandine E2 and 1 x Primocin (Vivogen). Rho kinase inhibitor was added for one day after seeding.

extract_protocol: Total RNA was isolated using RNeasy Kit (Qiagen) according to manufacturer’s protocol,

treatment_protocol: Organoids were grown for two days in complete Human Intestinal Stem Cell medium (HISC). Healthy and tumor organoids were grown in the same medium conditions.

value: CRC

tag: individual

value: patient 23

value: colon tumor


title: dobbi-00100: NCI_88_U133A

tag: Sex


title: cho-00156: CHTN-OE-040

value: F

value: endometrioid


title: p31t

description:
Sample name: ext0716
patient 31 organoids

value: patient 31


title: cho-00156: CHTN-OE-054


title: dobbi-00100: NCI_82

tag: cell line


title: cho-00156: CHTN-OE-027

tag: disease state


title: carpt-00469: RA53T

value: Prostate Cancer

value: Lung

value: metastatic tumor

value: male

value: Female


title: p9t

description:
Sample name: ext0712
patient 9 organoids

value: patient 9


title: dobbi-00100: NCI_C1_U133A


title: p14t

description:
Sample name: ext0713
patient 14 organoids

value: patient 14


title: cho-00156: CHTN-OE-036

value: Ovary cancer

tag: disease location

value: Ovary


title: cho-00156: CHTN-OE-018

tag: organism part


title: cho-00156: CHTN-OE-033

tag: disease stage


title: dobbi-00100: NCI_78_U133A

tag: histology


title: carpt-00469: RA45RM

value: Rib


title: dobbi-00100: NCI_89

tag: age


title: dobbi-00100: NCI_75_U133A

tag: tumor grading


title: p28t

description:
Sample name: ext0715
patient 28 organoids

value: patient 28


title: carpt-00469: RA49LT

value: Lymph Node


title: cho-00156: CHTN-OE-011


title: cho-00156: CHTN-OC-041

value: clear cell


title: p27t

description:
Sample name: ext0659
patient 27 organoids

value: CRC

value: patient 27

value: colon tumor


title: p27n

description:
Sample name: ext0658
patient 27 organoids

source_name: colon healthy tissue organoids

value: colon healthy/normal


title: dobbi-00100: NCI_73


title: Human classical B-cell-rep 3

description: Gene expression data from human classical B-cell, rep 3.

value: classical B-cell (CD10- CD19+ CD20+ CD21+ CD27+)


title: dobbi-00100: NCI_168_U133A

value: Non neoplastic liver with cirrosis

value: Liver


title: p28n

description:
Sample name: ext0660
patient 28 organoids


title: dobbi-00100: NCI_170_U133A

value: Ovarian Adenocarcinoma


title: p26t

description:
Sample name: ext0657
patient 26 organoids

value: patient 26


title: dobbi-00100: CL2003092309AA

value: Recurrent Renal Cell Carcinoma

value: Kidney

value: Recurrent Renal Cell Carcinoma, chromophobe cell type


title: cho-00156: CHTN-OE-005

source_name: Ovary

value: F

value: Ovary cancer

value: Ovary

value: endometrioid


title: dobbi-00100: NCI_171_U133A

value: Stomach Adenocarcinoma

value: Stomach


title: Huh7 U6 20 Cre 16 P3

city: Heidelberg

first: Tobias

last: Bauer

address: Im Neuenheimer Feld 280

department: Theoretical Bioinformatics

country: Germany

institute: German Cancer Research Center

description:
mRNA expression profile after integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells and knock out of miR-122
U6 20.16 P3

hyb_protocol: According to user manual GeneChip® 3’ IVT Express Kit, P/N 702646 Rev. 8: 12,5 ug of fragmented and labeled aRNA were hybridized for 17 hr at 45°C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays (P/N 702731).

data_processing: Raw data was quantile normalized and log2-transformed.

source_name: Huh7 cell line, shmiRNA integration and miR-122 ko, passage 3

label_protocol: The Affymetrix 3' IVT Express Kit is used to generate labeled single-stranded aRNA from input amounts of 100ng total RNA. Label: Biotin

growth_protocol: Huh7 cells were culture with DMEM supplemented with 10% FCS, 1% P/S and 1% NEAA

extract_protocol: To extract the total RNA the cells were harvested from one confluent 10 cm dish and resuspended in 5 ml of QIAzol Lysis Reagent (QIAGEN, Hilden, Germany). The QIAzol RNA extraction protocol recommended by QIAGEN was used for RNA purification.

tag: origin

value: Hepatocellular carcinoma

tag: gender

value: Male

tag: genotype/variation

value: shmiRNA integration and miR-122 ko

tag: passage


title: dobbi-00100: NCI_159_U133A

value: Large Cell Lymphoma


title: p26n

description:
Sample name: ext0656
patient 26 organoids

value: CRC

tag: tissue

value: colon healthy/normal


title: cho-00156: CHTN-OC-029

value: clear cell/serous


title: dobbi-00100: NCI_158

value: Squamous Cell Carcinoma

value: Lung


title: p25t

description:
Sample name: ext0655
patient 25 organoids

value: patient 25

value: colon tumor


title: cho-00156: CHTN-OC-026

value: F

value: clear cell


title: cho-00156: CHTN-OC-028

value: Ovary cancer

value: Ovary


title: Huh7 U6 20 Cre 16 P2

description:
mRNA expression profile after integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells and knock out of miR-122
U6 20.16 P2

source_name: Huh7 cell line, shmiRNA integration and miR-122 ko, passage 2


title: p24ta

description:
Sample name: ext0653
patient 24 tumor A organoids

value: patient 24


title: Huh7 TS 30 Cre 20 P3

description:
mRNA expression profile after integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells and mutation of miR-122
TS 30.20 P3

source_name: Huh7 cell line, shmiRNA integration and miR-122 mutation, passage 3


title: cho-00156: CHTN-OC-012


title: Huh7 U6 20 Cre 16

description:
mRNA expression profile after integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells and knock out of miR-122
U6 20.16 P1

source_name: Huh7 cell line, shmiRNA integration and miR-122 ko, passage 1


title: p24tb

description:
Sample name: ext0654
patient 24 tumor B organoids


title: dobbi-00100: NCI_152


title: Huh7 TS 30 Cre 20 P2

description:
mRNA expression profile after integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells and mutation of miR-122
TS 30.20 P2

source_name: Huh7 cell line, shmiRNA integration and miR-122 mutation, passage 2


title: dobbi-00100: NCI_157

value: Adrenal Cortical Adenoma

value: Adrenal Gland


title: p24n

description:
Sample name: ext0652
patient 24 organoids


title: cho-00156: CHTN-OC-004


title: p23n

description:
Sample name: ext0651
patient 23 organoids

value: patient 23


title: cho-00156: CHTN-OC-001


title: Huh7 TS 30 Cre 20

description:
mRNA expression profile after integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells and mutation of miR-122
TS 30.20 P1

source_name: Huh7 cell line, shmiRNA integration and miR-122 mutation, passage 1

value: Hepatocellular carcinoma

value: Male


title: cho-00156: UM-OS-010

value: serous


title: p20t

description:
Sample name: ext0650
patient 20 organoids

value: CRC

value: patient 20


title: cho-00156: UM-OS-001


title: p20n

description:
Sample name: ext0649
patient 20 organoids

value: colon healthy/normal


title: cho-00156: CU-OS-004


title: Huh7 T2 31 Cre 3 P3

description:
mRNA expression profile after integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells
T2 31.3 P3

source_name: Huh7 cell line, shmiRNA integration, passage 3

value: shmiRNA integration


title: cho-00156: CHTN-OS-139


title: p19tb

description:
Sample name: ext0648
patient 19 tumor B organoids

value: patient 19


title: dobbi-00100: NCI_136_U133A


title: dobbi-00100: NCI_138_U133A

value: Squamous Cell Carcinoma

value: Lung

value: Squamous Cell carcinoma


title: Huh7 T2 31 Cre 3 P2

description:
mRNA expression profile after integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells
T2 31.3 P2

source_name: Huh7 cell line, shmiRNA integration, passage 2


title: Huh7 wt

description:
mRNA expression profile of Huh7 wild-type cells
WT P1

source_name: Huh7 cell line, wild type, passage 1

value: wild type


title: Huh7 wt P3

description:
mRNA expression profile of Huh7 wild-type cells
WT P3

source_name: Huh7 cell line, wild type, passage 3


title: dobbi-00100: NCI_146

value: Metastatic Renal Cell Carcinoma

value: Kidney

value: Metastatic Renal Cell Carcinoma, clear cell type


title: dobbi-00100: NCI_135_U133A

value: Adrenal Cortical Adenoma

value: Adrenal Gland


title: cho-00156: CHTN-OS-116

value: F

value: Ovary cancer

value: Ovary


title: dobbi-00100: NCI_132_U133A

value: Recurrent Renal Cell Carcinoma

value: Recurrent Renal Cell Carcinoma, chromophobe cell type


title: Huh7 T2 31 Cre 3

description:
mRNA expression profile after integration of a an anti-HCV shmiRNA in the hcr locus of Huh7 wild type cells
T2 31.3 P1

source_name: Huh7 cell line, shmiRNA integration, passage 1

value: Hepatocellular carcinoma

value: Male


title: p18n

description:
Sample name: ext0645
patient 18 organoids

value: CRC

value: patient 18

value: colon healthy/normal


title: dobbi-00100: NCI_133_U133A

value: Stomach


title: p18t

description:
Sample name: ext0646
patient 18 organoids

value: colon tumor


title: cho-00156: CHTN-OS-098

value: serous


title: dobbi-00100: NCI_130_U133A

value: Stage IA

value: Lung

value: male

value: Lung Adenocarcinoma


title: p16t

description:
Sample name: ext0643
patient 16 organoids

value: patient 16


title: p19ta

description:
Sample name: ext0647
patient 19 tumor A organoids

value: patient 19


title: dobbi-00100: NCI_125R

value: Stage IB


title: Huh7 wt P2

description:
mRNA expression profile of Huh7 wild-type cells
WT P2

source_name: Huh7 cell line, wild type, passage 2

value: wild type


title: dobbi-00100: NCI_125_U133A

value: Squamous Cell Carcinoma


title: dobbi-00100: NCI_124_U133A

value: Stage IIIB

value: female


title: p16n

description:
Sample name: ext0642
patient 16 organoids

value: CRC


title: p11t

description:
Sample name: ext0641
patient 11 organoids

value: patient 11


title: dobbi-00100: NCI_121


title: cho-00156: CHTN-OS-084

value: F

value: Ovary cancer

value: Ovary


title: cho-00156: CHTN-OS-053

value: serous


title: cho-00156: CHTN-OE-023

value: endometrioid


title: dobbi-00100: NCI_113_U133A

value: Lung


title: cho-00156: CHTN-OS-049


title: cho-00156: CHTN-OS-046


title: cho-00156: CHTN-OS-081


title: cho-00156: CHTN-OS-068


title: p9n

description:
Sample name: ext0636
patient 9 organoids

value: patient 9

value: colon healthy/normal


title: p11n

description:
Sample name: ext0640
patient 11 organoids


title: dobbi-00100: NCI_115

value: Stomach Adenocarcinoma

value: Stomach

value: Adenocarcinoma


title: cho-00156: CHTN-OS-072


title: p10n

description:
Sample name: ext0638
patient 10 organoids

value: patient 10


title: cho-00156: CHTN-OS-038


title: cho-00156: CHTN-OS-025


title: dobbi-00100: NCI_110


title: dobbi-00100: NCI_114_U133A

value: Malignant Melanoma

value: Skin

value: carcinoma


title: cho-00156: UM-OM-001

value: mucinous


title: Patient 4750

first: Costa

last: Bachas

address: CCA 4.28, De Boelelaan 1117

department: Pediatric Oncology/ Hematology

institute: VU University Medical Center

description: primary pediatric relapsed AML bone marrow specimen

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Array Set HG-U133 Plus 2.0. After sample hybridization, GeneChips were stained using phycoerythrin-conjugated streptavidine in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner.

data_processing: The CEL files for these samples were read into R using the affy package and normalized at probe-level with vsn (Huber et al, Bioinformatics 2002). Measurements were summarized per probe set using median polish.

source_name: bone marrow or peripheral blood sample from child with acute myeloid leukemia

label_protocol: Biotinylated cRNA was produced according tot the Affymetrix protocol with the ENZO IVT labeling kit, using 5 ug total RNA as input (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: in patient/vivo

extract_protocol: Total RNA was isolated out of leukemic cells using Trizol reagent (GIBCO BRL, Life Technologies). Quality of RNA was checked using an Agilent 2100 Bio-analyzer.

treatment_protocol: If required, samples were enriched for leukemic cells were isolated by sucrose density centrifugation and non-leukemic cells were eliminated as previously described

tag: diagnosis

value: primary pediatric relapsed acute myeloid leukemia

tag: cytogenetic aml subgroup

value: Complex

tag: flt3/itd mutation status

value: wild type

tag: npm1 mutation status

tag: ras mutation status

value: mutated

tag: kit mutation status

tag: cebpa mutation status

tag: wt1 mutation status


title: p10t

description:
Sample name: ext0639
patient 10 organoids

tag: disease state

value: CRC

tag: individual

value: colon tumor


title: p8n

description:
Sample name: ext0634
patient 8 organoids

value: patient 8


title: dobbi-00100: NCI_106

source_name: U. Michigan Medical School

tag: cell line

value: Squamous Cell Carcinoma

tag: disease stage

tag: organism part

value: Lung

tag: Sex

tag: age

tag: histology


title: p17t

description:
Sample name: ext0644
patient 17 organoids

source_name: colon carcinoma organoids

value: patient 17

tag: tissue


title: dobbi-00100: NCI_105_U133A

tag: tumor grading


title: p7n

description:
Sample name: ext0632
patient 7 organoids

source_name: colon healthy tissue organoids

value: patient 7

value: colon healthy/normal


title: p7t

description:
Sample name: ext0633
patient 7 organoids


title: dobbi-00100: NCI_111_U133A

value: Kidney

value: metastatic renal cell carcinoma


title: p8t

description:
Sample name: ext0635
patient 8 organoids


title: cho-00156: CHTN-OS-016

source_name: Ovary

value: F

value: Ovary cancer

tag: disease location

value: Ovary

value: serous


title: p6t

description:
Sample name: ext0631
patient 6 organoids

value: patient 6


title: cho-00156: CHTN-OS-009


title: cho-00156: CHTN-OS-020


title: cho-00156: CHTN-OS-008


title: dobbi-00100: Mof Tumor 163

source_name: H. Lee Moffitt Cancer Center

value: Stomach

value: Malignant G1 Stromal Tumor


title: p5t

description:
Sample name: ext0629
patient 5 organoids

value: CRC

value: patient 5


title: cho-00156: CHTN-OS-003


title: dobbi-00100: Mof Tumor 151

value: Leiomyoma

value: Uterus


title: cho-00156: CHTN-OM-029

value: mucinous


title: dobbi-00100: Mof Tumor 166

value: Squamous Cell Carcinoma

value: Lung


title: cho-00156: CHTN-OE-096

value: endometrioid/serous


title: cho-00156: CHTN-OM-034


title: p5n

description:
Sample name: ext0628
patient 5 organoids

value: colon healthy/normal


title: dobbi-00100: Mof Tumor 150

value: Ovarian Adenocarcinoma

value: Papillary Serous Adenocarcinoma


title: dobbi-00100: Mof Tumor 155

value: Large Cell Lymphoma

value: Lymphoid tissue


title: cho-00156: CHTN-OE-080

value: F

value: Ovary cancer

value: Ovary

value: endometrioid


title: dobbi-00100: Mof Tumor 169

value: Stomach

value: Malignant G1 Stromal Tumor


title: dobbi-00100: Mof Tumor 154

value: Squamous cell carcinoma 85% tumor 15% Stroma


title: dobbi-00100: Mof Tumor 156


title: cho-00156: CHTN-OS-018

value: serous


title: dobbi-00100: Mof Tumor 124

value: Malignant Melanoma

value: Metastatic Malignant Melanoma


title: dobbi-00100: Mof Tumor 126

value: Recurrent Renal Cell Carcinoma

value: Recurrent Renal Cell Carcinoma, chromophobe cell type


title: Patient 3355

tag: diagnosis

value: primary pediatric relapsed acute myeloid leukemia

tag: cytogenetic aml subgroup

value: Unknown

tag: flt3/itd mutation status

value: wild type


title: Patient 4081

value: mutated

tag: npm1 mutation status

tag: ras mutation status

tag: kit mutation status


title: cho-00156: CHTN-OE-069

tag: disease state


title: Patient 3342

value: Other

tag: cebpa mutation status

tag: wt1 mutation status


title: dobbi-00100: Mof Tumor 139

tag: cell line

tag: disease stage

value: Liver

value: Non neoplastic liver with cirrosis


title: dobbi-00100: Mof Tumor 149

value: Adrenal Cortical Adenoma

tag: organism part

value: Adrenal Gland

tag: Sex


title: p6n

description:
Sample name: ext0630
patient 6 organoids

value: CRC

tag: individual

value: patient 6

value: colon healthy/normal


title: cho-00156: CHTN-OE-048

value: F

value: Ovary cancer

value: Ovary

tag: histology

value: endometrioid

value: U


title: cho-00156: CHTN-OE-039

tag: tumor grading


title: cho-00156: CHTN-OE-035

tag: disease location


title: cho-00156: CHTN-OE-029


title: cho-00156: CHTN-OE-019


title: cho-00156: CHTN-OE-046


title: dobbi-00100: Mof Tumor 105

tag: age


title: dobbi-00100: Mof Tumor 113

value: Large Cell Lymphoma

value: Lymphoid tissue


title: dobbi-00100: Mof Tumor 108

value: Squamous Cell Carcinoma

value: Lung


title: dobbi-00100: Mof Tumor 104

value: Leiomyoma

value: Uterus


title: Tet-mev-1 liver, normal diet 2

city: Isehara

first: Yutaka

last: Inagaki

state: Kanagawa

address: Shimokasuya 143

department: Regenerative Medicine

country: Japan

institute: Tokai University School of Medicine

hyb_protocol: The labelled cRNA was hybridized to the Agilent Whole Mouse Genome Microarray 4x44K v2 following manufacture's protocol.

scan_protocol: Arrays were scanned using Agilent G2565A Microarray Scanner System.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent Technology) using default parameters.
The raw signal intensities were log2 transformed and normalized by 75 percentile shift using Gene spring GX software (Agilent Technology).

source_name: Tet-mev-1 liver, normal diet

label_protocol: Cy3 labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA). cRNA was quantified with the NanoDrop ND-1000 Spectrophotometer

extract_protocol: Total RNA was extracted from liver tissues using RNeasy Mini kit (Qiagen, Valencia, CA) following manufacture's protocol. Extracted RNA quality was checked by the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain

tag: gender

value: Female

tag: genotype/variation

tag: protocol

value: normal diet

tag: tissue

value: liver


title: dobbi-00100: Mof Strat RNA 1

tag: disease state


title: Tet-mev-1 liver, high fat high sucrose diet 1

value: high fat high sucrose diet


title: Patient 3339

tag: diagnosis

value: primary pediatric relapsed acute myeloid leukemia

tag: cytogenetic aml subgroup

value: MLL

tag: flt3/itd mutation status

value: wild type

tag: npm1 mutation status

tag: ras mutation status

tag: kit mutation status

tag: cebpa mutation status


title: cho-00156: CHTN-OC-033

tag: Sex

value: F

value: Ovary cancer

tag: organism part

tag: histology

value: clear cell

tag: disease stage


title: cho-00156: CHTN-OC-045

tag: disease location

value: Ovary

tag: tumor grading


title: Wild type liver, high fat high sucrose diet 2

tag: strain

tag: gender

tag: genotype/variation

value: Wild type


title: dobbi-00100: Mof RNA 128

tag: cell line

tag: disease state

value: Stage IB

value: female

tag: age


title: dobbi-00100: Mof Tumor 109

value: Stomach Adenocarcinoma

value: Stomach


title: Tet-mev-1 liver, high fat high sucrose diet 2

tag: protocol

tag: tissue


title: Tet-mev-1 liver, normal diet 1


title: dobbi-00100: Mof RNA 127

value: Stage IIIB

value: Lung


title: dobbi-00100: Mof RNA 120

value: male


title: cho-00156: CHTN-OE-014

value: endometrioid


title: Wild type liver, high fat high sucrose diet 1

value: Female

value: high fat high sucrose diet

value: liver


title: cho-00156: CHTN-OE-017


title: dobbi-00100: Mof Cells 97


title: Wild type liver, normal diet 1

source_name: Wild type liver, normal diet

value: normal diet


title: dobbi-00100: Mof RNA 118

value: Stage IA


title: dobbi-00100: Mof Strat RNA 2


title: dobbi-00100: Mof RNA 122


title: dobbi-00100: Mof Cells 81


title: dobbi-00100: Mof Cells 91


title: dobbi-00100: Mof Cells 94


title: Wild type liver, normal diet 2


title: dobbi-00100: Mof Cells 77


title: becic-00235: D018: HG_U95B

status: Public on May 06 2015

tag: diseasestate

value: Normal

tag: tumorgrading

tag: diseasestaging

tag: organismpart

value: Prostate

value: at least 60% glandular no pathological alterations

tag: prostatetissue

value: normal


title: dobbi-00100: Mof Cells 111

tag: organism part

tag: Sex

tag: histology


title: dobbi-00100: Mof Cells 104

value: Leiomyoma

tag: tumor grading

tag: disease stage

value: Uterus


title: dobbi-00100: Mof Cells 102


title: dobbi-00100: Mof Cells 103


title: dobbi-00100: Mof Cells 74


title: becic-00235: PD010: HG_U95B


title: becic-00235: PD014: HG_U95B


title: becic-00235: PD001: HG_U95B


title: becic-00235: D024: HG_U95B

value: at least 60% glandular with inflammation


title: becic-00235: PT97: HG_U95B

value: pT T3a, pN N0, pM MX

value: ALI unknown, ECI focal, SVI no, SMI no

value: tumor


title: becic-00235: PD009: HG_U95B

value: male


title: becic-00235: PT93: HG_U95B

value: pT T3b, pN N0, pM MX

value: ALI yes, ECI multifocal, SVI yes, SMI no


title: becic-00235: PT99: HG_U95B

value: pT T3a, pN N1, pM MX

value: ALI unknown, ECI focal, SVI no, SMI yes


title: becic-00235: D019: HG_U95B


title: becic-00235: PD015: HG_U95B


title: becic-00235: PD22: HG_U95B

value: Ovary


title: becic-00235: PT94: HG_U95B

value: ALI no, ECI focal, SVI no, SMI no


title: becic-00235: PT90: HG_U95B


title: becic-00235: PT96: HG_U95B

value: ALI no, ECI multifocal, SVI yes, SMI extensive


title: becic-00235: PD002: HG_U95B

value: Normal

value: Prostate


title: becic-00235: PD013: HG_U95B

value: at least 60% glandular no pathological alterations

value: normal


title: becic-00235: PD006: HG_U95B


title: becic-00235: PD004: HG_U95B


title: becic-00235: PD016: HG_U95B


title: becic-00235: PD011: HG_U95B


title: becic-00235: PD012: HG_U95B


title: becic-00235: PT95: HG_U95B

value: pT T2b, pN N1, pM MX

value: ALI yes, ECI no, SVI no, SMI yes


title: becic-00235: PD005: HG_U95B


title: becic-00235: PD23: HG_U95B


title: becic-00235: PT89: HG_U95B

value: pT T2b, pN N0, pM MX

value: ALI unknown, ECI no, SVI no, SMI no


title: becic-00235: PD008: HG_U95B


title: becic-00235: PT91: HG_U95B

value: ALI no, ECI no, SVI no, SMI no

value: tumor


title: becic-00235: PD007: HG_U95B

value: male


title: becic-00235: PD25: HG_U95B


title: becic-00235: PT86: HG_U95B

value: pT T3b, pN N0, pM MX

value: ALI no, ECI multifocal, SVI yes, SMI no


title: becic-00235: PT87: HG_U95B

value: pT T2b, pN NX, pM MX

value: ALI unknown, ECI no, SVI no, SMI unknown


title: becic-00235: PT84: HG_U95B

value: pT T3b, pN N1, pM MX

value: ALI unknown, ECI multifocal, SVI yes, SMI yes


title: becic-00235: PT82: HG_U95B

value: pT T3a, pN N0, pM MX

value: ALI yes, ECI focal, SVI no, SMI yes


title: becic-00235: PT85: HG_U95B

value: Prostate

value: ALI unknown, ECI no, SVI no, SMI yes


title: becic-00235: PT83: HG_U95B


title: becic-00235: PT76: HG_U95B


title: becic-00235: PT80: HG_U95B


title: becic-00235: PT81: HG_U95B

value: pT T4, pN N0, pM MX

value: ALI unknown, ECI yes, SVI yes, SMI yes


title: becic-00235: PT88: HG_U95B

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PT75: HG_U95B

value: pT T2b, pN N0, pM MX

value: ALI unknown, ECI no, SVI no, SMI no


title: becic-00235: PT71: HG_U95B

value: tumor


title: becic-00235: PT66: HG_U95B

value: male


title: becic-00235: PT70: HG_U95B

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PT74: HG_U95B

value: pT T3a, pN N1, pM MX

value: ALI no, ECI multifocal, SVI no, SMI yes


title: becic-00235: PT72: HG_U95B

value: ALI unknown, ECI yes, SVI no, SMI yes


title: becic-00235: PT69: HG_U95B

value: ALI unknown, ECI multifocal, SVI no, SMI yes


title: becic-00235: PT60: HG_U95B


title: becic-00235: PT73: HG_U95B

value: ALI no, ECI focal, SVI no, SMI yes


title: becic-00235: PD003: HG_U95B

value: Normal

value: at least 60% glandular no pathological alterations

value: normal


title: becic-00235: PT68: HG_U95B

value: Prostate

value: ALI unknown, ECI no, SVI no, SMI yes


title: becic-00235: PT64: HG_U95B

value: pT T2a, pN N0, pM MX


title: becic-00235: PT57: HG_U95B


title: becic-00235: PT62: HG_U95B

value: pT T3a, pN N0, pM MX

value: ALI unknown, ECI yes, SVI no, SMI no


title: becic-00235: PT61: HG_U95B

value: pT T2b, pN N0, pM MX


title: becic-00235: PT65: HG_U95B

value: pT T3b, pN N0, pM MX

value: ALI yes, ECI multifocal, SVI yes, SMI no

value: tumor


title: becic-00235: PT63: HG_U95B

value: male

value: ALI unknown, ECI no, SVI no, SMI no


title: becic-00235: PT56: HG_U95B

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PT58: HG_U95B

value: ALI no, ECI yes, SVI no, SMI yes


title: becic-00235: PT67: HG_U95B

value: ALI no, ECI multifocal, SVI yes, SMI extensive


title: becic-00235: PT54: HG_U95B

value: pT T3a, pN N1, pM MX

value: ALI unknown, ECI multifocal, SVI no, SMI extensive


title: becic-00235: PT47: HG_U95B

value: ALI unknown, ECI multifocal, SVI yes, SMI yes


title: becic-00235: PT51: HG_U95B

value: Prostate

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PT45: HG_U95B


title: becic-00235: PT44: HG_U95B

value: pT T4a, pN N0, pM MX

value: ALI unknown, ECI multifocal, SVI no, SMI yes


title: becic-00235: PT50: HG_U95B

value: pT T3a, pN N0, pM MX


title: becic-00235: PT42: HG_U95B

value: ALI no, ECI focal, SVI no, SMI no


title: becic-00235: PT53: HG_U95B

value: pT T2b, pN N0, pM MX


title: becic-00235: PT41: HG_U95B

value: pT T3b, pN N0, pM MX

value: ALI unknown, ECI no, SVI yes, SMI no


title: becic-00235: PT39: HG_U95B

value: male

value: ALI unknown, ECI focal, SVI no, SMI yes

value: tumor


title: becic-00235: PT55: HG_U95B

value: ALI unknown, ECI no, SVI no, SMI no


title: becic-00235: PT35: HG_U95B

value: pT T2b, pN N0, pM M0

value: ALI no, ECI no, SVI no, SMI focal


title: becic-00235: PT38: HG_U95B


title: becic-00235: PT36: HG_U95B


title: becic-00235: PT46: HG_U95B

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PT48: HG_U95B

value: ALI unknown, ECI focal, SVI yes, SMI no


title: becic-00235: PT20: HG_U95B

value: Prostate

value: ALI unknown, ECI yes, SVI no, SMI yes


title: becic-00235: PT16: HG_U95B


title: becic-00235: PN95: HG_U95B

value: pT T2b, pN N1, pM MX

value: ALI yes, ECI no, SVI no, SMI yes

value: adjacent normal


title: becic-00235: PT10: HG_U95B

value: pT T2a, pN N0, pM MX


title: becic-00235: PT52: HG_U95B

value: pT T2b, pN N0, pM MX


title: becic-00235: PN99: HG_U95B

value: pT T3a, pN N1, pM MX


title: becic-00235: PN85: HG_U95B

value: ALI unknown, ECI no, SVI no, SMI yes


title: becic-00235: PT40: HG_U95B

value: male

value: pT T3a, pN N0, pM MX


title: becic-00235: PT107: HG_U95B

value: ALI no, ECI focal, SVI no, SMI no

value: tumor


title: becic-00235: PT101: HG_U95B

value: ALI unknown, ECI no, SVI no, SMI no


title: becic-00235: PT13: HG_U95B


title: becic-00235: PT34: HG_U95B

value: pT T3b, pN N0, pM MX

value: ALI yes, ECI focal, SVI yes, SMI focal


title: becic-00235: PN92: HG_U95B

value: pT T2b, pN N0, pM Mx

value: ALI no, ECI no, SVI no, SMI focal


title: becic-00235: PN84: HG_U95B

value: pT T3b, pN N1, pM MX

value: Prostate

value: ALI unknown, ECI multifocal, SVI yes, SMI yes


title: becic-00235: PN82: HG_U95B

value: ALI yes, ECI focal, SVI no, SMI yes

value: adjacent normal


title: becic-00235: PT100: HG_U95B

value: ALI unknown, ECI focal, SVI no, SMI yes


title: becic-00235: PT105: HG_U95B

value: ALI no, ECI established, SVI no, SMI extensive


title: becic-00235: PN79: HG_U95B

value: pT T3a, pN N0, pM Mx

value: ALI no, ECI focal, SVI no, SMI focal


title: becic-00235: PN75: HG_U95B

value: male

value: pT T2b, pN N0, pM MX


title: becic-00235: PN88: HG_U95B

value: pT T3a, pN N0, pM MX

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PN74: HG_U95B

value: pT T3a, pN N1, pM MX

value: ALI no, ECI multifocal, SVI no, SMI yes


title: becic-00235: PN87: HG_U95B

value: pT T2b, pN NX, pM MX

value: ALI unknown, ECI no, SVI no, SMI unknown


title: becic-00235: PN76: HG_U95B

value: ALI unknown, ECI no, SVI no, SMI yes


title: becic-00235: PN91: HG_U95B

value: Prostate

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PN83: HG_U95B


title: becic-00235: PN72: HG_U95B

value: ALI unknown, ECI yes, SVI no, SMI yes


title: becic-00235: PN73: HG_U95B

value: ALI no, ECI focal, SVI no, SMI yes

value: adjacent normal


title: becic-00235: PN71: HG_U95B


title: becic-00235: PN86: HG_U95B

value: pT T3b, pN N0, pM MX

value: ALI no, ECI multifocal, SVI yes, SMI no


title: becic-00235: PN90: HG_U95B


title: becic-00235: PN80: HG_U95B


title: becic-00235: PN81: HG_U95B

value: pT T4, pN N0, pM MX

value: ALI unknown, ECI yes, SVI yes, SMI yes


title: becic-00235: PT43: HG_U95B

value: male

value: ALI no, ECI yes, SVI no, SMI yes

value: tumor


title: becic-00235: PN77: HG_U95B

value: pT T3b, pN N0, pM Mx

value: ALI no, ECI established, SVI yes, SMI extensive


title: becic-00235: PN94: HG_U95B

value: pT T3a, pN N0, pM MX

value: ALI no, ECI focal, SVI no, SMI no


title: becic-00235: PN70: HG_U95B

value: pT T2b, pN N0, pM MX


title: becic-00235: PN67: HG_U95B

value: Prostate

value: ALI no, ECI multifocal, SVI yes, SMI extensive


title: becic-00235: PN62: HG_U95B

value: ALI unknown, ECI yes, SVI no, SMI no


title: becic-00235: PN66: HG_U95B_2ND_SCAN

value: ALI unknown, ECI multifocal, SVI yes, SMI yes


title: becic-00235: PN65: HG_U95B

value: ALI yes, ECI multifocal, SVI yes, SMI no

value: adjacent normal


title: becic-00235: PN66: HG_U95B

value: pT T3b, pN N0, pM MX


title: becic-00235: PN69: HG_U95B

value: ALI unknown, ECI multifocal, SVI no, SMI yes


title: becic-00235: PN61: HG_U95B

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PN63: HG_U95B

value: male

value: ALI unknown, ECI no, SVI no, SMI no


title: becic-00235: PN56: HG_U95B

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PN54: HG_U95B

value: pT T3a, pN N1, pM MX

value: ALI unknown, ECI multifocal, SVI no, SMI extensive


title: becic-00235: PN64: HG_U95B

value: pT T2a, pN N0, pM MX


title: becic-00235: PN68: HG_U95B

value: ALI unknown, ECI no, SVI no, SMI yes


title: becic-00235: PN58: HG_U95B

value: pT T3a, pN N0, pM MX

value: ALI no, ECI yes, SVI no, SMI yes


title: becic-00235: PN48: HG_U95B

value: Prostate

value: ALI unknown, ECI focal, SVI yes, SMI no


title: becic-00235: PN51: HG_U95B


title: becic-00235: PN47: HG_U95B

value: ALI unknown, ECI multifocal, SVI yes, SMI yes


title: becic-00235: PN53: HG_U95B

value: pT T2b, pN N0, pM MX


title: becic-00235: PN44: HG_U95B

value: pT T4a, pN N0, pM MX

value: adjacent normal


title: becic-00235: PN55: HG_U95B


title: becic-00235: PN45: HG_U95B


title: becic-00235: PN50: HG_U95B


title: becic-00235: PN60: HG_U95B

value: ALI unknown, ECI multifocal, SVI no, SMI yes


title: becic-00235: PN43: HG_U95B


title: becic-00235: PN46: HG_U95B


title: becic-00235: PN40: HG_U95B

value: ALI unknown, ECI focal, SVI no, SMI yes


title: becic-00235: PN42: HG_U95B

value: male

value: ALI no, ECI focal, SVI no, SMI no


title: becic-00235: PN41: HG_U95B

value: pT T3b, pN N0, pM MX

value: ALI unknown, ECI no, SVI yes, SMI no


title: becic-00235: PN38: HG_U95B

value: ALI unknown, ECI no, SVI no, SMI no


title: becic-00235: PN36: HG_U95B

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PN35: HG_U95B

value: pT T2b, pN N0, pM M0

value: ALI no, ECI no, SVI no, SMI focal


title: becic-00235: PN30: HG_U95B

value: pT T2b, pN N0, pM Mx


title: becic-00235: PN101: HG_U95B

value: Prostate


title: becic-00235: PN34: HG_U95B

value: ALI yes, ECI focal, SVI yes, SMI focal


title: becic-00235: PN107: HG_U95B

value: pT T3a, pN N0, pM MX


title: becic-00235: PN105: HG_U95B

value: ALI no, ECI established, SVI no, SMI extensive


title: Inactivated EV71 vaccine_PBMC, H06012

city: Kunming

first: Jie

last: Song

state: Yunnan

address: Number 935 Jiaoling Load

country: China

institute: Institute of Medical Biology, Chinese Academy of Medicine Science and Peking Union Medical College

description:
H06012
Gene expression after administrating of inactivated EV71 vaccine.

hyb_protocol: Each slide was hybridized with 1.65 μl of Cy3-labeled cRNA using the Gene Expression Hybridization Kit (Agilent) in a Hybridization Oven (Agilent). After 17 hours of hybridization, slides were washed in staining dishes (Thermo, MA, USA) with the Gene Expression Wash Buffer Kit (Agilent). Briefly, 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-014850 Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed with the Gene Expression Wash Buffer Kit (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: PBMC, inactivated EV71 vaccine

label_protocol: mRNA purified from total RNA after removal of rRNA was amplified and transcribed into fluorescent cRNA using the manufacturer’s Low Input Quick Amp Labeling protocol (Agilent). Labeled cRNA was purified using the RNeasy Mini Kit (QIAGEN, GmBH, Germany). Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from the PBMCs using TRIzol Reagent (Invitrogen, CA, USA) and purified using the RNeasy Mini Kit (QIAGEN, GmBH, Germany). The RNA Integrity Number (RIN) was also evaluated to inspect RNA integrity using an Agilent Bioanalyzer 2100 (Agilent, CA, USA).

treatment_protocol:
An inactivated EV71 vaccine or placebo was administered to infants (6 to 11 months).
Fresh peripheral blood from experiment or control infants was sampled, then was isolated the PBMCs.

tag: cell type

value: peripheral blood mononuclear cells

tag: treatment

value: inactivated EV71 vaccine

tag: developmental stage

value: infant


title: Inactivated EV71 vaccine_PBMC, H06016

description:
H06016
Gene expression after administrating of inactivated EV71 vaccine.


title: Inactivated EV71 vaccine_PBMC, H06008

description:
H06008
Gene expression after administrating of inactivated EV71 vaccine.


title: Inactivated EV71 vaccine_PBMC, H06005

description:
H06005
Gene expression after administrating of inactivated EV71 vaccine.


title: becic-00235: PN100: HG_U95B

value: ALI unknown, ECI focal, SVI no, SMI yes

value: adjacent normal


title: becic-00235: PN39: HG_U95B

value: male


title: Inactivated EV71 vaccine_PBMC, H06004

description:
H06004
Gene expression after administrating of inactivated EV71 vaccine.


title: Inactivated EV71 vaccine_PBMC, H06014

description:
H06014
Gene expression after administrating of inactivated EV71 vaccine.


title: Inactivated EV71 vaccine_PBMC, H06011

description:
H06011
Gene expression after administrating of inactivated EV71 vaccine.


title: Inactivated EV71 vaccine_PBMC, H06010

description:
H06010
Gene expression after administrating of inactivated EV71 vaccine.


title: Inactivated EV71 vaccine_PBMC, H06009

description:
H06009
Gene expression after administrating of inactivated EV71 vaccine.


title: Inactivated EV71 vaccine_PBMC, H06001

description:
H06001
Gene expression after administrating of inactivated EV71 vaccine.


title: Inactivated EV71 vaccine_PBMC, H06017

description:
H06017
Gene expression after administrating of inactivated EV71 vaccine.


title: Inactivated EV71 vaccine_PBMC_Placebo, Q167

description:
Q167
Gene expression after administrating of placebo.

source_name: PBMC, placebo

value: placebo


title: Inactivated EV71 vaccine_PBMC, H06013

description:
H06013
Gene expression after administrating of inactivated EV71 vaccine.


title: Inactivated EV71 vaccine_PBMC, H06007

description:
H06007
Gene expression after administrating of inactivated EV71 vaccine.


title: Inactivated EV71 vaccine_PBMC, H06002

description:
H06002
Gene expression after administrating of inactivated EV71 vaccine.


title: Inactivated EV71 vaccine_PBMC_Placebo, Q202

description:
Q202
Gene expression after administrating of placebo.


title: becic-00235: D025: HG_U95AV2

value: Normal

value: at least 60% glandular no pathological alterations

value: normal


title: Inactivated EV71 vaccine_PBMC, H06003

description:
H06003
Gene expression after administrating of inactivated EV71 vaccine.


title: Inactivated EV71 vaccine_PBMC, H06006

description:
H06006
Gene expression after administrating of inactivated EV71 vaccine.


title: Inactivated EV71 vaccine_PBMC_Placebo, Q161

description:
Q161
Gene expression after administrating of placebo.


title: becic-00235: D018: HG_U95AV2


title: Inactivated EV71 vaccine_PBMC_Placebo, Q182

description:
Q182
Gene expression after administrating of placebo.


title: becic-00235: D023: HG_U95AV2


title: becic-00235: PD24: HG_U95AV2

value: at least 60% glandular with inflammation


title: becic-00235: D022: HG_U95AV2

value: Ovary


title: becic-00235: D020: HG_U95AV2


title: becic-00235: PD012: HG_U95AV2


title: becic-00235: D019: HG_U95AV2


title: becic-00235: PD015: HG_U95AV2


title: becic-00235: PD005: HG_U95AV2


title: becic-00235: PD011: HG_U95AV2


title: becic-00235: PD016: HG_U95AV2


title: becic-00235: PD008: HG_U95AV2


title: becic-00235: PD014: HG_U95AV2


title: becic-00235: PD006: HG_U95AV2


title: becic-00235: PD004: HG_U95AV2


title: becic-00235: PD007: HG_U95AV2


title: becic-00235: PT96: HG_U95AV2

value: pT T3b, pN N0, pM MX

value: ALI no, ECI multifocal, SVI yes, SMI extensive

value: tumor


title: becic-00235: PD001: HG_U95AV2

value: Prostate


title: becic-00235: PD013: HG_U95AV2


title: becic-00235: PT94: HG_U95AV2

value: pT T3a, pN N0, pM MX

value: ALI no, ECI focal, SVI no, SMI no


title: becic-00235: PT97: HG_U95AV2

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PD010: HG_U95AV2


title: becic-00235: PD003: HG_U95AV2


title: becic-00235: D025: HG_U95C


title: becic-00235: PT93: HG_U95AV2

value: ALI yes, ECI multifocal, SVI yes, SMI no


title: becic-00235: PD024: HG_U95C


title: becic-00235: PT95: HG_U95AV2

value: pT T2b, pN N1, pM MX

value: ALI yes, ECI no, SVI no, SMI yes


title: becic-00235: PT91: HG_U95AV2

value: male

value: pT T2b, pN N0, pM MX

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PD009: HG_U95AV2

value: Normal

value: at least 60% glandular no pathological alterations


title: becic-00235: PT99: HG_U95AV2

value: pT T3a, pN N1, pM MX

value: ALI unknown, ECI focal, SVI no, SMI yes


title: becic-00235: D023: HG_U95C

value: normal


title: becic-00235: D022: HG_U95C

value: Ovary


title: becic-00235: PT88: HG_U95AV2

value: tumor


title: becic-00235: PT85: HG_U95AV2

value: Prostate

value: ALI unknown, ECI no, SVI no, SMI yes


title: becic-00235: PD014: HG_U95C


title: becic-00235: PD011: HG_U95C


title: becic-00235: PD002: HG_U95AV2


title: becic-00235: PD013: HG_U95C


title: becic-00235: PT87: HG_U95AV2

value: pT T2b, pN NX, pM MX

value: ALI unknown, ECI no, SVI no, SMI unknown


title: becic-00235: D019: HG_U95C


title: becic-00235: PT86: HG_U95AV2

value: pT T3b, pN N0, pM MX

value: ALI no, ECI multifocal, SVI yes, SMI no


title: becic-00235: PD009: HG_U95C


title: becic-00235: PT90: HG_U95AV2

value: pT T3a, pN N0, pM MX

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PT84: HG_U95AV2

value: male

value: pT T3b, pN N1, pM MX

value: ALI unknown, ECI multifocal, SVI yes, SMI yes


title: becic-00235: PT82: HG_U95AV2

value: ALI yes, ECI focal, SVI no, SMI yes


title: becic-00235: PT83: HG_U95AV2

value: pT T2b, pN N0, pM MX

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PT81: HG_U95AV2

value: pT T4, pN N0, pM MX

value: ALI unknown, ECI yes, SVI yes, SMI yes


title: becic-00235: PT89: HG_U95AV2

value: ALI unknown, ECI no, SVI no, SMI no

value: tumor


title: becic-00235: PD008: HG_U95C

value: Normal

value: Prostate

value: at least 60% glandular no pathological alterations

value: normal


title: becic-00235: PD007: HG_U95C


title: becic-00235: PD005: HG_U95C


title: becic-00235: PT74: HG_U95AV2

value: pT T3a, pN N1, pM MX

value: ALI no, ECI multifocal, SVI no, SMI yes


title: becic-00235: PT75: HG_U95AV2


title: becic-00235: PT76: HG_U95AV2

value: ALI unknown, ECI no, SVI no, SMI yes


title: becic-00235: PD015: HG_U95C

value: male


title: becic-00235: PD004: HG_U95C


title: becic-00235: PD012: HG_U95C


title: becic-00235: PT73: HG_U95AV2

value: pT T3a, pN N0, pM MX

value: ALI no, ECI focal, SVI no, SMI yes


title: becic-00235: PD003: HG_U95C


title: becic-00235: PD010: HG_U95C


title: becic-00235: PD002: HG_U95C


title: becic-00235: PT70: HG_U95AV2


title: becic-00235: PT80: HG_U95AV2


title: becic-00235: PT72: HG_U95AV2

value: ALI unknown, ECI yes, SVI no, SMI yes


title: becic-00235: PD006: HG_U95C


title: becic-00235: PT71: HG_U95AV2

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PD001: HG_U95C


title: becic-00235: PT68: HG_U95AV2

value: pT T2b, pN N0, pM MX


title: becic-00235: PT69: HG_U95AV2

value: ALI unknown, ECI multifocal, SVI no, SMI yes


title: becic-00235: PT96: HG_U95C

value: pT T3b, pN N0, pM MX

value: ALI no, ECI multifocal, SVI yes, SMI extensive


title: becic-00235: PT66: HG_U95AV2

value: ALI unknown, ECI multifocal, SVI yes, SMI yes

value: tumor


title: becic-00235: PT67: HG_U95AV2

value: Prostate


title: becic-00235: PT94: HG_U95C

value: ALI no, ECI focal, SVI no, SMI no


title: becic-00235: PT93: HG_U95C

value: ALI yes, ECI multifocal, SVI yes, SMI no


title: becic-00235: PT90: HG_U95C


title: becic-00235: PT88: HG_U95C


title: becic-00235: PT91: HG_U95C

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PT62: HG_U95AV2

value: ALI unknown, ECI yes, SVI no, SMI no


title: becic-00235: PT87: HG_U95C

value: pT T2b, pN NX, pM MX

value: ALI unknown, ECI no, SVI no, SMI unknown


title: becic-00235: PT95: HG_U95C

value: male

value: pT T2b, pN N1, pM MX

value: ALI yes, ECI no, SVI no, SMI yes


title: becic-00235: PT99: HG_U95C

value: pT T3a, pN N1, pM MX

value: ALI unknown, ECI focal, SVI no, SMI yes


title: becic-00235: PT58: HG_U95AV2

value: pT T3a, pN N0, pM MX

value: ALI no, ECI yes, SVI no, SMI yes


title: becic-00235: PT97: HG_U95C

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PT63: HG_U95AV2

value: pT T2b, pN N0, pM MX

value: ALI unknown, ECI no, SVI no, SMI no


title: becic-00235: PT57: HG_U95AV2

value: Prostate

value: ALI unknown, ECI no, SVI no, SMI yes

value: tumor


title: becic-00235: PT60: HG_U95AV2

value: ALI unknown, ECI multifocal, SVI no, SMI yes


title: becic-00235: PT65: HG_U95AV2

value: pT T3b, pN N0, pM MX

value: ALI yes, ECI multifocal, SVI yes, SMI no


title: becic-00235: PT61: HG_U95AV2

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PT64: HG_U95AV2

value: male

value: pT T2a, pN N0, pM MX


title: becic-00235: PT86: HG_U95C

value: ALI no, ECI multifocal, SVI yes, SMI no


title: becic-00235: PT89: HG_U95C


title: becic-00235: PT82: HG_U95C

value: ALI yes, ECI focal, SVI no, SMI yes


title: becic-00235: PT55: HG_U95AV2


title: becic-00235: PT81: HG_U95C

value: pT T4, pN N0, pM MX

value: ALI unknown, ECI yes, SVI yes, SMI yes


title: becic-00235: PT53: HG_U95AV2


title: becic-00235: PT56: HG_U95AV2

value: pT T3a, pN N0, pM MX


title: becic-00235: PT80: HG_U95C


title: becic-00235: PT76: HG_U95C


title: becic-00235: PT52: HG_U95AV2


title: becic-00235: PT74: HG_U95C

value: pT T3a, pN N1, pM MX

value: ALI no, ECI multifocal, SVI no, SMI yes


title: becic-00235: PT51: HG_U95AV2


title: becic-00235: PT54: HG_U95AV2

value: ALI unknown, ECI multifocal, SVI no, SMI extensive


title: becic-00235: PT73: HG_U95C

value: Prostate

value: ALI no, ECI focal, SVI no, SMI yes


title: becic-00235: PT52: HG_U95AV2_NEW

value: pT T2b, pN N0, pM MX

value: ALI unknown, ECI no, SVI no, SMI no

value: tumor


title: becic-00235: PT47: HG_U95AV2

value: pT T3b, pN N0, pM MX

value: ALI unknown, ECI multifocal, SVI yes, SMI yes


title: becic-00235: PT72: HG_U95C

value: male

value: ALI unknown, ECI yes, SVI no, SMI yes


title: becic-00235: PT75: HG_U95C


title: becic-00235: PT46: HG_U95AV2

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PT68: HG_U95C

value: ALI unknown, ECI no, SVI no, SMI yes


title: becic-00235: PT69: HG_U95C

value: ALI unknown, ECI multifocal, SVI no, SMI yes


title: becic-00235: PT42: HG_U95AV2

value: ALI no, ECI focal, SVI no, SMI no


title: becic-00235: PT48: HG_U95AV2

value: ALI unknown, ECI focal, SVI yes, SMI no


title: becic-00235: PT71: HG_U95C

value: pT T3a, pN N0, pM MX


title: becic-00235: PT41: HG_U95AV2

value: ALI unknown, ECI no, SVI yes, SMI no


title: becic-00235: PT65: HG_U95C

value: ALI yes, ECI multifocal, SVI yes, SMI no


title: becic-00235: PT50: HG_U95AV2

value: Prostate


title: becic-00235: PT67: HG_U95C

value: ALI no, ECI multifocal, SVI yes, SMI extensive


title: becic-00235: PT66: HG_U95C


title: becic-00235: PT35: HG_U95AV2

value: pT T2b, pN N0, pM M0

value: ALI no, ECI no, SVI no, SMI focal


title: becic-00235: PT45: HG_U95AV2

value: pT T2b, pN N0, pM MX

value: ALI unknown, ECI no, SVI no, SMI no

value: tumor


title: becic-00235: PT43: HG_U95AV2

value: male

value: ALI no, ECI yes, SVI no, SMI yes


title: becic-00235: PT44: HG_U95AV2

value: pT T4a, pN N0, pM MX


title: becic-00235: PT34: HG_U95AV2

value: pT T3b, pN N0, pM MX

value: ALI yes, ECI focal, SVI yes, SMI focal


title: becic-00235: PT60: HG_U95C

value: ALI unknown, ECI multifocal, SVI no, SMI yes


title: becic-00235: PT40: HG_U95AV2

value: ALI unknown, ECI focal, SVI no, SMI yes


title: becic-00235: PT83: HG_U95C

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PT58: HG_U95C

value: pT T3a, pN N0, pM MX


title: becic-00235: PT57: HG_U95C

value: ALI unknown, ECI no, SVI no, SMI yes


title: becic-00235: PT13: HG_U95AV2

value: Prostate

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PT54: HG_U95C

value: pT T3a, pN N1, pM MX

value: ALI unknown, ECI multifocal, SVI no, SMI extensive


title: becic-00235: PT107: HG_U95AV2

value: ALI no, ECI focal, SVI no, SMI no


title: becic-00235: PT100: HG_U95AV2


title: becic-00235: PT62: HG_U95C

value: ALI unknown, ECI yes, SVI no, SMI no


title: becic-00235: PT56: HG_U95C

value: tumor


title: becic-00235: PT52: HG_U95C

value: male

value: pT T2b, pN N0, pM MX

value: ALI unknown, ECI no, SVI no, SMI no


title: becic-00235: PT105: HG_U95AV2

value: ALI no, ECI established, SVI no, SMI extensive


title: becic-00235: PT53: HG_U95C


title: becic-00235: PT101: HG_U95AV2


title: becic-00235: PT10: HG_U95AV2

value: pT T2a, pN N0, pM MX


title: becic-00235: PT20: HG_U95AV2

value: ALI unknown, ECI yes, SVI no, SMI yes


title: becic-00235: PT61: HG_U95C


title: becic-00235: PT63: HG_U95C


title: becic-00235: PT50: HG_U95C


title: becic-00235: PN97: HG_U95AV2

value: adjacent normal


title: becic-00235: PNS96: HG_U95AV2

value: pT T3b, pN N0, pM MX

value: ALI no, ECI multifocal, SVI yes, SMI extensive


title: becic-00235: PT51: HG_U95C

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PT55: HG_U95C

value: Prostate


title: becic-00235: PN95: HG_U95AV2

value: pT T2b, pN N1, pM MX

value: ALI yes, ECI no, SVI no, SMI yes


title: becic-00235: PT47: HG_U95C

value: ALI unknown, ECI multifocal, SVI yes, SMI yes


title: becic-00235: PT48: HG_U95C

value: ALI unknown, ECI focal, SVI yes, SMI no


title: becic-00235: PN94: HG_U95AV2

value: pT T3a, pN N0, pM MX

value: ALI no, ECI focal, SVI no, SMI no


title: becic-00235: PN93: HG_U95AV2

value: male

value: ALI yes, ECI multifocal, SVI yes, SMI no


title: becic-00235: PN99: HG_U95AV2

value: pT T3a, pN N1, pM MX

value: ALI unknown, ECI focal, SVI no, SMI yes


title: becic-00235: PN92: HG_U95AV2

value: pT T2b, pN N0, pM Mx

value: ALI no, ECI no, SVI no, SMI focal


title: becic-00235: PT44: HG_U95C

value: pT T4a, pN N0, pM MX

value: ALI unknown, ECI multifocal, SVI no, SMI yes

value: tumor


title: becic-00235: PT45: HG_U95C

value: pT T2b, pN N0, pM MX

value: ALI unknown, ECI no, SVI no, SMI no


title: becic-00235: PN90: HG_U95AV2

value: Prostate

value: ALI unknown, ECI focal, SVI no, SMI no

value: adjacent normal


title: becic-00235: PN91: HG_U95AV2

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PN88: HG_U95AV2

value: pT T3a, pN N0, pM MX


title: becic-00235: PT43: HG_U95C

value: ALI no, ECI yes, SVI no, SMI yes


title: becic-00235: PT40: HG_U95C

value: male


title: becic-00235: PN86: HG_U95AV2

value: pT T3b, pN N0, pM MX

value: ALI no, ECI multifocal, SVI yes, SMI no


title: becic-00235: PN87: HG_U95AV2

value: pT T2b, pN NX, pM MX

value: ALI unknown, ECI no, SVI no, SMI unknown


title: becic-00235: PT39: HG_U95C

value: ALI unknown, ECI focal, SVI no, SMI yes


title: becic-00235: PT42: HG_U95C

value: ALI no, ECI focal, SVI no, SMI no


title: becic-00235: PT41: HG_U95C

value: ALI unknown, ECI no, SVI yes, SMI no


title: becic-00235: PN85: HG_U95AV2

value: ALI unknown, ECI no, SVI no, SMI yes


title: becic-00235: PN83: HG_U95AV2

value: pT T2b, pN N0, pM MX


title: becic-00235: PT35: HG_U95C

value: pT T2b, pN N0, pM M0

value: ALI no, ECI no, SVI no, SMI focal

value: tumor


title: becic-00235: PN82: HG_U95AV2

value: Prostate

value: ALI yes, ECI focal, SVI no, SMI yes

value: adjacent normal


title: becic-00235: PT38: HG_U95C

value: ALI unknown, ECI no, SVI no, SMI no


title: becic-00235: PN84: HG_U95AV2

value: male

value: pT T3b, pN N1, pM MX

value: ALI unknown, ECI multifocal, SVI yes, SMI yes


title: becic-00235: PT36: HG_U95C

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PT34: HG_U95C

value: pT T3b, pN N0, pM MX

value: ALI yes, ECI focal, SVI yes, SMI focal


title: becic-00235: PT20: HG_U95C

value: pT T3a, pN N0, pM MX

value: ALI unknown, ECI yes, SVI no, SMI yes


title: becic-00235: PN80: HG_U95AV2

value: ALI unknown, ECI no, SVI no, SMI yes


title: becic-00235: PT16: HG_U95C

value: pT T2b, pN N0, pM MX


title: becic-00235: PN79: HG_U95AV2

value: pT T3a, pN N0, pM Mx

value: ALI no, ECI focal, SVI no, SMI focal


title: becic-00235: PT13: HG_U95C

value: ALI unknown, ECI focal, SVI no, SMI no

value: tumor


title: becic-00235: PT107: HG_U95C

value: Prostate

value: ALI no, ECI focal, SVI no, SMI no


title: becic-00235: PN75: HG_U95AV2

value: ALI unknown, ECI no, SVI no, SMI no

value: adjacent normal


title: becic-00235: PN77: HG_U95AV2

value: male

value: pT T3b, pN N0, pM Mx

value: ALI no, ECI established, SVI yes, SMI extensive


title: becic-00235: PN76: HG_U95AV2


title: becic-00235: PT100: HG_U95C

value: ALI unknown, ECI focal, SVI no, SMI yes


title: becic-00235: PT101: HG_U95C


title: becic-00235: PT10: HG_U95C

value: pT T2a, pN N0, pM MX


title: becic-00235: PN73: HG_U95AV2

value: pT T3a, pN N0, pM MX

value: ALI no, ECI focal, SVI no, SMI yes


title: becic-00235: PT84: HG_U95C

value: pT T3b, pN N1, pM MX

value: ALI unknown, ECI multifocal, SVI yes, SMI yes


title: becic-00235: PN81: HG_U95AV2

value: pT T4, pN N0, pM MX

value: ALI unknown, ECI yes, SVI yes, SMI yes


title: becic-00235: PN95: HG_U95C

value: pT T2b, pN N1, pM MX

value: ALI yes, ECI no, SVI no, SMI yes


title: becic-00235: PN94: HG_U95C

value: Prostate


title: becic-00235: PN72: HG_U95AV2

value: ALI unknown, ECI yes, SVI no, SMI yes


title: becic-00235: PN91: HG_U95C

value: pT T2b, pN N0, pM MX

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PN74: HG_U95AV2

value: male

value: pT T3a, pN N1, pM MX

value: ALI no, ECI multifocal, SVI no, SMI yes

value: adjacent normal


title: becic-00235: PN71: HG_U95AV2

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PN92: HG_U95C

value: pT T2b, pN N0, pM Mx

value: ALI no, ECI no, SVI no, SMI focal


title: becic-00235: PN99: HG_U95C

value: ALI unknown, ECI focal, SVI no, SMI yes


title: becic-00235: PN70: HG_U95AV2


title: becic-00235: PN85: HG_U95C

value: ALI unknown, ECI no, SVI no, SMI yes


title: becic-00235: PN90: HG_U95C

value: pT T3a, pN N0, pM MX


title: becic-00235: PN83: HG_U95C


title: becic-00235: PN69: HG_U95AV2

value: ALI unknown, ECI multifocal, SVI no, SMI yes


title: becic-00235: PN68: HG_U95AV2


title: becic-00235: PN81: HG_U95C

value: pT T4, pN N0, pM MX

value: ALI unknown, ECI yes, SVI yes, SMI yes


title: becic-00235: PN82: HG_U95C

value: Prostate

value: ALI yes, ECI focal, SVI no, SMI yes


title: becic-00235: PN88: HG_U95C


title: becic-00235: PN87: HG_U95C

value: pT T2b, pN NX, pM MX

value: ALI unknown, ECI no, SVI no, SMI unknown


title: becic-00235: PN86: HG_U95C

value: male

value: pT T3b, pN N0, pM MX

value: ALI no, ECI multifocal, SVI yes, SMI no


title: becic-00235: PN67: HG_U95AV2

value: ALI no, ECI multifocal, SVI yes, SMI extensive

value: adjacent normal


title: becic-00235: PN80: HG_U95C

value: pT T2b, pN N0, pM MX


title: becic-00235: PN79: HG_U95C

value: pT T3a, pN N0, pM Mx

value: ALI no, ECI focal, SVI no, SMI focal


title: X8942326097_Control

city: Huddinge

first: Ingrid

last: Dahlman

address: Hälsovägen 7

department: Department of Medicine

institute: Karolinska Institute

description:
5959
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

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

data_processing: data was normalized and analyzed using Genom Studio software, R packages and Qlucore software.

label: Biotin

label_protocol: Standard Illumina protocol for Human Methylation 450K DNA Analysis bead chip

extract_protocol: Genomic DNA was prepared from fat cells using the  QiAamp DNA Mini kit (cat no. 51304, Qiagen, Hilden, Germany).

tag: gender

value: Female

value: Fat cell

tag: disease state

value: control

tag: bmi


title: X8942326097_PO2.3

description:
4971c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

value: postobese

tag: age


title: X8942326097_Control.2

description:
4978
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: becic-00235: PN77: HG_U95C

tag: diseasestate

value: pT T3b, pN N0, pM Mx

value: ALI no, ECI established, SVI yes, SMI extensive


title: becic-00235: PN66: HG_U95AV2

tag: tumorgrading

value: Prostate

value: ALI unknown, ECI multifocal, SVI yes, SMI yes


title: becic-00235: PT64: HG_U95C

tag: diseasestaging

value: pT T2a, pN N0, pM MX

value: ALI unknown, ECI no, SVI no, SMI no

value: tumor


title: becic-00235: PN76: HG_U95C

value: male

tag: organismpart

value: ALI unknown, ECI no, SVI no, SMI yes


title: X8942326097_Control.1

description:
406
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: becic-00235: PN75: HG_U95C

tag: prostatetissue

value: adjacent normal


title: becic-00235: PT16: HG_U95AV2

value: pT T2b, pN N0, pM MX


title: becic-00235: PN65: HG_U95AV2

value: pT T3b, pN N0, pM MX

value: ALI yes, ECI multifocal, SVI yes, SMI no


title: becic-00235: PN74: HG_U95C

value: pT T3a, pN N1, pM MX

value: ALI no, ECI multifocal, SVI no, SMI yes


title: X8942326097_PO2

description:
4979c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

value: Female

value: Fat cell


title: becic-00235: PN73: HG_U95C

value: pT T3a, pN N0, pM MX

value: ALI no, ECI focal, SVI no, SMI yes


title: X8942326097_PO2.2

description:
4946c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

value: postobese


title: becic-00235: PN72: HG_U95C

value: Prostate

value: ALI unknown, ECI yes, SVI no, SMI yes


title: becic-00235: PN63: HG_U95AV2

value: ALI unknown, ECI no, SVI no, SMI no


title: becic-00235: PT85: HG_U95C

value: tumor


title: becic-00235: PN71: HG_U95C

value: male

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PN70: HG_U95C

value: ALI no, ECI no, SVI no, SMI no

value: adjacent normal


title: becic-00235: PN64: HG_U95AV2

value: pT T2a, pN N0, pM MX


title: becic-00235: PN61: HG_U95AV2

value: pT T2b, pN N0, pM MX


title: becic-00235: PN62: HG_U95AV2

value: ALI unknown, ECI yes, SVI no, SMI no


title: becic-00235: PN68: HG_U95C

value: ALI unknown, ECI no, SVI no, SMI yes


title: becic-00235: PN67: HG_U95C

value: pT T3b, pN N0, pM MX

value: ALI no, ECI multifocal, SVI yes, SMI extensive


title: becic-00235: PN66: HG_U95C

value: ALI unknown, ECI multifocal, SVI yes, SMI yes


title: becic-00235: PN69: HG_U95C

value: pT T3a, pN N0, pM MX

value: ALI unknown, ECI multifocal, SVI no, SMI yes


title: becic-00235: PT46: HG_U95C

value: Prostate


title: becic-00235: PN65: HG_U95C

value: ALI yes, ECI multifocal, SVI yes, SMI no


title: becic-00235: PN64: HG_U95C

value: ALI unknown, ECI no, SVI no, SMI no


title: X8942326001_Control.1

description:
465
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

value: Female

value: Fat cell

value: control


title: becic-00235: PN60: HG_U95AV2

value: male


title: becic-00235: PN63: HG_U95C

value: adjacent normal


title: X8942326001_Control.2

description:
4993
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: X8942326001_PO2.3

description:
4966c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

value: postobese


title: becic-00235: PN58: HG_U95AV2

value: ALI no, ECI yes, SVI no, SMI yes


title: becic-00235: PN62: HG_U95C

value: ALI unknown, ECI yes, SVI no, SMI no


title: becic-00235: PT36: HG_U95AV2

value: pT T2b, pN N0, pM MX

value: ALI no, ECI no, SVI no, SMI no

value: tumor


title: X8942326097_PO2.1

description:
4666c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: becic-00235: PN56: HG_U95AV2

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PN61: HG_U95C


title: becic-00235: PN55: HG_U95AV2


title: becic-00235: PN58: HG_U95C

value: pT T3a, pN N0, pM MX


title: becic-00235: PN60: HG_U95C

value: ALI unknown, ECI multifocal, SVI no, SMI yes


title: X8942326001_PO2.1

description:
4595c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: becic-00235: PN54: HG_U95AV2

value: pT T3a, pN N1, pM MX

value: Prostate

value: ALI unknown, ECI multifocal, SVI no, SMI extensive


title: becic-00235: PN53: HG_U95AV2

value: ALI unknown, ECI no, SVI no, SMI no


title: becic-00235: PN55: HG_U95C


title: becic-00235: PN56: HG_U95C


title: becic-00235: PN53: HG_U95C


title: becic-00235: PN51: HG_U95C

value: pT T2a, pN N0, pM MX


title: becic-00235: PN54: HG_U95C


title: becic-00235: PN48: HG_U95C

value: pT T3b, pN N0, pM MX

value: ALI unknown, ECI focal, SVI yes, SMI no


title: becic-00235: PN47: HG_U95C

value: male

value: ALI unknown, ECI multifocal, SVI yes, SMI yes

value: adjacent normal


title: X8942326001_PO2.2

description:
4649c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

value: Female

value: Fat cell

value: postobese


title: becic-00235: PN50: HG_U95AV2


title: becic-00235: PN51: HG_U95AV2

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PN50: HG_U95C

value: ALI unknown, ECI focal, SVI no, SMI no


title: becic-00235: PN45: HG_U95C

value: pT T2b, pN N0, pM MX


title: becic-00235: PN46: HG_U95C

value: pT T3a, pN N0, pM MX


title: X8942326001_Control

description:
5886
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

value: control


title: becic-00235: PN48: HG_U95AV2

value: Prostate


title: X8942300210_Control

description:
5957
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: becic-00235: PN44: HG_U95C

value: pT T4a, pN N0, pM MX

value: ALI unknown, ECI multifocal, SVI no, SMI yes


title: becic-00235: PN47: HG_U95AV2


title: X8942326001_PO2

description:
4975c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: becic-00235: PN42: HG_U95C

value: ALI no, ECI focal, SVI no, SMI no


title: X8942300210_Control.1

description:
416
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: becic-00235: PN46: HG_U95AV2


title: becic-00235: PN43: HG_U95C

value: ALI no, ECI yes, SVI no, SMI yes


title: becic-00235: PN41: HG_U95C

value: pT T3b, pN N0, pM MX

value: ALI unknown, ECI no, SVI yes, SMI no


title: becic-00235: PN40: HG_U95C

value: male

value: ALI unknown, ECI focal, SVI no, SMI yes


title: becic-00235: PN39: HG_U95C

value: adjacent normal


title: becic-00235: PN38: HG_U95C

value: ALI unknown, ECI no, SVI no, SMI no


title: X8942300210_Control.2

description:
4613
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

value: Female

value: Fat cell


title: becic-00235: PN44: HG_U95AV2


title: becic-00235: PN36: HG_U95C

value: ALI no, ECI no, SVI no, SMI no


title: becic-00235: PN45: HG_U95AV2

value: pT T2b, pN N0, pM MX


title: becic-00235: PN34: HG_U95C

value: ALI yes, ECI focal, SVI yes, SMI focal


title: X8942300210_PO2

description:
4991c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

value: postobese


title: becic-00235: PN35: HG_U95C

value: pT T2b, pN N0, pM M0

value: Prostate

value: ALI no, ECI no, SVI no, SMI focal


title: becic-00235: PN30: HG_U95C

value: pT T2b, pN N0, pM Mx


title: becic-00235: PN43: HG_U95AV2

value: pT T3a, pN N0, pM MX

value: ALI no, ECI yes, SVI no, SMI yes


title: X8942300210_PO2.3

description:
4982c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: becic-00235: PN42: HG_U95AV2

value: ALI no, ECI focal, SVI no, SMI no


title: becic-00235: PN107: HG_U95C

value: male


title: X8942300210_PO2.2

description:
4957c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: becic-00235: PN100: HG_U95C

value: ALI unknown, ECI focal, SVI no, SMI yes


title: becic-00235: PN41: HG_U95AV2

value: pT T3b, pN N0, pM MX

value: ALI unknown, ECI no, SVI yes, SMI no

value: adjacent normal


title: X8942300210_Control.3

description:
5917
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

value: Female

value: Fat cell

value: control


title: becic-00235: PN101: HG_U95C

value: pT T2b, pN N0, pM MX

value: ALI unknown, ECI no, SVI no, SMI no


title: X8221932080_Control

description:
5960
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: X8221932080_Control.2

description:
4167
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: becic-00235: PN39: HG_U95AV2


title: Namalwa IRES GFP overexpression, replicate 2

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

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

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

data_processing: DNA microarray analyses were performed with R. RMA normalization and log2 transformation was used. Differentially expressed genes were called if FC ≥1.5 and p<0.05.

source_name: Namalwa IRES GFP overexpression

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

growth_protocol: HeLa and Namalwa cell lines (purchased from ATCC) were maintained in DMEM and RPMI respectively, containing 10% FBS,

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified with the RNAeasy kit from QIAGEN

treatment_protocol: Cells were infected with Sendai virus (+SV) for 6 and 12 hours. Double stranded shRNA sequences directed against macroH2A1 or a scramble sequence were cloned into the pLL3.7 vector harbouring GFP and recombinant lentiviral particles were produced and purified before transfection into the different cell lines.

tag: cell line

value: Namalwa

tag: expression

value: IRES GFP overexpression


title: Subject_10

city: Seattle

first: Daniel

middle: E

last: Sabath

state: WA

department: Laboratory Medicine

institute: University of Washington

description: Sri Lankan delta-beta thal

hyb_protocol: Labeled patient DNA and reference DNA were pooled and mixed with 2 μg of human Cot-1 DNA (Invitrogen, Carlsbad, CA), 4.5 μL of 10X blocking agent and 22.5 μL of 2X hybridization buffer (Agilent part no. 5188–5220) in a final volume of 45 μL. The mixture was denatured at 95°C for 3 minutes and incubated at 37°C for 30 minutes before loading on the array. Hybridization was performed for 18 to 24 hours at 65°C in a rotating oven (Agilent) at 10 rpm. After hybridization, the arrays were disassembled, washed for 5 minutes at room temperature in Agilent oligo array CGH wash buffer 1 and for 1 minute at 37°C in oligo array CGH wash buffer 2, and then were dried using compressed nitrogen.

scan_protocol: The arrays were scanned using an Agilent 2565BA DNA microarray scanner

data_processing: Array data were normalized using Feature Extraction Software version 9 (Agilent) and visualized using DNA Analytics software version 4.0.81 (Agilent)

label_protocol: Agilent Genomic DNA Labeling kit PLUS (Agilent part no. 5188-5309)

extract_protocol: DNA was extracted using Corbett automated DNA extractor

value: thalssemia/HPFH

source_name: Normal human DNA (Promega)

value: normal


title: Subject_11

description: 2.1 Mbp deletion


title: Subject_9

description: LCR deletion


title: Namalwa H2A overexpression, replicate 3

source_name: Namalwa H2A overexpression

value: H2A overexpression


title: Subject_8

description: 1.5 kb beta thal deletion


title: Namalwa IRES GFP overexpression, replicate 1


title: Namalwa IRES GFP overexpression, replicate 3


title: X8221932080_PO2.3

description:
4958c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

value: postobese


title: becic-00235: PN35: HG_U95AV2

tag: Sex

value: pT T2b, pN N0, pM M0

value: Prostate

tag: histology

value: ALI no, ECI no, SVI no, SMI focal


title: becic-00235: PN36: HG_U95AV2

value: male

value: ALI no, ECI no, SVI no, SMI no


title: Namalwa mH2A overexpression, replicate 3

source_name: Namalwa mH2A overexpression

value: mH2A overexpression


title: Namalwa H2A overexpression, replicate 1

description: Namalwa H2A overexpression, replicate 1


title: Subject_7

description: Kurdish beta thal


title: becic-00235: PN38: HG_U95AV2

value: adjacent normal


title: becic-00235: PN40: HG_U95AV2

value: pT T3a, pN N0, pM MX

value: ALI unknown, ECI focal, SVI no, SMI yes


title: Namalwa mH2A overexpression, replicate 1


title: Subject_6


title: Namalwa mH2A overexpression, replicate 2


title: X8942300210_PO2.1

description:
4885c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

value: Female

value: Fat cell


title: Namalwa H2A overexpression, replicate 2

value: Namalwa


title: X8221932080_PO2.1

description:
4640c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: HeLa IRES GFP overexpression, replicate 2

source_name: HeLa IRES GFP overexpression

value: HeLa

value: IRES GFP overexpression


title: HeLa IRES GFP overexpression, replicate 3


title: HeLa IRES GFP overexpression, replicate 1


title: X8221932080_PO2

description:
4985c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file


title: X8221932080_Control.3

description:
4911
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

value: control


title: Subject_5

description: SEA HPFH

value: thalssemia/HPFH

value: normal


title: becic-00235: PN34: HG_U95AV2

value: pT T3b, pN N0, pM MX

value: ALI yes, ECI focal, SVI yes, SMI focal


title: becic-00235: PN30: HG_U95AV2

value: pT T2b, pN N0, pM Mx

value: Prostate


title: HeLa H2A overexpression, replicate 3

source_name: HeLa H2A overexpression

value: H2A overexpression


title: becic-00235: PN107: HG_U95AV2

value: male

value: ALI no, ECI focal, SVI no, SMI no


title: HeLa mH2A overexpression, replicate 3

source_name: HeLa mH2A overexpression

value: mH2A overexpression


title: Subject_3

description: Hemoglobin Kenya


title: Subject_4

description: Hemoglobin E/beta0 thal


title: becic-00235: PN101: HG_U95AV2

value: pT T2b, pN N0, pM MX

value: ALI unknown, ECI no, SVI no, SMI no

value: adjacent normal


title: HeLa H2A overexpression, replicate 2


title: X8221932080_PO2.2

description:
4938c
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

value: Female

value: Fat cell

value: postobese


title: Subject_2


title: becic-00235: PN105: HG_U95AV2

value: pT T3a, pN N0, pM MX

value: ALI no, ECI established, SVI no, SMI extensive


title: HeLa mH2A overexpression, replicate 1

description: HeLa mH2A overexpression, replicate 1

value: HeLa


title: Subject_1

value: thalssemia/HPFH

value: normal


title: becic-00235: PN100: HG_U95AV2

value: ALI unknown, ECI focal, SVI no, SMI yes


title: HeLa mH2A overexpression, replicate 2


title: Namalwa shscr + SV 6 hours, replicate 3

source_name: Namalwa shscr + SV 6 hours

value: Namalwa

value: scramble sequence

tag: infection

value: Sendai virus (+SV) for 6 hours


title: Namalwa shmH2A1 + SV 6 hours, replicate 2

source_name: Namalwa shmH2A1 + SV 6 hours

value: shRNA sequences directed against macroH2A1


title: Namalwa shscr + SV 6 hours, replicate 1

description: Namalwa shscr + SV 6 hours, replicate 1


title: Namalwa shmH2A1 + SV 6 hours, replicate 3


title: WT ProB and PreB bone marrow cells, biological replicate 3

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description:
SAMPLE 17
Gene expression data from WT ProB and PreB bone marrow cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

source_name: WT ProB and PreB bone marrow cells

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

growth_protocol: Animals were housed in conventional facility and they have been exposed to common pathogens.

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

treatment_protocol: Not applicable

tag: strain background

tag: genotype/variation

value: wild type

tag: tissue/cell type

value: Bone marrow ProB and PreB Cells


title: Namalwa shscr, replicate 3

source_name: Namalwa shscr

tag: treatment


title: X8221932080_Control.1

description:
1753
Unmethylated and methylated signal intensities provided in signal_intensities.txt Series supplementary file

tag: gender

tag: cell type

tag: disease state

value: control