title: Tumor, rep54

city: Oslo

first: Ann Rita

last: Halvorsen

address: Montebello

country: Norway

institute: OUS- The Norwegian Radium Hospital

hyb_protocol: Cy3-labeled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was hybridized at 100°C for 5 minutes in a reaction containing 1x Agilent hybridization buffer and 2x Agilent blocking agent following the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol miRNA_107_sep09_patch and Grid:070156_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: breast tumor tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Trizol for tumor samples and Exiqon RNA isolation for biofluids (TIF).

treatment_protocol: Fresh-frozen tumor tissue.

tag: disease state

value: breast cancer

value: breast tumor


title: Tumor, rep53

status: Public on May 01 2017

type: RNA

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: CB LPS, rep1

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were normalised using quantile normalisation in Partek Genomic Suite. Expression values from different chip types (AB from HG-U133A, CB from HG-U133_Plus_2) were combined, keeping only probes with information from both chip types, resulting in 22277 probes. Further, only one probe per gene symbol was left by selecting the probes with the highest variance among all samples, resulting in 13515 unique transcripts.

label: biotin

source_name: Cord blood monocytes, LPS

label_protocol: cRNA were prepared and SAGE-labeled according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA) from 5 ug total RNA.

growth_protocol: Monocytes were isolated by Ficoll-Paque density gradient centrifugation and by using the Monocyte Isolation Kit II (Miltenyi Biotec, Bergisch Gladbach, Germany).

extract_protocol: Total RNA was isolated from monocytes using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: After o/n culture in teflon bags in McCoys modified medium supplemented with 1% glutamine, 1% penicillin-streptomycin and 15% FBS, monocytes were incubated for 4h with 10 ng/ml LPS.

tag: cell type

value: Monocytes

tag: tissue source

value: Cord blood

tag: treatment

value: Lipopolysaccharide (LPS)

tag: array


title: Tumor, rep52


title: glioma_14_nopressure_noAF

city: San Francisco

first: David

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

country: USA

institute: UCSF

hyb_protocol: 90 microliters of hybridization sample were incubated in the Affymetrix GeneTitan Hybridization Oven instrument for 16 hours at 48C

scan_protocol: Arrays were processed with the Affymetrix GeneTitan Fluidics Station instrument, using the HuGene-2_1-st-16 fluidics script and GeneTitan Hybridization, Wash, and Stain Kit for WT Array Plates. Arrays were scanned in the Affymetrix GeneTitan Multi-Channel (MC) instrument with the AGCC GeneTitan Instrument Control.

data_processing: Arrays were quantile normalized and log2 transformed

source_name: glioma, patient 14, nopressure, noAF

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

extract_protocol: Immediately upon completion of compression studies, HA gels were removed from the bioreactor assembly and the triplicates combined in a single Eppendorf tubes with either RNA (700 μL) or protein (300 μL) lysis buffers. Gels were then crushed mechanically, sonicated briefly, and RNA/proteins were allowed to diffuse out into the supernatant on ice for 2 hours. Subsequently, HA gel-RNA/protein solution was sonicated at maximum speed at 4 °C for 10 minutes; supernatant was then aliquoted into new tubes. RNA was isolated using RNAeasy mini kit (Qiagen) and further purified to remove any remaining glycosaminoglycans (Zymo Research); all samples were then flash-frozen on dry ice and stored in -80 °C. The concentration and quality of RNA was determined using Nanodrop followed by use of a RNA 6000 Nano Kit (Agilent) and bioanalyzer chips (Applied Biosystems) to determine RIN values. We then sent 300 ng total RNA (50 ng/ml) to the UCSF Institute for Human Genetics for further processing. In brief, 150 ng was used in the first and second strand cDNA synthesis and IVT cRNA synthesis.  We then performed cRNA purification and samples were normalized to 13.33 μg cRNA in 24 μl volume.  Samples then go through a second cycle of cDNA synthesis and RNase H hydrolysis. The cDNA was purified and normalized to 5.5 μg cDNA in 31.2 μl volume.

treatment_protocol: Human GBM tumorspheres (GBM5, GBM14, GBM34, and GBM43) embedded in HA-gels were subjected to no compression or compression (48h, 30%, 50 mmHg) using a compression force bioreactor with/without incubation with 1 ng/ml AF peptide.

value: FALSE

tag: individual

value: patient 14

value: patient-derived GBM tumorsphere


title: glioma_5_nopressure_noAF

source_name: glioma, patient 5, nopressure, noAF

value: patient 5


title: RatATII_AdHIF1a_Rep4

city: Denver

first: Sonia

middle: M

last: Leach

state: Colorado

address: 1400 Jackson St

institute: National Jewish Health

description: Gene expression in rat ATII cells transduced with AdHIF1a

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Affymetrix RaGene-2_0-st array analyzed by Expression Console using apt v1.2.1.20 with the following parameters: #%affymetrix-algorithm-param-apt-opt-analysis-spec=rma-bg,quant-norm.sketch=-1.bioc=true.lowprecision=false.usepm=true.target=0.doavg=false.subsetmd5=ef0a56c0e12e99397a1529009ff2ffa8,pm-only,med-polish.FixFeatureEffect=false.UseInputModel=false.FitFeatureResponse=true.expon=false.attenuate=true.l=0.005.h=-

organism: Rattus norvegicus

source_name: Rat ATII HIF1a

label_protocol: Affymetrix protocol

growth_protocol: Freshly isolated rat ATII cells were resuspended in DMEM + 2% FBS. AdGFP or AdHIF1a was added at an MOI of 20. Cells were incubated at 37 degrees C for 3 hours and then plated on 80% rat tail collagen / 20% matrigel in DMEM with 5% rat serum. RNA was harvested 24 h later.

extract_protocol: Qiagen RNEasy Kit according to the manufacturer's instructions

value: Alveolar Epithelial Type II Cells

tag: strain

value: Sprague Dawley

tag: gender

value: Male

tag: extractiondate


title: RatATII_AdHIF1a_Rep3

treatment_protocol: Freshly isolated rat ATII cells were resuspended in DMEM + 2% FBS. AdGFP or AdHIF1a was added at an MOI of 20. Cells were incubated at 37 degrees C for 3 hours and then plated on 80% rat tail collagen / 20% matrigel in DMEM with 5% rat serum. RNA was harvested 24 h later.


title: cord-blood from 755343-3RN

type: genomic

city: Campinas

first: Mariana

last: Maschietto

state: São Paulo

address: Rua Márcia Mendes, 619

department: Research Center

country: Brazil

institute: Boldrini Children's Hospital

description:
bisulfite converted DNA from 755343-3RN
DNA extracted from cord blood

hyb_protocol: As per Illumina protocol

scan_protocol: iScan SQ scanner (Illumina) using  GenomeStudio software (v.2011.1)

data_processing:
Unreliable measurements were identified using Greedycut (p>0.05) that removed 1,478 probes. Probes located in SNPs (n=4,776) as well those located in specific contexts (n=5,926, non-CpG sites and additional SNPs) were also excluded. Samples were retained only if >99% of sites assayed had detection p>0.05. The background was corrected using noob method, which is based on a normal-exponential convolution using out-of-band probes. Signal intensities values from probes type I and II were normalized using SWAN method that adjusts the intensities based on a quantile approach.
Normalized data (SWAN and noob) were transformed into M-values for statistical analyses

label: Cy5 and Cy3

molecule: genomic DNA

source_name: cord blood, 755343-3RN

label_protocol: As per Illumina protocol

extract_protocol: QIAamp DNA BloodMidi Kit as per protocol

treatment_protocol: DNA treated with sodium bisulfite

tag: age of the mother

tag: smoking cigarettes during pregnancy

value: No

tag: gestational stress


title: cord-blood from 470326-3RN

description:
bisulfite converted DNA from 470326-3RN
DNA extracted from cord blood

source_name: cord blood, 470326-3RN

value: Female


title: cord-blood from 2064320-1RN

description:
bisulfite converted DNA from 2064320-1RN
DNA extracted from cord blood

source_name: cord blood, 2064320-1RN

value: Yes


title: cord-blood from 2166265-3RN

description:
bisulfite converted DNA from 2166265-3RN
DNA extracted from cord blood

source_name: cord blood, 2166265-3RN


title: cord-blood from 2166181-2RN

description:
bisulfite converted DNA from 2166181-2RN
DNA extracted from cord blood

source_name: cord blood, 2166181-2RN


title: Tumor, rep51


title: cord-blood from 2107154-1RN

description:
bisulfite converted DNA from 2107154-1RN
DNA extracted from cord blood

source_name: cord blood, 2107154-1RN


title: RatATII_AdGFP_Rep4

description: Gene expression in rat ATII cells transduced with AdGFP

source_name: Rat ATII GFP


title: RatATII_AdHIF1a_Rep2


title: Tumor, rep50


title: Tumor, rep49


title: RatATII_AdGFP_Rep2


title: RatATII_AdGFP_Rep3


title: Tumor, rep48


title: Tumor, rep47


title: RatATII_AdHIF1a_Rep1


title: cord-blood from 569099-1RN

description:
bisulfite converted DNA from 569099-1RN
DNA extracted from cord blood

source_name: cord blood, 569099-1RN


title: cord-blood from 2163251-1RN

description:
bisulfite converted DNA from 2163251-1RN
DNA extracted from cord blood

source_name: cord blood, 2163251-1RN


title: Tumor, rep45


title: cord-blood from 2157134-1RN

description:
bisulfite converted DNA from 2157134-1RN
DNA extracted from cord blood

source_name: cord blood, 2157134-1RN


title: Tumor, rep46


title: RatATII_AdGFP_Rep1


title: Tumor, rep44


title: cord-blood from 2166325-2RN

description:
bisulfite converted DNA from 2166325-2RN
DNA extracted from cord blood

source_name: cord blood, 2166325-2RN


title: Blood CD8+T cell-Control3-Rep1

city: weifang

first: yurong

last: fu

address: No.7166, Baotong Xi (Western) Street, Weicheng District, Department of Laboratory Medicine, Shandong Provincial Key Laboratory of Clinical Laboratory Diagnostics, Weifang Medical University

country: China

institute: weifang medical universtiy

description: Gene expression in peripheral blood CD8+T cells isolated from  healthy controls

hyb_protocol: Arraystar Human LncRNA Microarray V3.0 is designed for the global profiling of human LncRNAs and protein-coding transcripts, which is updated from the previous Microarray V2.0. About 30,586 LncRNAs and 26,109 coding transcripts can be detected by our third-generation LncRNA microarray.1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) .

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: Peripheral blood CD8+T cell, Control3(one of three control subjects),replicate 1

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: For RNA preparation, total RNA was isolated from purified CD8+T cells using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA) and further purified with RNeasy mini kit (Qiagen, Hilden, Germany). Quantification and quality check were performed with Nanodrop ND-1000 (NanoDrop Technologies,Wilmington, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies Europe, Waldbroon, Germany), respectively. RNA integrity was assessed by standard denaturing gel electrophoresis.

treatment_protocol: For preparation of circulating CD8+ T cells, whole blood from each patient and healthy volunteer was taken into EDTA containing tubes. Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using density gradient centrifugation. CD8+ T cells were separated from PBMCs by means of negative selection with CD8+ T Cell Isolation Kit (R&D Systems, Minneapolis, MN, USA)  according to the manufacturer’s protocol. CD8+ T cells were recovered by removal of undesired cells employing a magnet. Flow cytometric analysis was used to measure purity of isolated CD8+ T cells and only cell sample with purity >90% was used for further downstream processing. Qualified samples were immediately stored in liquid nitrogen until further use.

value: CD8+Tcell from peripheral blood

tag: age

value: female

value: control


title: cord-blood from 015357-2RN

description:
bisulfite converted DNA from 015357-2RN
DNA extracted from cord blood

source_name: cord blood, 015357-2RN


title: cord-blood from 805473-3RN

description:
bisulfite converted DNA from 805473-3RN
DNA extracted from cord blood

source_name: cord blood, 805473-3RN


title: Blood CD8+T cell-Control2-Rep1

description: Gene expression in peripheral blood CD8+T cells isolated from healthy controls

source_name: Peripheral blood CD8+T cell, Control2(one of three control subjects),replicate 1

value: CD8+T cell from peripheral blood

value: male


title: Tumor, rep43

source_name: breast tumor tissue

value: breast cancer

value: breast tumor


title: Tumor, rep42


title: Tumor, rep41


title: cord-blood from 2162868-1RN

description:
bisulfite converted DNA from 2162868-1RN
DNA extracted from cord blood

source_name: cord blood, 2162868-1RN


title: Blood CD8+T cell-Control1-Rep1

source_name: Peripheral blood CD8+T cell, Control1(one of three control subjects),replicate 1


title: Tumor, rep40


title: Blood CD8+T cell-ATB3-Rep1

description: Gene expression in peripheral blood CD8+T cells isolated from patients with active TB

source_name: Peripheral blood CD8+T cell, ATB3(one of three active TB subjects),replicate 1

value: ATB


title: cord-blood from 729466-2RN

description:
bisulfite converted DNA from 729466-2RN
DNA extracted from cord blood

source_name: cord blood, 729466-2RN


title: Blood CD8+T cell-ATB2-Rep1

source_name: Peripheral blood CD8+T cell, ATB2(one of three active TB subjects),replicate 1


title: cord-blood from 2163133-3RN

description:
bisulfite converted DNA from 2163133-3RN
DNA extracted from cord blood

source_name: cord blood, 2163133-3RN


title: Blood CD8+T cell-ATB1-Rep1

source_name: Peripheral blood CD8+T cell, ATB1(one of three active TB subjects),replicate 1


title: cord-blood from 2164987-1RN

description:
bisulfite converted DNA from 2164987-1RN
DNA extracted from cord blood

source_name: cord blood, 2164987-1RN


title: Tumor, rep38


title: Patient S_S-F074

city: Belfast

first: Philip

last: Dunne

address: Lisburn Road

country: United Kingdom

institute: Queens University Belfast

description: Gene expression data from central region of colorectal cancer

hyb_protocol: 5µg biotinylated cRNA were hybridized for 18 hrs at 45 degrees

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000

data_processing: Normalisation was performed using RMA

source_name: colorectal cancer_central tumour

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

extract_protocol: RNA was extracted using NuGen FFPE RNA extraction kits

tag: subject id

value: Patient S

tag: subject status

value: Colorectal cancer patient

tag: region of origin

value: central tumour


title: Tumor, rep37

tag: disease state


title: Tumor, rep39

tag: tissue


title: cord-blood from 2164121-1RN

description:
bisulfite converted DNA from 2164121-1RN
DNA extracted from cord blood

source_name: cord blood, 2164121-1RN


title: Patient U_S-F071

value: Patient U


title: cord-blood from 2163925-2RN

description:
bisulfite converted DNA from 2163925-2RN
DNA extracted from cord blood

source_name: cord blood, 2163925-2RN


title: cord-blood from 2169834-3RN

description:
bisulfite converted DNA from 2169834-3RN
DNA extracted from cord blood

source_name: cord blood, 2169834-3RN


title: cord-blood from 2163432-3RN

description:
bisulfite converted DNA from 2163432-3RN
DNA extracted from cord blood

source_name: cord blood, 2163432-3RN


title: cord-blood from 2163727-3RN

description:
bisulfite converted DNA from 2163727-3RN
DNA extracted from cord blood

source_name: cord blood, 2163727-3RN


title: Patient R_S-F068

value: Patient R


title: Tumor, rep36


title: Tumor, rep35


title: cord-blood from 527855-3RN

description:
bisulfite converted DNA from 527855-3RN
DNA extracted from cord blood

source_name: cord blood, 527855-3RN


title: cord-blood from 562913-2RN

description:
bisulfite converted DNA from 562913-2RN
DNA extracted from cord blood

source_name: cord blood, 562913-2RN


title: Patient T_S-F063

value: Patient T


title: Patient N_S-F069

value: Patient N


title: Tumor, rep33

source_name: breast tumor tissue


title: Tumor, rep32


title: Tumor, rep31


title: cord-blood from 2163159-3RN 2G

description:
bisulfite converted DNA from 2163159-3RN 2G
DNA extracted from cord blood

source_name: cord blood, 2163159-3RN 2G

value: Male

value: No


title: Patient W_S-F059

value: Patient W


title: Patient Y_S-F051

value: Patient Y


title: Patient X_S-F058

value: Patient X


title: Patient V_S-F065

value: Patient V


title: Patient K_S-F047

value: Patient K


title: cord-blood from 2078795-2RN

description:
bisulfite converted DNA from 2078795-2RN
DNA extracted from cord blood

source_name: cord blood, 2078795-2RN

value: Yes


title: cord-blood from 2169829-1RN

description:
bisulfite converted DNA from 2169829-1RN
DNA extracted from cord blood

source_name: cord blood, 2169829-1RN

value: Female


title: Tumor, rep29

value: breast cancer

value: breast tumor


title: Tumor, rep28


title: Tumor, rep27


title: Tumor, rep30


title: Tumor, rep26


title: Patient Q_S-F032

value: Patient Q

value: Colorectal cancer patient


title: Tumor, rep25


title: Patient I_S-F035

value: Patient I

value: central tumour


title: Patient J_S-F039

value: Patient J


title: cord-blood from 2166316-1RN

description:
bisulfite converted DNA from 2166316-1RN
DNA extracted from cord blood

source_name: cord blood, 2166316-1RN


title: Patient L_S-F034

value: Patient L


title: Tumor, rep34


title: Tumor, rep24


title: cord-blood from 21664951-1RN

description:
bisulfite converted DNA from 21664951-1RN
DNA extracted from cord blood

source_name: cord blood, 21664951-1RN


title: cord-blood from 2163501-1RN

description:
bisulfite converted DNA from 2163501-1RN
DNA extracted from cord blood

source_name: cord blood, 2163501-1RN

value: Male


title: cord-blood from 2164435-2RN

description:
bisulfite converted DNA from 2164435-2RN
DNA extracted from cord blood

source_name: cord blood, 2164435-2RN

value: No


title: Patient P_S-F026

value: Patient P


title: Patient A_S-F021

value: Patient A


title: Patient O_S-F029

value: Patient O


title: Tumor, rep23


title: Chol (-) fed_2nd

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip C. elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with GeneSpring 12.5 GX. Expression signals of probe sets were calculated using RMA algorithm.

organism: Caenorhabditis elegans

source_name: Day 4_adult_fed under cholesterol deprivation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Synchronized were grown on NGM plates until young adult and then transferred to FUDR-containig plates.

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

treatment_protocol: Cholesterol deprivation were started when worms hatched. Worms were exposed to fasting for 48 hr since day 2 adult.

tag: food

value: fed

tag: cholesterol

value: cholesterol (-)


title: cord-blood from 789057-2RN

description:
bisulfite converted DNA from 789057-2RN
DNA extracted from cord blood

source_name: cord blood, 789057-2RN

value: Yes


title: Patient D_S-F020

source_name: colorectal cancer_central tumour

value: Patient D


title: cord-blood from 472702-2RN

description:
bisulfite converted DNA from 472702-2RN
DNA extracted from cord blood

source_name: cord blood, 472702-2RN


title: Chol (+) fasting_2nd

source_name: Day 4_adult_after 24 hr fasting

value: fasting

value: cholesterol (+)


title: Tumor, rep22

value: breast cancer

value: breast tumor


title: Patient C_S-F017

description: Gene expression data from central region of colorectal cancer

value: Patient C

value: Colorectal cancer patient


title: cord-blood from 2166201-3RN

description:
bisulfite converted DNA from 2166201-3RN
DNA extracted from cord blood

source_name: cord blood, 2166201-3RN


title: Tumor, rep20


title: Tumor, rep19


title: cord-blood from 2163443-3RN

description:
bisulfite converted DNA from 2163443-3RN
DNA extracted from cord blood

source_name: cord blood, 2163443-3RN


title: Patient G_S-F012

value: Patient G

value: central tumour


title: Patient E_S-F011

value: Patient E


title: Chol (-) fasting_2nd

source_name: Day 4_adult_after 24 hr fasting under cholesterol deprivation


title: cord-blood from 781616-3RN

description:
bisulfite converted DNA from 781616-3RN
DNA extracted from cord blood

source_name: cord blood, 781616-3RN

value: Male

value: No


title: Patient F_S-F007

value: Patient F


title: Chol (+) fasting_1st


title: Tumor, rep21

source_name: breast tumor tissue


title: Chol (+) fed_2nd

source_name: Day 4_adult_fed


title: Tumor, rep17


title: Patient H_S-F004

value: Patient H


title: cord-blood from 51693-2RN

description:
bisulfite converted DNA from 51693-2RN
DNA extracted from cord blood

source_name: cord blood, 51693-2RN


title: cord-blood from 883730-3RN

description:
bisulfite converted DNA from 883730-3RN
DNA extracted from cord blood

source_name: cord blood, 883730-3RN


title: Tumor, rep16


title: cord-blood from 2165228-1RN

description:
bisulfite converted DNA from 2165228-1RN
DNA extracted from cord blood

source_name: cord blood, 2165228-1RN


title: Tumor, rep12


title: Tumor, rep11


title: Tumor, rep10


title: Tumor, rep13


title: Tumor, rep9


title: Tumor, rep14


title: Tumor, rep15


title: Tumor, rep8


title: Tumor, rep6


title: Chol (+) fed_1st

value: fed


title: Patient S_LN-F054

description: Gene expression data from lymph node of colorectal cancer

source_name: colorectal cancer_lymph node

value: Patient S

value: lymph node


title: Tumor, rep18


title: Patient I_LN-F044

value: Patient I


title: Patient W_LN-F067

value: Patient W


title: Patient N_LN-F064

value: Patient N


title: Patient J_LN-F041

value: Patient J


title: Patient R_LN-F062a

value: Patient R


title: Patient B_S-F002

value: Patient B


title: Patient X_LN-F053

value: Patient X

value: Colorectal cancer patient


title: Patient Y_LN-F056

value: Patient Y


title: Patient U_LN-F052

value: Patient U


title: Patient V_LN-F070

value: Patient V


title: Patient P_LN-F046

value: Patient P


title: Tumor, rep5

value: breast cancer

value: breast tumor


title: Tumor, rep4


title: Tumor, rep7


title: Chol (-) fed_1st

value: fed

value: cholesterol (-)


title: Tumor, rep1


title: Patient T_LN-F061

value: Patient T

value: lymph node


title: Tumor, rep2


title: Tumor, rep3


title: TIF, rep12

source_name: tumor interstitial fluid

value: tumor interstitial fluid


title: Patient Q_LN-F036

value: Patient Q


title: TIF, rep14


title: TIF, rep13


title: Patient K_LN-F038

value: Patient K


title: TIF, rep10


title: Patient G_LN-F024

value: Patient G


title: Chol (-) fasting_1st

value: fasting


title: TIF, rep11


title: TIF, rep9


title: Patient L_LN-F025

value: Patient L


title: TIF, rep8


title: Patient O_LN-F028

value: Patient O

value: Colorectal cancer patient


title: SW1463_radio resistant_rep 3

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

hyb_protocol: 1.65 μg of labeled cRNA was fragmentized and hybridized overnight to a 4 x 44k gene expression microarray (Agilent Technologies)

scan_protocol: Arrays were scanned on an Agilent DNA microarray scanner G2505B (Agilent Technologies) at 5-micron resolution.

data_processing: Raw data were log2 transformed and normalized to 75 percentile according to Agilent protocol. Probes with intensity no less than 100 in at least one sample were kept for analysis.

source_name: Dukes' type C, colorectal adenocarcinoma

label_protocol: 200 ng of total RNA was reverse transcribed, amplified, and labeled with Cy3 using the Low RNA Input Linear Amplification Kit PLUS (Agilent Technologies)

growth_protocol: Cell lines, SW1463 directly from the American Type Culture Collection (ATCC, Manassas, VA). Cells were cultured in their recommended media, supplemented with 10% fetal bovine serum and 2 mM l-glutamine, and discarded no later than 15 passages. Periodically, mycoplasma contamination was determined using the MycoAlert® Mycoplasma Detection Kit.

extract_protocol: For each condition (i.e., no irradiation or 6 hours after exposure to 4 Gy of X-rays), total RNA was isolated from logarithmic growing cells at three different passages (passages four to six after thawing) using the RNeasy Mini kit (Qiagen, Hilden, Germany), according to the manufacturer's instructions, including the optional on-column DNase digestion. Quantity and purity of isolated RNA was assessed using a NanoDrop ND-1000 spectrophotometer (ThermoFischer, Waltham, MA); RNA integrity was assessed by Agilent 2100 Bioanalyzer electrophoresis (Agilent Technologies, Palo Alto, CA). Only samples with an RNA integrity number >9.5 were considered for additional experiments.

treatment_protocol: SW1463 cells were repeatedly irradiated with 2 Gy of X-rays for 34 cycles, equaling to a cumulative dose of 68 Gy. Specifically, cells were seeded into six-well plates, irradiated the next day, and cultured in fresh medium. At 70-80% confluence, they were exposed to the next cycle of irradiation.

tag: irradiated (4gy)

value: NO

tag: radioresistant

value: Radioresistant

tag: overexpression beta cat


title: SW1463_radio resistant_rep 2


title: SW1463_radio resistant_4Gy_rep 2

value: irradiated (4Gy)


title: SW1463_radio resistant_4Gy_rep 3


title: SW1463_radio resistant_4Gy_rep 1


title: Patient D_LN-F023

value: Patient D


title: Patient B_LN-F019

value: Patient B


title: Patient A_LN-F016

value: Patient A


title: Patient F_LN-F013

value: Patient F


title: Patient C_LN-F010

value: Patient C


title: TIF, rep7

value: breast cancer


title: SW1463_radio resistant_rep 1


title: TIF, rep6

value: tumor interstitial fluid


title: TIF, rep3


title: SW1463_wild type_4Gy_rep 3

value: No


title: TIF, rep5


title: Patient W_D-F073

description: Gene expression data from invasive front of colorectal cancer

source_name: colorectal cancer_invasive front

value: Patient W

value: invasive front


title: Patient H_LN-F001

value: Patient H

value: lymph node


title: Patient X_D-F075

value: Patient X


title: SW1463_wild type_rep 3


title: SW1463_wild type_4Gy_rep 2


title: Patient R_D-F066

value: Patient R

value: Colorectal cancer patient


title: TIF, rep1


title: Control

source_name: Control

value: control


title: TIF, rep4


title: TIF, rep2


title: SW1463_wild type_4Gy_rep 1

value: irradiated (4Gy)


title: Patient N_D-F060

value: Patient N


title: SW1463_wild type_rep 1

value: NO


title: SW1463_wild type_rep 2


title: Patient Y_D-F055

value: Patient Y


title: Patient S_D-F072

value: Patient S


title: Patient K_D-F048

value: Patient K


title: Patient T_D-F050

value: Patient T


title: OhrR regulon replicate 3

city: Ribeirao Preto

first: Jose

middle: Freire

last: da Silva Neto

state: Sao Paulo SP

address: Av Bandeirantes 3900

department: Biologia Celular e Molecular e Bioagentes Patogenicos

institute: Universidade de Sao Paulo

description: Biological replicate 3 of 3

hyb_protocol: Pooled labeled cRNA samples were fragmented and hybridized to the C. violaceum microarray slides. After hybridization, slides were washed sequential according to the Agilent Two-Color Microarray-Based Exon Analysis Protocol, version 1.0 (Agilent Technologies)

scan_protocol: The slides were scanned with the G2505C Agilent DNA Microarray Scanner

data_processing: Data were extracted and normalized (LOWESS normalization) using the Agilent Feature Extraction software, version 10.5.

organism: Chromobacterium violaceum

source_name: C. violaceum WT untretaed

label_protocol: The fluorescence-labeled cRNA (complementary RNA) was generated of total RNA derived from each experimental condition using the Low Input Quick Amp WT Two-Color kit (Agilent Technologies)

growth_protocol: Bacteria were grown at 37 °C in LB medium until mid-log phase (OD600 of 0.8 to 1.0)

extract_protocol: Total RNA was extracted using Trizol reagent (Ambion) and purified with the illustra RNAspin Mini RNA Isolation Kit (GE Healthcare)

treatment_protocol: For CHP stress, cultures were treated with 100 µM CHP for 10 minutes

tag: strain

tag: growth

value: midlog phase LB

source_name: C. violaceum ∆ohrR untretaed

value: ∆ohrR mutant (JF0210)


title: Patient U_D-F057

value: Patient U


title: OhrR regulon replicate 2

description: Biological replicate 2 of 3


title: Patient O_D-F042

value: Patient O

value: invasive front


title: Patient V_D-F049

value: Patient V


title: Patient L_D-F043

value: Patient L


title: Patient I_D-F033

value: Patient I


title: OhrR regulon replicate 1

description: Biological replicate 1 of 3


title: Patient P_D-F040

value: Patient P

value: Colorectal cancer patient


title: CHP stimulon replicate 2

description: Biological replicate 2 of 3

source_name: C. violaceum WT CHP 10 min

value: midlog phase LB 100 µM CHP 10 min


title: CHP stimulon replicate 3

description: Biological replicate 3 of 3


title: Patient J_D-F030

value: Patient J


title: Patient Q_D-F031

value: Patient Q


title: Patient G _D-F008

value: Patient G


title: CHP stimulon replicate 1

description: Biological replicate 1 of 3


title: Patient B_D-F014

value: Patient B


title: Patient E_D-F018

value: Patient E


title: Patient H_D-F003

value: Patient H


title: Patient D_D-F005

value: Patient D


title: Patient F_D-F022

value: Patient F


title: Patient C_D-F009

value: Patient C


title: BLCA_Cx_307

status: Public on Mar 13 2017

city: Lund

first: Pontus

last: Eriksson

state: Select:

address: Scheelevägen 2

department: Department of Clinical Sciences

country: Sweden

institute: Lund University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor R package Affy. Probe intensities were normalized in labeling batches of 24 using RMA. Batches were combined and RMA normalized.
The file Processed_Data_Supplement.txt contains ready-to-use median centered gene expression data for 307 tumor samples, with EntrezID and GeneSymbol. Sample order is derived from ConsensusClusterPlus, performed on the top 50% variance genes (n=7031) and matches the Sjodahl 2017 publication. Metadata: CEL Filename, GEO_SampleName, Labeling Batch, Hybridisation Number, TURB Stage, TURB Grade, Lund 2012 Taxonomy By Centroid Correlation, ConsensusClusterPlus Cluster, Sjodahl 2017 mRNA-cluster/Phenotype, Publication Heatmap Order.

source_name: FFPE tissue specimen

label_protocol: SensationPlus FFPE Amplification and WT labeling kit

extract_protocol: High Pure FFPET RNA isolation kit (Roche)

value: bladder cancer

tag: stage and grade

value: pT2   G3

tag: labeling batch


title: BLCA_Cx_300


title: BLCA_Cx_299


title: BLCA_Cx_291


title: BLCA_Cx_293


title: BLCA_Cx_301


title: BLCA_Cx_297


title: BLCA_Cx_294


title: BLCA_Cx_295


title: BLCA_Cx_303


title: BLCA_Cx_302


title: BLCA_Cx_290


title: Patient E_LN-F006

value: lymph node


title: Patient A_D-F015

value: Patient A

value: invasive front


title: BLCA_Cx_292


title: BLCA_Cx_288

value: pT1   G3


title: BLCA_Cx_286


title: BLCA_Cx_304


title: BLCA_Cx_289


title: BLCA_Cx_287


title: BLCA_Cx_284


title: BLCA_Cx_278


title: BLCA_Cx_276


title: BLCA_Cx_279


title: BLCA_Cx_281


title: BLCA_Cx_273

value: pT1   G2


title: BLCA_Cx_275


title: BLCA_Cx_274


title: BLCA_Cx_267

value: pTx   G3


title: BLCA_Cx_282


title: BLCA_Cx_269


title: BLCA_Cx_270


title: BLCA_Cx_266

value: pT2   G2


title: BLCA_Cx_271


title: BLCA_Cx_277


title: BLCA_Cx_259

value: pTa   G2


title: BLCA_Cx_264


title: BLCA_Cx_263


title: BLCA_Cx_257


title: BLCA_Cx_272


title: BLCA_Cx_261


title: BLCA_Cx_254


title: BLCA_Cx_246


title: BLCA_Cx_253


title: BLCA_Cx_252


title: BLCA_Cx_245


title: BLCA_Cx_249

value: pTa   G3


title: BLCA_Cx_250


title: BLCA_Cx_251

value: pT2   Gx


title: BLCA_Cx_265


title: BLCA_Cx_230


title: BLCA_Cx_237


title: BLCA_Cx_238


title: BLCA_Cx_242


title: BLCA_Cx_223


title: BLCA_Cx_231


title: BLCA_Cx_233


title: BLCA_Cx_239


title: BLCA_Cx_232


title: BLCA_Cx_236


title: BLCA_Cx_224


title: BLCA_Cx_228


title: BLCA_Cx_221


title: BLCA_Cx_227


title: BLCA_Cx_218


title: BLCA_Cx_214


title: BLCA_Cx_226


title: BLCA_Cx_225


title: BLCA_Cx_243


title: BLCA_Cx_217


title: BLCA_Cx_216


title: BLCA_Cx_213


title: BLCA_Cx_209


title: BLCA_Cx_211


title: BLCA_Cx_222


title: BLCA_Cx_210


title: BLCA_Cx_206


title: BLCA_Cx_220


title: BLCA_Cx_207


title: BLCA_Cx_202


title: BLCA_Cx_190


title: BLCA_Cx_199


title: BLCA_Cx_191


title: BLCA_Cx_203


title: BLCA_Cx_194


title: BLCA_Cx_208


title: BLCA_Cx_177


title: BLCA_Cx_185


title: BLCA_Cx_181


title: BLCA_Cx_183


title: BLCA_Cx_205


title: BLCA_Cx_176


title: BLCA_Cx_196


title: BLCA_Cx_195


title: BLCA_Cx_184


title: BLCA_Cx_182


title: BLCA_Cx_215


title: BLCA_Cx_175


title: BLCA_Cx_192


title: BLCA_Cx_180


title: BLCA_Cx_193


title: BLCA_Cx_172


title: BLCA_Cx_174


title: BLCA_Cx_189


title: BLCA_Cx_173


title: BLCA_Cx_179


title: BLCA_Cx_186


title: BLCA_Cx_171


title: BLCA_Cx_170


title: BLCA_Cx_166

value: pTx   Gx


title: BLCA_Cx_168


title: BLCA_Cx_158


title: BLCA_Cx_164


title: BLCA_Cx_155


title: BLCA_Cx_146


title: BLCA_Cx_163


title: BLCA_Cx_148


title: BLCA_Cx_165

value: pT4   G3


title: BLCA_Cx_145


title: BLCA_Cx_160


title: BLCA_Cx_144


title: BLCA_Cx_141


title: BLCA_Cx_169


title: BLCA_Cx_149


title: BLCA_Cx_142


title: BLCA_Cx_154


title: BLCA_Cx_147


title: BLCA_Cx_161


title: BLCA_Cx_159


title: BLCA_Cx_162


title: BLCA_Cx_157


title: BLCA_Cx_153


title: BLCA_Cx_152


title: BLCA_Cx_150


title: BLCA_Cx_137


title: BLCA_Cx_139


title: BLCA_Cx_136


title: BLCA_Cx_135


title: BLCA_Cx_140


title: BLCA_Cx_138


title: BLCA_Cx_151


title: BLCA_Cx_121


title: BLCA_Cx_127


title: BLCA_Cx_114


title: BLCA_Cx_116


title: BLCA_Cx_117


title: BLCA_Cx_120


title: BLCA_Cx_109


title: BLCA_Cx_128


title: BLCA_Cx_133


title: BLCA_Cx_132


title: BLCA_Cx_126


title: BLCA_Cx_129


title: BLCA_Cx_103


title: BLCA_Cx_107


title: BLCA_Cx_113


title: BLCA_Cx_124


title: BLCA_Cx_122


title: BLCA_Cx_112


title: BLCA_Cx_111


title: BLCA_Cx_115


title: BLCA_Cx_99


title: BLCA_Cx_110


title: BLCA_Cx_119


title: BLCA_Cx_104


title: BLCA_Cx_93


title: BLCA_Cx_97


title: BLCA_Cx_108


title: BLCA_Cx_94


title: BLCA_Cx_92


title: BLCA_Cx_86


title: BLCA_Cx_88


title: BLCA_Cx_102


title: BLCA_Cx_106


title: BLCA_Cx_100


title: BLCA_Cx_105


title: BLCA_Cx_81


title: BLCA_Cx_96


title: BLCA_Cx_74


title: BLCA_Cx_77


title: BLCA_Cx_90


title: BLCA_Cx_87


title: BLCA_Cx_89


title: BLCA_Cx_85


title: BLCA_Cx_91


title: BLCA_Cx_80


title: BLCA_Cx_83


title: BLCA_Cx_78


title: BLCA_Cx_95

value: pTis   G3


title: BLCA_Cx_79


title: BLCA_Cx_76


title: BLCA_Cx_63


title: BLCA_Cx_67


title: BLCA_Cx_69


title: BLCA_Cx_68


title: BLCA_Cx_75


title: BLCA_Cx_72


title: BLCA_Cx_71


title: BLCA_Cx_60


title: BLCA_Cx_66


title: BLCA_Cx_53


title: BLCA_Cx_52


title: BLCA_Cx_61


title: BLCA_Cx_62


title: BLCA_Cx_51


title: BLCA_Cx_49


title: BLCA_Cx_48


title: BLCA_Cx_65


title: BLCA_Cx_45


title: BLCA_Cx_56


title: BLCA_Cx_55


title: BLCA_Cx_54


title: BLCA_Cx_59


title: BLCA_Cx_58


title: BLCA_Cx_50


title: BLCA_Cx_70


title: BLCA_Cx_43


title: BLCA_Cx_47


title: BLCA_Cx_39


title: BLCA_Cx_42


title: BLCA_Cx_38


title: BLCA_Cx_34


title: BLCA_Cx_44


title: BLCA_Cx_40


title: BLCA_Cx_37


title: BLCA_Cx_33


title: BLCA_Cx_36


title: BLCA_Cx_32


title: BLCA_Cx_41


title: BLCA_Cx_30


title: BLCA_Cx_21


title: BLCA_Cx_22


title: BLCA_Cx_24


title: BLCA_Cx_27


title: BLCA_Cx_26


title: BLCA_Cx_28


title: BLCA_Cx_31


title: BLCA_Cx_57


title: BLCA_Cx_29


title: BLCA_Cx_17


title: BLCA_Cx_18


title: BLCA_Cx_23


title: BLCA_Cx_20


title: BLCA_Cx_25


title: BLCA_Cx_16


title: BLCA_Cx_19


title: BLCA_Cx_13


title: BLCA_Cx_15


title: BLCA_Cx_14


title: BLCA_Cx_7


title: BLCA_Cx_8

value: pT1   Gx


title: BLCA_Cx_11


title: ChIP-seq from OCI-LY7 (ENCLB716RUG)

status: Public on Mar 12 2017

type: SRA

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR850QKN/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR850QKN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR063AUO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB716RUG
size range: 200-600
nucleic acid starting quantity: 94.5
nucleic acid starting quantity units: ng

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens OCI-LY7 immortalized cell line

tag: antibody

tag: line

value: immortalized cell line

tag: description

value: established from the peripheral blood sample of a 48-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma, DLCL, stage 2A, at relapse) in 1984

tag: biosample encode accession

tag: dev stage

value: adult

tag: Sex

value: male

value: 48 year

tag: health state

value: B cell lymphoma

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS040MJM at ENCODE; https://www.encodeproject.org/ENCBS040MJM/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1881; http://web.expasy.org/cellosaurus/CVCL_1881


title: ChIP-seq from SK-N-SH (ENCLB800FFG)

description:
https://www.encodeproject.org/experiments/ENCSR978CNH/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR978CNH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2016-11-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB800FFG
size range: 200-600

source_name: Homo sapiens SK-N-SH immortalized cell line

value: SK-N-SH

tag: age

value: 4 year

value: child

value: female

tag: passage number

value: ENCBS018DDZ at ENCODE; https://www.encodeproject.org/ENCBS018DDZ/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531


title: BLCA_Cx_12

tag: tissue

value: bladder cancer

value: pT2   G3


title: ChIP-seq from body of pancreas (ENCLB110YUR)

description:
https://www.encodeproject.org/experiments/ENCSR689SFJ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR689SFJ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR888RBQ
encode release date: 2016-11-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB110YUR
size range: 200-600
nucleic acid starting quantity: 106.2
nucleic acid starting quantity units: ng

source_name: Homo sapiens body of pancreas tissue male adult (37 years)

value: body of pancreas

value: tissue

value: adult

value: 37 year

value: ENCBS869MHP at ENCODE; https://www.encodeproject.org/ENCBS869MHP/

value: Derived from ENCODE donor ENCDO845WKR; https://www.encodeproject.org/ENCDO845WKR/


title: ChIP-seq from neural cell (ENCLB755ZJQ)

description:
https://www.encodeproject.org/experiments/ENCSR873EIA/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR873EIA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR308JFE
encode release date: 2016-10-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB755ZJQ
size range: 200-600
nucleic acid starting quantity: 10.34
nucleic acid starting quantity units: ng

source_name: Homo sapiens neural in vitro differentiated cells male embryo

value: neural cell

value: in vitro differentiated cells

value: embryonic

value: male

value: unknown

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS504GFW at ENCODE; https://www.encodeproject.org/ENCBS504GFW/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: ChIP-seq from SK-N-MC (ENCLB141OPB)

description:
https://www.encodeproject.org/experiments/ENCSR899XXQ/
***************
biological replicate number: 2
technical replicate number: 2
description: Control ChIP-seq using SK-N-MC cell line which was previously described as a neuroepithelioma (ATCC HTB-10). However recent evidence reveals it is Ewing's Sarcoma (www.ncbi.nlm.nih.gov/pubmed/15548687, www.ncbi.nlm.nih.gov/biosample/3151999, www.ncbi.nlm.nih.gov/pubmed/25453903).
experiment encode accession: ENCSR899XXQ
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB141OPB
size range: 200-600

source_name: Homo sapiens SK-N-MC immortalized cell line

value: Control

value: SK-N-MC

value: immortalized cell line

value: Please note:This cell line was previously described as a neuroepithelioma (ATCC HTB-10).  However recent evidence reveals it is Ewing's Sarcoma (http://www.ncbi.nlm.nih.gov/pubmed/15548687, http://www.ncbi.nlm.nih.gov/biosample/3151999, http://www.ncbi.nlm.nih.gov/pubmed/25453903).

value: child

value: female

value: 14 year

value: Ewing's sarcoma

value: ENCBS203EZT at ENCODE; https://www.encodeproject.org/ENCBS203EZT/

value: Derived from ENCODE donor ENCDO000ABC; https://www.encodeproject.org/ENCDO000ABC/

value: ENCODE dbxrefs Cellosaurus CVCL_0530; http://web.expasy.org/cellosaurus/CVCL_0530


title: ChIP-seq from SK-N-MC (ENCLB097DSA)

description:
https://www.encodeproject.org/experiments/ENCSR899XXQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq using SK-N-MC cell line which was previously described as a neuroepithelioma (ATCC HTB-10). However recent evidence reveals it is Ewing's Sarcoma (www.ncbi.nlm.nih.gov/pubmed/15548687, www.ncbi.nlm.nih.gov/biosample/3151999, www.ncbi.nlm.nih.gov/pubmed/25453903).
experiment encode accession: ENCSR899XXQ
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB097DSA
size range: 200-600


title: BLCA_Cx_6

value: bladder cancer

value: pT2   G3


title: ChIP-seq from neuroepithelial stem cell (ENCLB833JZM)

description:
https://www.encodeproject.org/experiments/ENCSR842NGQ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR842NGQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR803UDX
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB833JZM
size range: 200-600
nucleic acid starting quantity: 1.87
nucleic acid starting quantity units: ng

source_name: Homo sapiens neuroepithelial stem in vitro differentiated cells female embryo (5 days) stably expressing C-terminal eGFP-HES5 fusion protein

value: neuroepithelial stem cell

value: in vitro differentiated cells

value: Neuroepithelial cells were collected at day 12 of differentiation (see protocol)

value: embryonic

value: 5 day

value: healthy

value: ENCBS709ZNP at ENCODE; https://www.encodeproject.org/ENCBS709ZNP/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: ChIP-seq from H1-hESC (ENCLB711BTD)

description:
https://www.encodeproject.org/experiments/ENCSR814XPE/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR814XPE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AMI
encode release date: 2016-11-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB711BTD
size range: 200-600

source_name: Homo sapiens H1-hESC stem cell male embryo

value: stem cell

value: male

value: unknown

value: Bradley Bernstein, Broad

value: ENCBS952IPA at ENCODE; https://www.encodeproject.org/ENCBS952IPA/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: BLCA_Cx_10


title: ChIP-seq from H1-hESC (ENCLB227LCT)

description:
https://www.encodeproject.org/experiments/ENCSR814XPE/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR814XPE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AMI
encode release date: 2016-11-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB227LCT
size range: 200-600

value: ENCBS364BFI at ENCODE; https://www.encodeproject.org/ENCBS364BFI/


title: ChIP-seq from K562 (ENCLB987AGN)

description:
https://www.encodeproject.org/experiments/ENCSR700IEB/
***************
biological replicate number: 15
technical replicate number: 1
description: Reverse Crosslink Control ChIP-seq on human K562 (fragmentation date 02-26-14)
experiment encode accession: ENCSR700IEB
assay title: ChIP-seq
encode release date: 2015-11-13
lab: Richard Myers, HAIB
library encode accession: ENCLB987AGN
size range: 100-500

source_name: Homo sapiens K562 immortalized cell line

value: Control

value: immortalized cell line

value: K562, myelogenous leukemia

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: ENCBS577JGM at ENCODE; https://www.encodeproject.org/ENCBS577JGM/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/

value: ENCODE dbxrefs Cellosaurus CVCL_0004; http://web.expasy.org/cellosaurus/CVCL_0004

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-243.aspx


title: ChIP-seq from K562 (ENCLB212MWS)

description:
https://www.encodeproject.org/experiments/ENCSR948QLZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562-human
experiment encode accession: ENCSR948QLZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000FCA, ENCSR962APM
encode release date: 2016-02-05
lab: Richard Myers, HAIB
library encode accession: ENCLB212MWS

value: ENCBS602AAA at ENCODE; https://www.encodeproject.org/ENCBS602AAA/


title: BLCA_Cx_5

value: bladder cancer

value: pT2   G3


title: ChIP-seq from neural cell (ENCLB581TGM)

description:
https://www.encodeproject.org/experiments/ENCSR958ZMM/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR958ZMM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR308JFE
encode release date: 2016-10-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB581TGM
size range: 200-600
nucleic acid starting quantity: 244.2
nucleic acid starting quantity units: ng

value: neural cell

value: in vitro differentiated cells

value: embryonic

value: male

value: unknown

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS504GFW at ENCODE; https://www.encodeproject.org/ENCBS504GFW/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: ChIP-seq from MCF-7 (ENCLB408LWH)

description:
https://www.encodeproject.org/experiments/ENCSR752UOD/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR752UOD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2016-06-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB408LWH
size range: 200-600

source_name: Homo sapiens MCF-7 immortalized cell line

value: immortalized cell line

value: mammary epithelium, doubling time ~ 29hoursATCC HTB-22

value: 69 year

value: adult

value: female

value: breast cancer (adenocarcinoma)

value: ENCBS967MVZ at ENCODE; https://www.encodeproject.org/ENCBS967MVZ/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/products/all/HTB-22.aspx


title: ChIP-seq from HCT116 (ENCLB411IZW)

description:
https://www.encodeproject.org/experiments/ENCSR661KMA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR661KMA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2016-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB411IZW
size range: 200-600

source_name: Homo sapiens HCT116 immortalized cell line

value: cells obtained from ATCC

value: colorectal carcinoma

value: ENCBS847SOB at ENCODE; https://www.encodeproject.org/ENCBS847SOB/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ATCC sample source; http://www.atcc.org/products/all/CCL-247.aspx#357C3571006A4259B64650D34DF19048


title: ChIP-seq from SK-N-SH (ENCLB559GFR)

description:
https://www.encodeproject.org/experiments/ENCSR564IGJ/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR564IGJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2016-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB559GFR
size range: 200-600

value: SK-N-SH

value: 4 year

value: child

value: Bradley Bernstein, Broad

value: ENCBS500EWH at ENCODE; https://www.encodeproject.org/ENCBS500EWH/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531


title: ChIP-seq from Loucy (ENCLB675GWW)

description:
https://www.encodeproject.org/experiments/ENCSR648HLP/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR648HLP
assay title: ChIP-seq
encode release date: 2014-11-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB675GWW
size range: 200-600

source_name: Homo sapiens Loucy immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/ab9a4628-0877-468f-bdfe-78aada2fdb96/@@download/attachment/ChIP_Protocol_For_Fresh_or_Frozen_Cells_v8.2_exp.pdf

value: Control

value: Loucy

value: immortalized cell line

value: Established in 1987 from the peripheral blood of a patient with T-cell acute lymphoblastic leukemia (T-ALL) obtained two months prior to her death. May be of value in evaluating the role of t(16;20) in the etiology of T-ALL.

value: adult

value: female

value: 38 year

value: T-cell acute lymphoblastic leukemia cell line ATCC CRL-2629

value: ENCBS170DPY at ENCODE; https://www.encodeproject.org/ENCBS170DPY/

value: Derived from ENCODE donor ENCDO732PDS; https://www.encodeproject.org/ENCDO732PDS/

value: ENCODE dbxrefs Cellosaurus CVCL_1380; http://web.expasy.org/cellosaurus/CVCL_1380

value: ATCC sample source; http://www.atcc.org/Products/All/CRL-2629.aspx


title: BLCA_Cx_4

value: bladder cancer

value: pT2   G3


title: ChIP-seq from HepG2 (ENCLB452JBW)

description:
https://www.encodeproject.org/experiments/ENCSR476TKW/
***************
biological replicate number: 10
technical replicate number: 1
description: Reverse Crosslink Control ChIP-seq on human HepG2 (fragmentation date 02-20-14)
experiment encode accession: ENCSR476TKW
assay title: ChIP-seq
encode release date: 2016-01-08
lab: Richard Myers, HAIB
library encode accession: ENCLB452JBW
size range: 100-500

source_name: Homo sapiens HepG2 immortalized cell line

value: HepG2, hepatocellular carcinoma

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS614CMA at ENCODE; https://www.encodeproject.org/ENCBS614CMA/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/

value: ENCODE dbxrefs Cellosaurus CVCL_0027; http://web.expasy.org/cellosaurus/CVCL_0027

value: ATCC sample source; http://www.atcc.org/products/all/HB-8065.aspx


title: BLCA_Cx_3

value: pT2   Gx


title: BLCA_Cx_2


title: BLCA_Cx_98

value: pT1   G3


title: ChIP-seq from HCT116 (ENCLB507LPC)

description:
https://www.encodeproject.org/experiments/ENCSR474DOV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR474DOV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2017-01-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB507LPC
size range: 200-600

value: immortalized cell line

value: cells obtained from ATCC

value: unknown

value: colorectal carcinoma

value: Bradley Bernstein, Broad

value: ENCBS494OPB at ENCODE; https://www.encodeproject.org/ENCBS494OPB/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ATCC sample source; http://www.atcc.org/products/all/CCL-247.aspx#357C3571006A4259B64650D34DF19048


title: ChIP-seq from MM.1S (ENCLB312OXA)

status: Public on Mar 09 2017

description:
https://www.encodeproject.org/experiments/ENCSR264HOB/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR264HOB
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB312OXA
size range: 300-600

source_name: Homo sapiens MM.1S immortalized cell line

value: Control

value: The parent cell line, MM.1, was established from peripheral blood of a multiple myeloma patient who had become resistant to steroid-based therapy. this line is sensitive to dexamethasone

value: adult

value: female

value: 42 year

value: immunoglobulin A lambda myeloma

value: ENCBS205VYW at ENCODE; https://www.encodeproject.org/ENCBS205VYW/

value: Derived from ENCODE donor ENCDO697GBW; https://www.encodeproject.org/ENCDO697GBW/

value: ENCODE dbxrefs Cellosaurus CVCL_8792; http://web.expasy.org/cellosaurus/CVCL_8792


title: ChIP-seq from induced pluripotent stem cell (ENCLB695IXS)

description:
https://www.encodeproject.org/experiments/ENCSR249YGG/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR249YGG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695IXS
size range: 200-600
nucleic acid starting quantity: 123.75
nucleic acid starting quantity units: ng

source_name: Homo sapiens induced pluripotent stem cell line male adult (53 years) derived from fibroblast of arm

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

value: These are induced pluripotent stem cells (iPSC) created from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS373AAA at ENCODE; https://www.encodeproject.org/ENCBS373AAA/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F182; http://web.expasy.org/cellosaurus/CVCL_F182

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23338&PgId=166


title: ChIP-seq from SUDHL6 (ENCLB509CVO)

description:
https://www.encodeproject.org/experiments/ENCSR307DQT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR307DQT
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR179YLS
encode release date: 2016-11-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB509CVO
size range: 200-600

source_name: Homo sapiens SUDHL6 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/a47aaf7e-38f5-4326-914a-98991f61345a/@@download/attachment/Alon%27s%20SCN%20revised.pdf

value: immortalized cell line

value: also called SU-DHL-6 (diffuse histiocytic lymphoma) - disease:large cell lymphoma; diffuse mixed histiocytic and lymphocytic lymphoma; follicular B cell lymphoma; ATCC CRL-2959

value: 43 year

value: adult

value: Bradley Bernstein, Broad

value: ENCBS107PVI at ENCODE; https://www.encodeproject.org/ENCBS107PVI/

value: Derived from ENCODE donor ENCDO353AAA; https://www.encodeproject.org/ENCDO353AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2206; http://web.expasy.org/cellosaurus/CVCL_2206


title: ChIP-seq from mid-neurogenesis radial glial cells (ENCLB089XWR)

description:
https://www.encodeproject.org/experiments/ENCSR113LFZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR113LFZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR287XMW
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB089XWR
size range: 200-600

source_name: Homo sapiens mid-neurogenesis radial glial in vitro differentiated cells female embryo (5 days) derived from H9 stably expressing C-terminal eGFP-HES5 fusion protein

value: mid-neurogenesis radial glial cells

value: in vitro differentiated cells

value: Mid neurogenesis radial glial cells were collected at day 35 of differentiation (see protocol)

value: embryonic

value: female

value: 5 day

value: healthy

value: ENCBS741FXQ at ENCODE; https://www.encodeproject.org/ENCBS741FXQ/

value: Derived from ENCODE donor ENCDO222AAA; https://www.encodeproject.org/ENCDO222AAA/


title: ChIP-seq from neural cell (ENCLB300OZD)

description:
https://www.encodeproject.org/experiments/ENCSR308JFE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR308JFE
assay title: ChIP-seq
encode release date: 2016-10-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB300OZD
size range: 200-600

extract_protocol: not provided

value: Control

value: neural cell

value: male

value: unknown

value: ENCBS737HIZ at ENCODE; https://www.encodeproject.org/ENCBS737HIZ/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/


title: ChIP-seq from SK-N-MC (ENCLB606MTX)

description:
https://www.encodeproject.org/experiments/ENCSR111QAW/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against H3K9ac using SK-N-MC cell line which was previously described as a neuroepithelioma (ATCC HTB-10). However recent evidence reveals it is Ewing's Sarcoma (www.ncbi.nlm.nih.gov/pubmed/15548687, www.ncbi.nlm.nih.gov/pubmed/25453903, www.ncbi.nlm.nih.gov/biosample/3151999).
experiment encode accession: ENCSR111QAW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR899XXQ
encode release date: 2017-01-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB606MTX
size range: 200-600
nucleic acid starting quantity: 25.08
nucleic acid starting quantity units: ng

value: SK-N-MC

value: immortalized cell line

value: Please note:This cell line was previously described as a neuroepithelioma (ATCC HTB-10).  However recent evidence reveals it is Ewing's Sarcoma (http://www.ncbi.nlm.nih.gov/pubmed/15548687, http://www.ncbi.nlm.nih.gov/biosample/3151999, http://www.ncbi.nlm.nih.gov/pubmed/25453903).

value: child

value: 14 year

value: Ewing's sarcoma

value: Bradley Bernstein, Broad

value: ENCBS203EZT at ENCODE; https://www.encodeproject.org/ENCBS203EZT/

value: Derived from ENCODE donor ENCDO000ABC; https://www.encodeproject.org/ENCDO000ABC/

value: ENCODE dbxrefs Cellosaurus CVCL_0530; http://web.expasy.org/cellosaurus/CVCL_0530


title: ChIP-seq from GM12878 (ENCLB417ZGG)

description:
https://www.encodeproject.org/experiments/ENCSR136WQZ/
***************
biological replicate number: 13
technical replicate number: 2
description: Reverse Crosslink Control ChIP-seq on human GM12878 (fragmentation date 02-20-14)
experiment encode accession: ENCSR136WQZ
assay title: ChIP-seq
encode release date: 2016-01-08
lab: Richard Myers, HAIB
library encode accession: ENCLB417ZGG
size range: 100-500

source_name: Homo sapiens GM12878 immortalized cell line

value: GM12878, B-lymphocyte, lymphoblastoid

value: adult

value: female

value: Richard Myers, HAIB

value: ENCBS057BBL at ENCODE; https://www.encodeproject.org/ENCBS057BBL/

value: Derived from ENCODE donor ENCDO000AAK; https://www.encodeproject.org/ENCDO000AAK/

value: ENCODE dbxrefs Cellosaurus CVCL_7526; http://web.expasy.org/cellosaurus/CVCL_7526

value: Coriell sample source; https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=CC


title: ChIP-seq from SK-N-SH (ENCLB432IXA)

description:
https://www.encodeproject.org/experiments/ENCSR125IJY/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR125IJY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2016-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB432IXA
size range: 200-600
nucleic acid starting quantity: 18.575
nucleic acid starting quantity units: ng

value: SK-N-SH

value: immortalized cell line

value: 4 year

value: ENCBS018DDZ at ENCODE; https://www.encodeproject.org/ENCBS018DDZ/

value: Derived from ENCODE donor ENCDO000ABD; https://www.encodeproject.org/ENCDO000ABD/

value: ENCODE dbxrefs Cellosaurus CVCL_0531; http://web.expasy.org/cellosaurus/CVCL_0531


title: BLCA_Cx_1

source_name: FFPE tissue specimen

value: bladder cancer

value: pT2   G3


title: ChIP-seq from H1-hESC (ENCLB695AGW)

description:
https://www.encodeproject.org/experiments/ENCSR000AMI/
***************
biological replicate number: 5
technical replicate number: 1
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR000AMI
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AGW

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f10bdd36-e370-4777-a7f3-83091c115749/@@download/attachment/wgEncodeBroadHistone.html.pdf

value: Control

value: stem cell

value: embryonic

value: male

value: unknown

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS380OBH at ENCODE; https://www.encodeproject.org/ENCBS380OBH/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771


title: ChIP-seq from K562 (ENCLB933UPZ)

description:
https://www.encodeproject.org/experiments/ENCSR000AKY/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on human K562
experiment encode accession: ENCSR000AKY
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB933UPZ
size range: 200-600

value: immortalized cell line

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS979ZKW at ENCODE; https://www.encodeproject.org/ENCBS979ZKW/

value: Derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: ChIP-seq from K562 (ENCLB915JNJ)

description:
https://www.encodeproject.org/experiments/ENCSR000AKY/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq on human K562
experiment encode accession: ENCSR000AKY
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB915JNJ
size range: 200-600

value: Control

value: ENCBS775RXB at ENCODE; https://www.encodeproject.org/ENCBS775RXB/


title: ChIP-seq from H1-hESC (ENCLB372PRI)

description:
https://www.encodeproject.org/experiments/ENCSR000AMI/
***************
biological replicate number: 2
technical replicate number: 4
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR000AMI
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB372PRI
size range: 200-600

value: stem cell

value: embryonic

value: ENCBS011NFB at ENCODE; https://www.encodeproject.org/ENCBS011NFB/


title: BLCA_Cx_9

value: bladder cancer

value: pT2   G3


title: ChIP-seq from MCF-7 (ENCLB339BDV)

description:
https://www.encodeproject.org/experiments/ENCSR155VDK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on MCF7-human
experiment encode accession: ENCSR155VDK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR610GTD, ENCSR511PAE
encode release date: 2016-04-25
lab: Richard Myers, HAIB
library encode accession: ENCLB339BDV

value: MCF-7, mammary gland adenocarcinoma

value: 69 year

value: breast cancer (adenocarcinoma)

value: Richard Myers, HAIB

value: ENCBS143XXF at ENCODE; https://www.encodeproject.org/ENCBS143XXF/

value: Derived from ENCODE donor ENCDO000AAE; https://www.encodeproject.org/ENCDO000AAE/

value: ENCODE dbxrefs Cellosaurus CVCL_0031; http://web.expasy.org/cellosaurus/CVCL_0031

value: ATCC sample source; http://www.atcc.org/Products/All/HTB-22.aspx


title: ChIP-seq from H1-hESC (ENCLB695AKK)

description:
https://www.encodeproject.org/experiments/ENCSR000AMI/
***************
biological replicate number: 5
technical replicate number: 2
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR000AMI
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AKK

value: male

value: unknown

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS380OBH at ENCODE; https://www.encodeproject.org/ENCBS380OBH/

value: Derived from ENCODE donor ENCDO000AAW; https://www.encodeproject.org/ENCDO000AAW/

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771


title: ChIP-seq from SK-N-MC (ENCLB263HJZ)

description:
https://www.encodeproject.org/experiments/ENCSR287VPM/
***************
biological replicate number: 2
technical replicate number: 2
description: ChIP-seq against H3K4me3 using SK-N-MC cell line which was previously described as a neuroepithelioma (ATCC HTB-10). However recent evidence reveals it is Ewing's Sarcoma (www.ncbi.nlm.nih.gov/pubmed/15548687, www.ncbi.nlm.nih.gov/biosample/3151999, www.ncbi.nlm.nih.gov/pubmed/25453903).
experiment encode accession: ENCSR287VPM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR899XXQ
encode release date: 2016-11-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB263HJZ
size range: 200-600

value: SK-N-MC

value: immortalized cell line

value: Please note:This cell line was previously described as a neuroepithelioma (ATCC HTB-10).  However recent evidence reveals it is Ewing's Sarcoma (http://www.ncbi.nlm.nih.gov/pubmed/15548687, http://www.ncbi.nlm.nih.gov/biosample/3151999, http://www.ncbi.nlm.nih.gov/pubmed/25453903).

value: child

value: female

value: 14 year

value: Ewing's sarcoma

value: ENCBS203EZT at ENCODE; https://www.encodeproject.org/ENCBS203EZT/

value: Derived from ENCODE donor ENCDO000ABC; https://www.encodeproject.org/ENCDO000ABC/

value: ENCODE dbxrefs Cellosaurus CVCL_0530; http://web.expasy.org/cellosaurus/CVCL_0530


title: Dystrophic mouse quadriceps, prednisolone-treated, biological replicate 3

status: Public on Mar 07 2017

city: Columbus

first: Jill

last: Rafael-Fortney

state: OH

address: 460 W. 12th Ave

department: Physiology & Cell Biology

institute: The Ohio State University

hyb_protocol: Labeled cDNA targets were hybridized to Affymetrix GeneChip® Mouse Transcriptome array 1.0 for 16 h at 45 ⁰C rotating at 60 rpm.

scan_protocol: The arrays were washed and stained using the Fluidics Station 450 and scanned using the GeneChip Scanner 3000.

data_processing: For gene expression analysis, arrays were normalized using Gene Level SST RMA algorithm in Expression Console and comparisons made in Transcriptome Analysis Console (Affymetrix).

organism: Mus musculus

label_protocol: 5.5 µg of cDNA was labeled and fragmented using the GeneChip WT PLUS reagent kit (Affymetrix) following the manufacturer's instructions.

growth_protocol: Mouse quadriceps muscles dissected from 6-week-old dystrophic mice.

extract_protocol: RNA was isolated using TRIzol reagent (Life Technologies), according to manufacturer’s instructions. RNA concentration was determined spectrophotometrically using a Nanodrop ND-100 (Nanodrop Technologies). Samples were DNase treated using RQ1 DNase (Promega) for 30 minutes at 37⁰C, reaction was stopped with a 25:24:1 phenol: chloroform: isoamyl alcohol mixture (Malinckrodt, Fischer, Sigma) and centrifuged 5 minutes (14,000 x g; room temperature). A chloroform phase separation was performed; the aqueous layer was removed and ethanol (Fisher) precipitated. The pellet was washed (75% ethanol), centrifuged (14,000 x g, 10 minutes, 4⁰C), air dried (5 minutes) and re-suspended in autoclaved Millipore filtered water. DNase treated RNA concentration was determined spectrophotometrically and samples were stored at -80⁰C. Samples for microarray analysis were further purified using the RNeasy mini kit (Qiagen) RNA cleanup protocol and final RNA concentrations were determined. RNA integrity was interrogated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). A 100 ng aliquot of total mRNA was linearly amplified.

treatment_protocol: 20 mg/kg x day lisinopril plus 100 mg/kg x day spironolactone delivered via medicated pellets from 4-6 weeks-of-age, 20 mg/kg x day lisinopril plus 200 mg/kg x day eplerenone delivered via medicated pellets from 4-6 weeks-of-age, 1.5 mg/kg x day prednisolone delivered via water bottle from 4-6 weeks-of-age or untreated normal chow.

tag: strain/background

tag: genotype/variation

value: utrn+/-;mdx

value: 6 weeks

value: male

value: quadriceps muscle

tag: treatment

value: prednisolone


title: Dystrophic mouse quadriceps, prednisolone-treated, biological replicate2


title: Dystrophic mouse quadriceps, spironolactone plus lisinopril-treated, biological replicate 3

source_name: quadriceps, utrn+/-;mdx, spironolactone plus lisinopril-treated

value: spironolactone plus lisinopril


title: Dystrophic mouse quadriceps, spironolactone plus lisinopril-treated, biological replicate 2


title: Dystrophic mouse quadriceps, eplerenone plus lisinopril-treated, biological replicate 2

source_name: quadriceps, utrn+/-;mdx, eplerenone plus lisinopril-treated

value: eplerenone plus lisinopril


title: Dystrophic mouse quadriceps, prednisolone-treated, biological replicate 1


title: Dystrophic mouse quadriceps, untreated, biological replicate 3

source_name: quadriceps, utrn+/-;mdx, untreated


title: Dystrophic mouse quadriceps, eplerenone plus lisinopril-treated, biological replicate 3


title: Dystrophic mouse quadriceps, spironolactone plus lisinopril-treated, biological replicate 1


title: Dystrophic mouse quadriceps, eplerenone plus lisinopril-treated, biological replicate 1


title: Dystrophic mouse quadriceps, untreated, biological replicate 2


title: Dystrophic mouse quadriceps, untreated, biological replicate 1


title: case9_T6_Meth

status: Public on Oct 18 2016

city: FUKUOKA

first: RYUTARO

last: UCHI

state: FUKUOKA

institute: KYUSHUUNIVERSItY

description: SAMPLE 74

hyb_protocol: Illumina standard protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Mean background-corrected and normalized signal intensities of the methylation (M) and unmethylated (U) estimates for each CpG locus were extracted using Illumina BeadStudio software
the non_normalized.txt contains unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: case9_Primary colorectal tumor tissue

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: case id

tag: gender

tag: tissue type

value: Primary colorectal tumor tissue

tag: primary tumor defferentiation

value: moderately differentiated

tag: tumor or normal colon location

value: ascending colon


title: case9_N_Meth

description: SAMPLE 70

source_name: case9_Normal colon tissue tissue

value: Normal colon tissue tissue


title: case9_T3_Meth

description: SAMPLE 73

value: female


title: case8_T1_Meth

description: SAMPLE 64

source_name: case8_Primary colorectal tumor tissue

value: sigmoid colon


title: case9_T8_Meth

description: SAMPLE 75


title: case9_T1_Meth

description: SAMPLE 71


title: case8_N_Meth

description: SAMPLE 63

source_name: case8_Normal colon tissue tissue


title: case8_T4_Meth

description: SAMPLE 66


title: case8_T8_Meth

description: SAMPLE 69


title: case7_T8_Meth

description: SAMPLE 62

source_name: case7_Primary colorectal tumor tissue

value: well to moderately differentiated

value: rectum


title: case9_T2_Meth

description: SAMPLE 72


title: case6_T8_Meth

description: SAMPLE 55

source_name: case6_Primary colorectal tumor tissue


title: case8_T3_Meth

description: SAMPLE 65


title: case7_T4_Meth

description: SAMPLE 59


title: case7_T6_Meth

description: SAMPLE 60


title: case7_T2_Meth

description: SAMPLE 58


title: case8_T5_Meth

description: SAMPLE 67


title: case8_T6_Meth

description: SAMPLE 68


title: case7_N_Meth

description: SAMPLE 56

source_name: case7_Normal colon tissue tissue


title: case6_T2_Meth

description: SAMPLE 51


title: case6_T6_Meth

description: SAMPLE 53


title: case7_T7_Meth

description: SAMPLE 61


title: case6_T7_Meth

description: SAMPLE 54


title: case5_T8_Meth

description: SAMPLE 48

source_name: case5_Primary colorectal tumor tissue

value: well differentiated


title: case5_T5_Meth

description: SAMPLE 46


title: case5_T6_Meth

description: SAMPLE 47


title: case6_T1_Meth

description: SAMPLE 50


title: case6_N_Meth

description: SAMPLE 49

source_name: case6_Normal colon tissue tissue


title: case6_T3_Meth

description: SAMPLE 52


title: case5_T3_Meth

description: SAMPLE 45


title: case5_N_Meth

description: SAMPLE 42

source_name: case5_Normal colon tissue tissue


title: case7_T1_Meth

description: SAMPLE 57


title: case5_T1_Meth

description: SAMPLE 43


title: case5_T2_Meth

description: SAMPLE 44


title: case4_N_Meth

description: SAMPLE 36

source_name: case4_Normal colon tissue tissue


title: case4_T8_Meth

description: SAMPLE 41

source_name: case4_Primary colorectal tumor tissue


title: case4_T4_Meth

description: SAMPLE 38


title: case3_Liver_Meth

description: SAMPLE 27

source_name: case3_Liver metastasis tumor tissue

value: Liver metastasis tumor tissue

value: Liver


title: case3_Q_Meth

description: SAMPLE 33

source_name: case3_Primary colorectal tumor tissue

value: descending colon


title: case4_T3_Meth

description: SAMPLE 37

value: male


title: case3_po2_Meth

description: SAMPLE 31


title: case3_S_Meth

description: SAMPLE 35


title: case3_F1_Meth

description: SAMPLE 20


title: case4_T6_Meth

description: SAMPLE 40


title: case3_C_Meth

description: SAMPLE 16


title: case3_O_Meth

description: SAMPLE 29


title: case3_po3_Meth

description: SAMPLE 32


title: case3_J_Meth

description: SAMPLE 26


title: case3_G2_Meth

description: SAMPLE 23


title: case4_T5_Meth

description: SAMPLE 39


title: case3_I_Meth

description: SAMPLE 25


title: case3_D_Meth

description: SAMPLE 17


title: case3_G1_Meth

description: SAMPLE 22


title: case3_F2_Meth

description: SAMPLE 21


title: case3_R_Meth

description: SAMPLE 34


title: case3_M_Meth

description: SAMPLE 28


title: case3_po1_Meth

description: SAMPLE 30


title: case3_H_Meth

description: SAMPLE 24


title: case3_E1_Meth

description: SAMPLE 18


title: case3_normal_Meth

description: SAMPLE 14

source_name: case3_Normal colon tissue tissue


title: case3_E3_Meth

description: SAMPLE 19


title: case2_I3_Meth

description: SAMPLE 10

source_name: case2_Primary colorectal tumor tissue


title: Subject 4 Post

status: Public on Jun 01 2016

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

institute: Karolinska Institutet

description: Subject 4 Human Vastus lateralis muscle, Subject 4, Post EECP Post EECP

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HuGene-1_0-st 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: The probe-set level intensities of the arrays were normalized using the Robust Multi-array Analysis method (RMA) implemented within the R statistical software environment using the 'oligo' package (Bioconductor project).

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

extract_protocol: Biopsies were obtained from the vastus lateralis muscle using the Bergström needle technique. The biopsies were immediately stored in liquid nitrogen until processing. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: Vastus lateralis

value: Post EECP

value: Male

tag: subject

value: Subject 4


title: Subject 5 Post

description: Subject 5 Human Vastus lateralis muscle, Subject 5, Post EECP Post EECP

value: Subject 5


title: Subject 1 Post

description: Subject 1 Human Vastus lateralis muscle, Subject 1, Post EECP Post EECP

value: Subject 1


title: Subject 5 Pre

description: Subject 5 Human Vastus lateralis muscle, Subject 5, Pre EECP Pre EECP

value: Pre EECP


title: Subject 1  Pre

description: Subject 1 Human Vastus lateralis muscle, Subject 1, Pre EECP Pre EECP


title: case3_B_Meth

description: SAMPLE 15

value: Primary colorectal tumor tissue


title: Subject 6 Pre

description: Subject 6 Human Vastus lateralis muscle, Subject 6, Pre EECP Pre EECP

value: Subject 6


title: Subject 2 Pre

description: Subject 2 Human Vastus lateralis muscle, Subject 2, Pre EECP Pre EECP

value: Subject 2


title: Subject 3 Pre

description: Subject 3 Human Vastus lateralis muscle, Subject 3, Pre EECP Pre EECP

value: Subject 3


title: Subject 4 Pre

description: Subject 4 Human Vastus lateralis muscle, Subject 4, Pre EECP Pre EECP


title: case2_E2_Meth

description: SAMPLE 5


title: case2_G3_Meth

description: SAMPLE 9


title: case2_Liver1_Meth

description: SAMPLE 11

source_name: case2_Liver metastasis tumor tissue


title: mAbs 31E10E7 R2 peptide array

status: Public on May 27 2016

type: protein

city: Siena

first: Erika

last: Bartolini

state: Italy

address: Via Fiorentina 1

department: AIMB

country: Italy

institute: GSK Vaccines

hyb_protocol: Peptide arrays were first blocked 60 min in Blocking Buffer (Block it, Arrayit Sunnyvale, CA 94085, USA). The array was then incubated 1h a room temperature with mAb diluted 1:200 for anti-mouse IgG-specific analysis. After washing with 0.1% Tween 20 in PBS buffer (PBST), arrays were incubated with an AlexaFluor®647-labelled anti-mouse secondary antibody (1:800 – Jackson Immunoresearch) at RT for 1 h to detect interactions. Slides were washed again as before, then rinsed in sterile water and dried.

scan_protocol: Fluorescence signals were detected by using a Powerscanner (Tecan Trading AG, Switzerland) and the 16-bit images were generated with Powerscanner software at 10 µm per pixel resolution.

data_processing: Images were processed using ImaGene 9.0 software (Biodiscovery Inc, CA, USA). Elaboration and analysis of image raw fluorescence Intensity (FI) data was performed using in-house developed software and R scripts. For each sample, the mean fluorescence intensity (MFI) of replicated spots was determined, after subtraction of the background value surrounding each spot.

molecule: protein

source_name: purified murine monoclonal antibody

label_protocol: The secondary antibody used for arrays was from Jackson Immunoresearch, (872 W Baltimore Pike, West Grove, PA 19390 USA). It was conjugated to the Alexafluor dye (Alexa 647) by the company.

extract_protocol: The murine anti-NHBA 31E10/E7 IgG2a mAb was produced and purified by conventional hybridoma production methods. The mAb was purified from culture supernatants by Protein G affinity columns (GE Healthcare). The mAb subclass was determined using a mouse mAb isotyping kit (Roche).

tag: antigen

value: Neisserial Heparin Binding Antigen

tag: antibody subclass

tag: antibody production

value: hybridoma cell line


title: mAbs 31E10E7 R3 peptide array

label: AlexaFluor®647-labelled anti-mouse secondary antibody


title: case2_E3_Meth

description: SAMPLE 6

value: well differentiated


title: mAbs 31E10E7 R1 peptide array


title: case2_F2_Meth

description: SAMPLE 8


title: case2_Liver3_Meth

description: SAMPLE 13

value: Liver metastasis tumor tissue

value: Liver


title: case2_Liver2_Meth

description: SAMPLE 12

value: male


title: Subject 6 Post

description: Subject 6 Human Vastus lateralis muscle, Subject 6, Post EECP Post EECP

value: Vastus lateralis


title: mAbs 31E10E7 R2 protein array

hyb_protocol: Protein arrays were first blocked 60 min in Blocking Buffer (Block it, Arrayit Sunnyvale, CA 94085, USA). The array was then incubated 1h a room temperature with mAb diluted 1:2000 for anti-mouse IgG-specific analysis. After washing with 0.1% Tween 20 in PBS buffer (PBST), arrays were incubated with an AlexaFluor®647-labelled anti-mouse secondary antibody (1:800 – Jackson Immunoresearch) at RT for 1 h to detect interactions. Slides were washed again as before, then rinsed in sterile water and dried.


title: case2_D3_Meth

description: SAMPLE 4

value: descending colon


title: mAbs 31E10E7 R3 protein array


title: Subject 2 Post

description: Subject 2 Human Vastus lateralis muscle, Subject 2, Post EECP Post EECP

value: Post EECP

value: Male


title: case2_C2_Meth

description: SAMPLE 2


title: mAbs 31E10E7 R1 protein array


title: Reference strain-rep3

status: Public on Mar 01 2016

city: TOULOUSE

first: CEREN

last: ALKIM

address: Laboratoire d'Ingénierie des Systèmes Biologiques & des Procédés

country: France

institute: INRA

description: Gene expression under non-stress condition after growth in minimal media until OD600 of 1.

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast V2 Oligo Microarrays (G4813A-016322) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321).  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.5 µg RNA using the One-color Low Input Quick Amp Kit (Agilent) according to the manufacturer's instructions, followed by Agilent Nano-prep RNA purification (Agilent, Santa Clara, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-2000 spectrophotometer.

growth_protocol: Fresh precultures of yeast cells were diluted to an OD600 of 0.1 in fresh minimal medium. They were cultivated at 30°C and 150 rpm untill they reach the OD600 value of about 1.00. Cells were harvested at this OD600 value.

extract_protocol: Total RNA of yeast cells were extracted by using RNeasy Mini Kit supplied from QIAGEN according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Yeast cells were not treated with any special agent.

tag: strain

value: CEN.PK 113.7D

tag: mating type

value: MATa


title: Reference strain-rep1

source_name: Saccharomyces cerevisiae, replicate 1


title: Reference strain-rep2

source_name: Saccharomyces cerevisiae, replicate 2


title: Subject 3 Post

description: Subject 3 Human Vastus lateralis muscle, Subject 3, Post EECP Post EECP


title: case2_normal_Meth

description: SAMPLE 1

source_name: case2_Normal colon tissue tissue

tag: age

value: Normal colon tissue tissue


title: case2_E4_Meth

description: SAMPLE 7

value: Primary colorectal tumor tissue


title: case2_D2_Meth

description: SAMPLE 3


title: myometrial_vehicle_sample 1 B7_2

status: Public on Aug 13 2015

city: london

first: kaiyu

last: lei

state: London

address: ducan road

department: Surgery and Cancer

institute: imperial college london

description:
Gene expression data from myometrial cells treated with vehicle for 6h
B7_2

hyb_protocol: 25 µg of labelled cRNA was fragmented using 5× fragmentation buffer and Rnase-free water at 94oC for 35 min. 15 µg of the fragmented, biotin-labelled cRNA was made up in a hybridization cocktail and hybridized to the HgU133 Plus 2.0 array at 45oC for 16 hours. Following hybridization the arrays were washed and stained using the Affymetrix Fluidics Station 450.

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

data_processing: All steps of the process were quality controlled by measuring yield (µg), concentration (µg/l) and 260:280 ratios via spectrophotometry using the Nanodrop ND-1000 and sample integrity using the Agilent 2100 bioanalyser (Agilent Technologies, Inc.). After general array Quality Control and data export, the data were normalised using Robust Multichip Average and imported into Partek Genomic Suite. Array data were then identified for any potential outliers and overall grouping/separation using Principal Component Analysis. The gene lists were generated by a sequential filtering approach based on the fold-change (normalisation to the control group) and the confidence (fold-change p value). The less-stringent gene list was resulted from the fold-change greater than 1.5 by comparing the treatment group to the control group. The stringent gene list was retained by further filtering with fold-change p<0.05.

label_protocol: cDNA generated from 2 µg of total RNA using the GeneChip® Expression 3’-Amplification One-Cycle cDNA Synthesis Kit, in conjunction with the GeneChip® Eukaryotic PolyA RNA Control Kit (Affymetrix, Inc.). The cDNA was cleaned up using the GeneChip® Sample Cleanup Module and subsequently processed to generate biotin-labelled cRNA using the GeneChip® Expression 3’-Amplification IVT Labelling Kit (Affymetrix, Inc.).

growth_protocol: Primary human myometrial cells were isolated using a mixture of collagenases {1 mg/ml of collagenase 1A and 1 mg/ml of collagenase XI (Sigma)} and cultured in DMEM medium containing phenol red 7.5% fetal calf serum, L-glutamine and 100 mU/mL penicillin and 100µg/mL streptomycin in an atmosphere of 5% CO2: 95% air at 37oC.

extract_protocol: Total RNA was extracted and purified from myometrial cells grown in 6-well culture plates using RNAeasy mini kit (Qiagen).

treatment_protocol: Cells were exposed to IL-1β, P4 either alone or in combination; ethanol was used as the vehicle control for 6 h.

value: uterine smooth muscle

tag: individual

value: patient 1

tag: passage

value: cell passage 4


title: myometrial_IL-1β_sample 3 F8_2

description:
Gene expression data from myometrial cells treated with IL-1β for 6h
F8_2

tag: tissue

value: patient 3


title: myometrial_vehicle_sample 3 F7_2

description:
Gene expression data from myometrial cells treated with vehicle for 6h
F7_2


title: myometrial_P4_sample 3 F10_1

description:
Gene expression data from myometrial cells treated with P4 for 6h
F10_1

source_name: myometrial cells treated with P4 for 6h


title: myometrial_vehicle_sample 3 F7_1

description:
Gene expression data from myometrial cells treated with vehicle for 6h
F7_1


title: myometrial_IL-1β+P4_sample 2 C12_2

description:
Gene expression data from myometrial cells treated with IL-1β+P4 for 6h
C12_2

value: patient 4


title: myometrial_IL-1β+P4_sample 3 F12_2

description:
Gene expression data from myometrial cells treated with IL-1β+P4 for 6h
F12_2


title: myometrial_IL-1β_sample 1 B8_2

description:
Gene expression data from myometrial cells treated with IL-1β for 6h
B8_2


title: myometrial_IL-1β_sample 2 C8_2

description:
Gene expression data from myometrial cells treated with IL-1β for 6h
C8_2


title: myometrial_vehicle_sample 2 C7_2

description:
Gene expression data from myometrial cells treated with vehicle for 6h
C7_2


title: myometrial_P4_sample 2 D10_1

description:
Gene expression data from myometrial cells treated with P4 for 6h
D10_1

value: patient 2


title: myometrial_IL-1β+P4_sample 1 B12_2

description:
Gene expression data from myometrial cells treated with IL-1β+P4 for 6h
B12_2


title: myometrial_vehicle_sample 2 D7_1

description:
Gene expression data from myometrial cells treated with vehicle for 6h
D7_1


title: myometrial_P4_sample 1 B10_1

description:
Gene expression data from myometrial cells treated with P4 for 6h
B10_1


title: spheroids_rep2

status: Public on Jan 03 2014

city: indianapolis

first: salvatore

last: condello

address: 980 west walnut street

institute: iu school of medicine

hyb_protocol: Standar hybridization cocktail, hybed 17 hours at 45C.

scan_protocol: Standard wash and stain controlled by GCOS

data_processing: Cel Files generated by GCOS, imported into Partek (ver. 6.2) and RMA signals were generated for only the core probe sets (28,869).   RMA signals were generated for the core probe sets using the RMA background correction, quantile normalization and summarization by Median Polish.  Summarized signals for each probe set were log2 transformed.

source_name: ovarian cancer cell line IGROV-1

label_protocol: Standard Affymetrix WT labeling and control kit.

extract_protocol: standard RNA extraction. Trizol

tag: cell type

value: ovarian cancer

tag: phenotype

value: spheroids


title: spheroids_rep3


title: myometrial_vehicle_sample 1 B7_1

description:
Gene expression data from myometrial cells treated with vehicle for 6h
B7_1


title: spheroids to monolayer_rep2

value: spheroids to monolayer


title: monolayer_rep2

value: monolayer


title: spheroids to monolayer_rep3


title: monolayer_rep3


title: monolayer_rep1


title: spheroids to monolayer_rep1


title: Replicate 3

status: Public on Oct 08 2014

city: Suzhou

first: Yiqiang

last: Wang

state: Jiangsu

address: 111 Renai Road

institute: Xi'an Jiaotong-Liverpool University

hyb_protocol: An Agilent SurePrint G3 Human Gene Expression 8x60K (Cat# G2543-60015. Agilent) was used

scan_protocol: G2505C was used to scan the arrys and images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Normalized with GENESPRING12.0 (Silicon Genetics, Redwood City, CA)

label_protocol: Low Input Quick-Amp Labeling Kit of Agilent was used to amplify and label cRNA, the FlgE treated or control samples labeled with Cy3 and Cy5 fluorescence respectively.

growth_protocol: The SV40-immortalized human corneal epithelial cell line (HCEC, ATCC CRL-11135) were seeded in 24well plates at 1.5×104 in 500μL Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen, Carlsbad, CA, USA) at 37℃.

extract_protocol: mirVana RNA Isolation Kit (ABS p/n AM1556) was used to extract RNA

treatment_protocol: When 80%-90% confluence was reached, the cells were starved for 4 hours in culture medium without bovine serum, and then FlgE was added to 20ug/mL for 4 hours in triplicates. Control wells were added with PBS instead.

tag: cell line

value: HCEC

value: SV40-immortalized human corneal epithelial cells

tag: treated with

value: 20ug/mL FlgE for 4hrs

value: PBS for 4hrs