title: T2DR [DR278]

description:
DR278
DNA methylation data from whole blood samples of Taiwanese patients with non-proliferative retinopathy of Type-2 Diabetes (T2NPDR).

value: Whole blood

value: Type-2 Diabetes with non-proliferative retinopathy

value: Mild NPDR (Microaneurysms only) in both eyes

value: Glucose (AC):132 mg/dL; HbA1C:8.8%.

value: Taiwanese


title: T2DR [DR248]

status: Public on Jan 07 2020

type: genomic

city: Taichung

first: Fuu-Jen

last: Tsai

address: No.2, Yude Rd., North Dist.

department: Department of Medical Research

country: Taiwan

institute: China Medical University Hospital

description:
DR248
DNA methylation data from whole blood samples of Taiwanese patients with non-proliferative retinopathy of Type-2 Diabetes (T2NPDR).

hyb_protocol: The hybridization was performed against the Affymetrix GeneChip® Human Promoter 1.0R array by following the Affymetrix protocol for 17 hours at 45oC and 60 rpm.

scan_protocol: The arrays were subsequently washed (Affymetrix Fluidics Station 450) and stained with streptavidin-phycoerythrin (GeneChip® Hybridization, Wash, and Stain Kit, 900720), and were scanned on an Affymetrix GeneChip® Scanner 3000 7G.

data_processing:
The output data was annotated and the differential methylation of the compared arrays was performed with the tilling analysis software (TAS) of Affymetrix update to 1.0.3 version. It resulted in CHP files and text files.
The differential methylation levels were determined by the MAT (Model-based Analysis of Tiling-array) score which based on T value of ANOVA method, which was performed by the Partek Genomics suite (version 7.18.0723).

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood, T2DR

label_protocol: The 50 ng of methylated DNA from MeDIP immunoprecipitations and MBD-Capture reactions was amplified with GenomePlex Single Cell Whole Genome Amplification Kit (Sigma, Catalog No. WGA4) in each amplification performance was instructed by the company protocol. Then, cDNA was purified using cDNA cleanup columns (Affymetrix, Catalog No. 900371), and 7.5 ug of amplified DNA was fragmented and labeled following Affymetrix Chromatin Immunoprecipitation Assay Protocol (P/N: 702238 Rev. 3).

growth_protocol: The patients have been diagnosed with resulting to classified groups as Control, Type-2 diabetes with non-complication (T2D), Type-2 diabetes with nephropathy (T2DN), Type-2 diabetes with non-proliferative retinopathy (T2NPDR) and Type-2 diabetes with proliferative retinopathy (T2PDR). The blood samples were collected individually for the only research purposes with their voluntary participation. Whole blood of these samples was contained individually in the EDTA tubes for further steps of array analysis.

extract_protocol: The MethylMiner Methylated DNA Enrichment Kit (Invitrogen) was used to isolate the methylated DNA. One microgram of genomic DNA was sonicated to 100–500 bp. Then 3.5 mg (7 mL) of MBD-Biotin Protein was coupled to 10 mL of Dynabeads M-280 Streptavidin according to the manufacturer’s instructions.

treatment_protocol: Not applicable.

tag: tissue

tag: disease group

tag: phenotype

tag: blood glucose

value: Glucose (AC):186 mg/dL; HbA1C:8.3%.

tag: bmi (kg/m2)

tag: duration (yr)

tag: age (yr)

tag: gender

value: male

tag: population


title: OVCAR8 parental control-2 [272 DS-14]

type: SRA

city: Nashville

first: Dhivya

last: Sudhan

state: TN

address: 777 Preston Research Building

department: Hematology/Oncology Division

country: USA

institute: Vanderbilt University

library_source: transcriptomic

data_processing:
Quality control on raw reads was performed using FastQC.
STAR v2.5.3a used for reads mapping.
FeatureCounts v1.15.2 was used to count the number of mapped reads to each gene.
BiomaRt package was used to map mouse genes to human genes, and only uniquely mapped genes between human and mouse were kept.
Significantly differentially expressed genes with FDR-adjusted p-value≤0.01 and absolute fold-change≥2.0 were detected by DESeq2 (v1.18.1).
Genome Ontology and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway over-representation analysis was performed on differentially expressed genes using the WebGestaltR package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

molecule: total RNA

source_name: OVCAR8 parental control

growth_protocol: 5637NR and OVCAR8NR cells were maintained under drug-free conditions for 1 week prior to seeding.

extract_protocol:
RNA was extracted using ReliaPrep RNA Cell Miniprep system (Promega). Total RNA was quantified using the Quant-iT Ribo-Green RNA Assay Kit (Invitrogen).
Automated Illumina  Tru Seq Sample Preparation protocol was used to separate mRNA from total RNA, followed by cDNA  18  synthesis. Libraries were prepared using TruSeq® Stranded mRNA Library Prep kit (Illumina). Following  quality check, the libraries were quantified using the KAPA Library Quantification Kits for Next-Generation  Sequencing (Kapa biosystems), pooled and sequenced on the HiSEq3000 platform targeting 50 million  paired end reads/sample.

treatment_protocol: Parental and neratinib-resistant cells were seeded in triplicate in 10-cm dishes and then treated with or without neratinib (5637 – 600 nM; OVCAR8 – 1 μM); 24h later, cells were harvested and RNA was extracted.

tag: cell line

value: parental

tag: treatment

value: control


title: T2DR [DR240]

description:
DR240
DNA methylation data from whole blood samples of Taiwanese patients with non-proliferative retinopathy of Type-2 Diabetes (T2NPDR).

value: female


title: RNAPolII_ChIP_rep2

city: Farmington

first: Chia-Lin

last: Wei

state: CT

address: 10 Discovery Drive

department: Genome Technologies

institute: The Jackson Laboratory

description:
RNAPolII_ChIP_treat.bigWig
RNAPolII_ChIP_foldEnrich.bigWig
RNAPolII_ChIP.narrowPeak.gz

library_source: genomic

data_processing:
Raw reads were quality trimmed along with the adapter using cutadapt v1.14  (options: -e 0.2 -a AGATCGGAAGAGC --minimum-length 20 --trim-n -n 3). The trimmed-reads were mapped on the mm10 genome using BWA v0.7.12  (options: aln –l 25 followed by samse). Only the de-duplicated uniquely mapped reads were used for downstream analysis.
Peak calling was performed on the pair of ChIP and input dataset with MACS v2.1.1.20160309 (options: --nomodel --extsize 250 -B –SPMR -g mm ; broad peak additional options: --broad --broad-cutoff 0.1). bedGraphToBigWig from kentUtils was used to convert MACS2 generated bedgraph to bigWig format. Fold enrichment was computed with MACS2 bdgcmp and the output bedgraph file was converted to bigWig with bedGraphToBigWig.
Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced.
Genome_build: mm10

organism: Mus musculus

source_name: Mouse embryonic stem cells

growth_protocol: ES E14 were cultured routinely under feeder-free conditions on 0.1% gelatin coated dishes in Knockout DMEM supplemented with 15% FBS, 2 mM L-glutamine , 0.1 mM non-essential amino acids, 100 U/ml Penicillin/Streptomycin, 0.05 mM 2-mercaptoethanol, 1,000 U/ml ESGRO mouse LIF Medium Supplement (Leukemia Inhibitory Factor) and maintained at 37ºC with 5% CO2.

extract_protocol:
Cells were lysed using SDS-based lysis buffer and sonicated, protein-DNA complexes were then isolated with antibody.
Immunoprecipitated protein-DNA complex were ligated with illumina-compatible adaptors, amplified by PCR and sequenced.

value: E14 cell line

tag: cell type

value: embryonic stem cells

tag: ip antibody

value: RNA polymerase II clone (Covance MMS126R-500)


title: OVCAR8 parental control-1 [272 DS-13]


title: RNAPolII_ChIP_rep1


title: T2DR [DR218]

description:
DR218
DNA methylation data from whole blood samples of Taiwanese patients with non-proliferative retinopathy of Type-2 Diabetes (T2NPDR).


title: water column RNA_ETSP_Sample2_300m

type: mixed

city: Princeton

first: Bess

middle: B

last: Ward

state: NJ

address: Washington Road

department: Geosciences

institute: Princeton University

hyb_protocol: Samples were hybridized to duplicate arrays by overnight incubation at 64°C and washed.

scan_protocol: The arrays were scanned with a laser scanner (Molecular Devices 4300) Images were analyzed with Gene Pix Pro 6.0 software (Molecular Devices)

data_processing: Quality control was employed to remove noise by eliminating features 1) in which the Cy3 signal was not at least twice the value of the control probes, and 2) in which the Cy3/Cy5 could not pass a Z test to find out the outlier values. The Z test was performed by calculating Zi = ri/(s/square root of 3), i = 1, 2, or 3, where ri represents Cy3/Cy5, s the standard deviation of the triplicate Cy3/Cy5 values. A feature is considered as an outlier if the Z is greater than 1.9 (CI = 80%).

molecule: other

organism: synthetic construct

source_name: Universal Internal Standard + 70-mer

label_protocol: PCR products derived from both DNA and cDNA were labeled with amino-allyl-dUTP (Ambion) during linear amplification using random octamers and a Klenow polymerase (Applied Biosystems). The reaction contained 3.96 mM d(AGC)TP, 0.44 mM dTTP, and 4.84 mM dUaa and was amplified for 3 h at 37°C. The Klenow product was purified and conjugated with Cy3. The Cy3-labelled target (200 ng) was combined with 2x hybridization buffer (1x final concentration; Agilent) and 0.25 pmol of a Cy5-labelled complementary 20-mer standard oligonucleotide and incubated at 95°C for 5 min before being cooled to room temperature.

extract_protocol: DNA and RNA were extracted simultaneously from the same filters using the AllPrep DNA/RNA Mini Kit (Qiagen Sciences, Maryland, USA) with slight modifications (as in Rees et al. 2016).

tag: sample type

value: 20-mer DNA oligo

organism: seawater metagenome

source_name: seawater

tag: location

value: Oxygen Minimum Zone nitrogen cycling experiments in the Eastern Tropical South Pacific Ocean

tag: depth

value: PCR fragment amplified from total cDNA prepared from RNA extract


title: T2D [DN279]

description:
DN279
DNA methylation data from whole blood samples of Taiwanese patients with non-complication of Type-2 Diabetes (T2D).

source_name: Blood, T2D

value: Type-2 Diabetes without complication

value: Hyperglycemia related to T2D without complication according to China Medical Hospital's medical records

value: Glucose (AC):175 mg/dL; HbA1C:8.9%.


title: water column RNA_ETSP_Sample1_350m


title: 5637 NR Tx-2 [272 DS-11]

source_name: 5637 NR Tx

value: neratinib-resistant cells

value: neratinib


title: 5637 NR Tx-3 [272 DS-12]


title: water column DNA_ETSP_Sample19_145m

value: PCR fragment amplified from total DNA extract


title: Unk_neuron_H2O2_1

city: Clemson

first: William

middle: S

last: Baldwin

state: South Carolina

address: 230 Parkway Dr

department: Biological Sciences

institute: Clemson University

data_processing:
Illumina NextSeq 550 Control Software/Real-Time Analysis (RTA) was used for base-calling.
Samples were sequenced to an average sequencing depth of 16,000,000 read pairs with a 2 x 150 paired-end module.
Quality metrics were checked using FastQC on all samples sequenced, and Trimmomatic was used to trim low quality bases.
Trimmed reads were aligned to the human reference genome (GRCh38.p12) using GSNAP.  Subread feature counts software finds reads that aligned with known genes.
Raw read counts and EdgeR were used to determine differential gene expression.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Tab-deliminated text file includes raw counts for each sample.

source_name: neuron

growth_protocol: Primary fibroblasts were cultured in an incubator at 37°C with 5% CO2 with Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum, 1% insulin-transferrin-selenium, and 1% penicillin-streptomycin-glutamine.

extract_protocol:
Cells were removed from the plate with accutase, pelleted and resuspended 2X prior to lysis.  Lysis and RNA isolation were performed using the GenEluteTM Total RNA Miniprep Kit with the On-Column DNase I Digestion Set.
Libraries were prepared using TruSeq Total RNA Library Prep kit.

treatment_protocol: Primary fibroblasts from ASD-postive and ASD-negative patients were differentiated into cortical neurons from primary fibroblasts and were either left unexposed or exposed to 800 uM hydrogen peroxide for 17 hours prior to RNA extraction.

tag: patient id

tag: condition

value: ASD -

tag: Sex

value: neuron

value: H2O2 treated for 17 hours


title: water column DNA_ETSP_Sample21_140m


title: T2D [DN020]

description:
DN020
DNA methylation data from whole blood samples of Taiwanese patients with non-complication of Type-2 Diabetes (T2D).

tag: tissue

value: Whole blood

tag: disease group

tag: phenotype

value: Glucose (AC):136 mg/dL; HbA1C:8.1%.

value: male

value: Taiwanese


title: 5637 NR Tx-1 [272 DS-10]


title: Unk_neuron_H2O2_3


title: Unk_neuron_UT_3

value: Untreated (UT)


title: RNAPolII_ChIP_rep4

value: E14 cell line

value: embryonic stem cells

value: RNA polymerase II clone (Covance MMS126R-500)


title: OVCAR8 parental control-3 [272 DS-15]

value: parental

value: control


title: 5637 NR control-3 [272 DS-9]

source_name: 5637 NR control


title: T2D [DN195]

description:
DN195
DNA methylation data from whole blood samples of Taiwanese patients with non-complication of Type-2 Diabetes (T2D).

value: Type-2 Diabetes without complication

value: Hyperglycemia related to T2D without complication according to China Medical Hospital's medical records

tag: blood glucose

value: Glucose (AC):114 mg/dL; HbA1C:5.8%.

tag: bmi (kg/m2)

tag: duration (yr)


title: water column RNA_ETSP_Sample3_260m

value: 20-mer DNA oligo

value: Oxygen Minimum Zone nitrogen cycling experiments in the Eastern Tropical South Pacific Ocean

value: PCR fragment amplified from total cDNA prepared from RNA extract


title: Unk_neuron_UT_2

value: ASD -

value: neuron


title: 5637 NR control-2 [272 DS-8]

value: neratinib-resistant cells


title: water column DNA_ETSP_Sample20_150m

value: PCR fragment amplified from total DNA extract


title: Unk_neuron_UT_1

value: male


title: T2D [DN147]

description:
DN147
DNA methylation data from whole blood samples of Taiwanese patients with non-complication of Type-2 Diabetes (T2D).

value: Whole blood

value: Glucose (AC):97 mg/dL; HbA1C:7.1%.

tag: age (yr)

tag: gender

tag: population

value: Taiwanese


title: 5637 NR control-1 [272 DS-7]

tag: cell line

tag: treatment


title: F34_neuron_H2O2_3

tag: cell type

value: H2O2 treated for 17 hours


title: water column DNA_ETSP_Sample13_125m

tag: sample type

tag: location


title: water column DNA_ETSP_Sample12_180m

tag: depth


title: T2D [DN246]

description:
DN246
DNA methylation data from whole blood samples of Taiwanese patients with non-complication of Type-2 Diabetes (T2D).

value: Glucose (AC):98 mg/dL; HbA1C:7.2%.

value: female


title: F34_neuron_H2O2_2

tag: patient id

tag: condition


title: 5637 parental Tx-3 [272 DS-6]

source_name: 5637 parental Tx

value: parental

value: neratinib


title: T2D [DN035]

description:
DN035
DNA methylation data from whole blood samples of Taiwanese patients with non-complication of Type-2 Diabetes (T2D).

tag: tissue

value: Type-2 Diabetes without complication

value: Hyperglycemia related to T2D without complication according to China Medical Hospital's medical records

value: Glucose (AC):143 mg/dL; HbA1C:6.8%.


title: T2D [DN192]

description:
DN192
DNA methylation data from whole blood samples of Taiwanese patients with non-complication of Type-2 Diabetes (T2D).

tag: disease group

value: Glucose (AC):128 mg/dL; HbA1C:6.1%.


title: water column DNA_ETSP_Sample11_120m

value: 20-mer DNA oligo

value: Oxygen Minimum Zone nitrogen cycling experiments in the Eastern Tropical South Pacific Ocean


title: 5637 parental Tx-1 [272 DS-4]

tag: phenotype


title: 5637 parental Tx-2 [272 DS-5]


title: F34_neuron_UT_2

value: ASD -

tag: Sex

value: neuron

value: Untreated (UT)


title: T2D [DN073]

description:
DN073
DNA methylation data from whole blood samples of Taiwanese patients with non-complication of Type-2 Diabetes (T2D).

value: Whole blood

tag: blood glucose

value: Glucose (AC):149 mg/dL; HbA1C:7.4%.

tag: bmi (kg/m2)


title: T2D [DN093]

description:
DN093
DNA methylation data from whole blood samples of Taiwanese patients with non-complication of Type-2 Diabetes (T2D).

value: Glucose (AC):154 mg/dL; HbA1C:6.6%.

value: not available

tag: duration (yr)

tag: age (yr)

value: Taiwanese


title: F34_neuron_UT_3

value: male


title: 5637 parental control-3 [272 DS-3]

source_name: 5637 parental control

value: parental

value: control


title: water column DNA_ETSP_Sample9_190m

value: PCR fragment amplified from total DNA extract


title: water column DNA_ETSP_Sample18_5m


title: F34_neuron_UT_1


title: T2D [DN097]

description:
DN097
DNA methylation data from whole blood samples of Taiwanese patients with non-complication of Type-2 Diabetes (T2D).

value: Type-2 Diabetes without complication

value: Hyperglycemia related to T2D without complication according to China Medical Hospital's medical records

value: Glucose (AC):158 mg/dL; HbA1C:10%.

tag: gender

value: female

tag: population


title: 5637 parental control-1 [272 DS-1]

tag: cell line

tag: treatment


title: E91_neuron_H2O2_3

value: ASD +

tag: cell type

value: H2O2 treated for 17 hours


title: 5637 parental control-2 [272 DS-2]


title: Control [33071]

description:
33071
DNA methylation data from whole blood samples of Taiwanese without Type-2 Diabetes.

source_name: Blood, Control

value: Non-diabetes

value: Unrelated to T2D according to China Medical Hospital's medical records

value: not applicable


title: E91_neuron_H2O2_2

value: neuron


title: water column DNA_ETSP_Sample17_100m

tag: sample type

value: 20-mer DNA oligo

tag: location

value: Oxygen Minimum Zone nitrogen cycling experiments in the Eastern Tropical South Pacific Ocean


title: water column DNA_ETSP_Sample16_10m

tag: depth


title: E91_neuron_UT_3

tag: patient id

tag: condition

value: Untreated (UT)


title: Control [33070]

description:
33070
DNA methylation data from whole blood samples of Taiwanese without Type-2 Diabetes.

tag: tissue

value: Whole blood

tag: disease group

value: not available

value: male

value: Taiwanese


title: water column DNA_ETSP_Sample15_130m

value: PCR fragment amplified from total DNA extract


title: E91_neuron_UT_1

tag: Sex


title: Control [27385]

description:
27385
DNA methylation data from whole blood samples of Taiwanese without Type-2 Diabetes.

tag: phenotype

tag: blood glucose


title: water column DNA_ETSP_Sample10_30m


title: Sample 31: 1417F7L

city: Madrid

first: Cristina

last: Ovilo

address: Ctra Coruña km 7.5

country: Spain

institute: INIA-CSIC

data_processing:
Sequence reads were analyzed using the Tuxedo protocol (Trapnell et al, 2012).
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of raw sequencing data.
TrimGalore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to quality trim data with default settings and to remove the sequencing adaptors and poly A and T tails (stringency of 6 bp, -s 6) keeping only paired-end reads where both pairs were longer than 40 bp.
Filtered reads were mapped against the pig reference genome (Sscrofa11.1) using TopHat v.2.1.0 (Kim et al., 2013) with Bowtie2 (v.2.2.7.0) applying default settings except that reads were first aligned to the ENSEMBL (11.1.90) transcriptome annotation (-G option), and the distance between both pairs was set to 100 bp (inner-mean distance) and the standard deviation to 150 bp.
Transcripts were assembled using Cufflinks (v2.2.1.), following the protocol proposed by the developer and including the Cufflinks, Cuffmerge and Cuffdiff steps (Trapnell et al., 2012); and transcript abundances were estimated as FPKM (fragments per kilobase of transcript per million mapped reads).
Genome_build: Sscrofa 11.1
Supplementary_files_format_and_content: Processed data file includes normalized expression values (FPKM) for all genes in all 32 samples

organism: Sus scrofa

source_name: Longissimus dorsi muscle

growth_protocol: All tissues were collected within 15 min postmortem, snap-frozen in liquid nitrogen, and then stored at -80° C until processing.

extract_protocol:
Total RNA was extracted from 50-100mg samples of muscle using the RiboPure TM of High Quality total RNA kit (Ambion, Austin, TX, USA) following the manufacturer’s recommendations. RNA was quantified using a NanoDrop-100 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The quality of the RNA was evaluated using the RNA Integrity Number (RIN) value from the Agilent 2100 Bioanalyzer device (Agilent technologies, Santa Clara, CA, USA). The RIN values ranged from 7.8 to 9.8
Sequencing libraries were made using the mRNA-Seq sample preparation kit (Illumina Inc., Cat. # RS-100-0801) according to manufacturer’s protocol. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode with the read length 2x76bp on a on a HiSeq2000 sequence analyzer (Illumina, Inc). Images from the instrument were processed using the manufacturer’s software to generate FASTQ sequence files.

treatment_protocol: 50-100 mg samples of each tissue were ground in liquid nitrogen with mortar and pestle.

value: Longissimus dorsi muscle

tag: age

value: gestation day 77

tag: genotype

value: crossbred Iberian x Large White


title: Sample 32: 1417F9L

value: female


title: water column DNA_ETSP_Sample1_250m


title: water column DNA_ETSP_Sample14_90m


title: Sample 30: 1417F6L

value: pure Iberian


title: water column DNA_ETSP_Sample7_270m


title: B26_fibroblast_UT_3

source_name: fibroblast

value: ASD +

value: fibroblast


title: Control [27189]

description:
27189
DNA methylation data from whole blood samples of Taiwanese without Type-2 Diabetes.

value: Non-diabetes

value: Unrelated to T2D according to China Medical Hospital's medical records

tag: bmi (kg/m2)

tag: duration (yr)

value: not applicable

tag: age (yr)

tag: gender


title: Sample 29: 1417F5L


title: B26_fibroblast_UT_1

tag: cell type

tag: treatment


title: B26_neuron_H2O2_3

value: neuron

value: H2O2 treated for 17 hours


title: water column DNA_ETSP_Sample6_305m

tag: sample type

value: 20-mer DNA oligo

tag: location

value: Oxygen Minimum Zone nitrogen cycling experiments in the Eastern Tropical South Pacific Ocean


title: Sample 28: 1417F3L


title: water column DNA_ETSP_Sample5_75m

tag: depth


title: Control [33068]

description:
33068
DNA methylation data from whole blood samples of Taiwanese without Type-2 Diabetes.

value: Whole blood

value: not available

tag: population


title: Sample 27: 1417F2L

tag: tissue


title: B26_neuron_H2O2_2

tag: patient id

tag: condition

value: male


title: Control [33069]

description:
33069
DNA methylation data from whole blood samples of Taiwanese without Type-2 Diabetes.

tag: disease group

tag: phenotype

value: Taiwanese


title: Control [33067]

description:
33067
DNA methylation data from whole blood samples of Taiwanese without Type-2 Diabetes.

tag: blood glucose


title: water column DNA_ETSP_Sample4_220m

value: PCR fragment amplified from total DNA extract


title: Control [27237]

description:
27237
DNA methylation data from whole blood samples of Taiwanese without Type-2 Diabetes.


title: Control [27169]

description:
27169
DNA methylation data from whole blood samples of Taiwanese without Type-2 Diabetes.


title: B26_neuron_H2O2_1

tag: Sex


title: B26_neuron_UT_3

value: Untreated (UT)


title: water column DNA_ETSP_Sample1_350m


title: Control [27160]

description:
27160
DNA methylation data from whole blood samples of Taiwanese without Type-2 Diabetes.

tag: bmi (kg/m2)

value: female


title: Sample 24: 1412F2L

value: Longissimus dorsi muscle

tag: age

value: gestation day 77

tag: genotype

value: crossbred Iberian x Large White


title: Sample 26: 1417F1L


title: B26_neuron_UT_2

value: ASD +


title: Sample 23: 1410F6L

value: pure Iberian


title: B26_neuron_UT_1


title: water column DNA_ETSP_Sample2_300m


title: AK10_fibroblast_UT_3

value: fibroblast


title: 1394.1 Sample 2

city: Tampa

first: Derek

last: Wildman

state: FL

address: 3720 Spectrum Blvd

institute: University of South Florida

description:
Right; Disc 1
Z2129

data_processing:
low quality bases and adaptor sequences were trimmed
sequences were aligned to the marmoset genome using the bwa-meth R package
methylation status was determined using PileOMeth R pacakges
Genome_build: C_jacchus 3.2.1, verson 85 (GCA_000004665.1)

organism: Callithrix jacchus

source_name: placenta

extract_protocol:
genomic DNA was extracted using qiagen DNAeasy Blood and Tissue Kit
RRBS uses MspI which is a methylation insensitive restriction enzyme that recognizes CCGG sites. As MspI is insensitive to methylation status, all CCGG sites were cut between the two C's resulting in small fragments with a high frequency of potential CpG methylation sites. Following MspI digestion, the fragments underwent adaptor ligation, final repair, bisulfite conversion, and PCR amplification to produce the final libraries for sequencing. The 5 pools were sequenced on 5 lanes in the HiSeq 4000 (Illumina, San Diego, CA) with paired-end reads 100nt in length
RRBS Methyl-Seq System 1-16

tag: maternal weight day 60

tag: maternal weight day 90

tag: maternal weight day 120


title: 1427.1 Sample 1

description:
Right; Disc 1
Z2130


title: KC-L7-rep3

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Sequencing reads were aligned to genome assembly dm3 using Bowtie2 (version 2.2.9) with default parameters and “--local” to allow soft clipping of ends.
Alignments were further processed by SAMtools (version 0.1.19) to remove low quality alignments (“-q 10”), PCR duplicates (“rmdup -s”) and mitochondrial reads.
For visualization, each individual library was normalized to 10 million reads per library and then track for each library subtracting its corresponding Input control was generated using BEDtools (“genomecov”) and Deeptools (“bigwigCompare –ratio=subtract --binSize=10”).
BigWig files were then converted from bedgraph files using command "bedGraphToBigWig".
Genome_build: dm3
Supplementary_files_format_and_content: Bedgraph files were generated for each library using Bedtools 'genomecov' with scale normalized to 10 million reads per library. IgG were then subtracted from IP bedgraph files using Deeptools 'bigwigCompare'. Bigwig files were converted from bedgraph files.

organism: Drosophila melanogaster

source_name: embryonic cells

extract_protocol:
Lysates from embryonic cells or 3rd instar brains were clarified from sonicated nuclei and lamin-DNA complexes were isolated with specific antibody
Libraries were prepared according to Illumina's instructions for HiSeq 2000 for KC or S2 cells and NextSeq 500/550 High Output Kit when brains were analyzed.

tag: cell line

value: KC

tag: chip antibody

value: lamin L7 antibody

tag: genotype/variation

value: wild type


title: Sample 22: 1410F5L


title: water column DNA_ETSP_Sample3_260m

tag: sample type

value: 20-mer DNA oligo

tag: location

value: Oxygen Minimum Zone nitrogen cycling experiments in the Eastern Tropical South Pacific Ocean

tag: depth


title: 1466.2 Sample 2

description:
Central; Disc 1
Z2127


title: Sample 21: 1410F3L

tag: tissue


title: 1394.1 Sample 1

description:
Central; Disc 1
Z2128


title: Sample 19: 1410F1L


title: AK10_neuron_H2O2_2

tag: patient id

tag: condition

tag: cell type

value: neuron

tag: treatment

value: H2O2 treated for 17 hours


title: URB597_treated_cells

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: none provided by the submitter

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given RNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: HepG2 cells

label_protocol: none provided by the submitter

growth_protocol: DMEM supplemented with 10% FBS.

extract_protocol: RNeasy mini kit was used for the RNA extraction.

treatment_protocol: Control DMSO or URB597 treatment for 24 h was performed.

value: Liver carcinoma


title: KC-Input

description: control for KC libraries


title: Sample 20: 1410F2L

tag: Sex


title: KC-L7-rep2


title: 1427.1 Sample 2

description:
Central; Disc 1
Z2131


title: 1333.6 Sample 2

description:
Right; Disc 1
Z2123


title: 1466.2 Sample 1

description:
Central; Disc 2
Z2126


title: AK10_neuron_H2O2_1


title: DMSO_treated_cells


title: AK10_neuron_H2O2_3


title: KC-L7-rep1


title: 1333.6 Sample 1

description:
Central; Disc 1
Z2122


title: Sample 18: 1404F7L

tag: age

value: male


title: Sample 17: 1404F5L

tag: genotype


title: AK10_neuron_UT_3

value: Untreated (UT)


title: AK10_neuron_UT_2

value: female


title: 1357.3 Sample 2

description:
Right; Disc 1
Z2121

tag: maternal weight day 60


title: HEK293T cells_-NAEK_rpt2 (Ribo-seq)

city: Beijing

first: Yiming

last: Wu

state: Beijing

address: No 38 Xueyuan Road

department: Chemical Bilogy

country: China

institute: Peking University Health Science Center

description:
ribosome protected mRNA
Ribosome_profiling_of_transgenic_and_HEK293T_cells.xlsx

data_processing:
Library strategy: Ribo-Seq
UGENE software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 all transcripts using bowtie v1.2.2 with parameters -p 10 -l 25
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a python script. In short, the number of reads falling in the coding region of the transcript were counted and normalized by the length of the transcript and by the total number of the reads.
Genome_build: hg38
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample

source_name: HEK293T cells_-NAEK

extract_protocol: using TruSeq Ribo Profile kits (illumina)


title: Sample 16: 1404F3L

value: Longissimus dorsi muscle


title: AK10_neuron_UT_1


title: 1357.3 Sample 1

description:
Central; Disc 1
Z2120

tag: maternal weight day 90


title: HEK293T cells_+NAEK_rpt2 (Ribo-seq)

source_name: HEK293T cells_+NAEK

value: with the addition of 1mM NAEK


title: HEK293T cells_-NAEK_rpt1 (Ribo-seq)


title: Sample 15: 1404F2L

value: gestation day 77


title: Sample 14: 1404F1L


title: 1322.5 Sample 2

description:
Central; Disc 1
Z2119

tag: maternal weight day 120


title: HEK293T cells_+NAEK_rpt1 (Ribo-seq)

tag: cell line


title: Transgenic cells_-NAEK_rpt2 (Ribo-seq)

source_name: Transgenic cells_-NAEK

value: HEK293T cells stably transfected with Mb pyltRNA


title: Sample 13: 1401F8L

value: pure Iberian


title: 29-RKn16-dose10-041818-LNCD4

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the Rhesus macaque (MacaM v7) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf)
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Macaca mulatta

source_name: Sorted Lymph Node cells

extract_protocol:
RNA was purified from 50,000 peripheral blood or lymph node derived CD4+ T cells, which were purified by flow cytometry and lysed in in 350 μl of RLT buffer at −80°C, using Qiagen Micro RNEasy columns, and RNA quality was assessed using an Agilent Bioanalyzer.
Two nanograms of total RNA was used as input for mRNA amplification using 5′ template switch PCR with the Clontech SMART-Seq v4 ultra-low-input RNA kit according to manufacturer's instructions. Amplified mRNA was fragmented and appended with dual-indexed bar codes using Illumina NexteraXT DNA library preparation kits. Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled, and sequenced on an Illumina HiSeq 3000 using 100-bp SR at an average depth of 25 M reads.

treatment_protocol: AZD5582 was infused weekly intravenously at 0.1 mg/kg. Three RMs received 3 doses of AZD5582 and were sacrificed 48 h after the last dose. Three RMs received 10 doses of AZD5582 and were sacrificed 48 h after the last dose.

tag: subjectid

tag: sampletime


title: 28-RDm16-dose10-041818-LNCD4


title: Sample 12: 1401F7L

value: crossbred Iberian x Large White


title: 1269.1 Sample 2

description:
Central; Disc 1
Z2117


title: 27-RDl16-dose10-041818-LNCD4


title: Transgenic cells_+NAEK_rpt2 (Ribo-seq)

source_name: Transgenic cells_+NAEK


title: Sample 11: 1401F4L


title: Transgenic cells_-NAEK_rpt1 (Ribo-seq)


title: 1322.5 Sample 1

description:
Right; Disc 1
Z2118


title: 23-RLu16-dose3-022818-LNCD4


title: 1269.1 Sample 1

description:
Right; Disc 1
Z2116


title: 22-RNp16-dose3-022818-LNCD4


title: 1466.1 Sample 2

description:
Central; Disc 1
Z2113


title: Sample 9: 1401F1L


title: Transgenic cells_+NAEK_rpt1 (Ribo-seq)


title: GLOR07_1964-1980_WGBS

city: Milan

first: Federico

last: Rossi

address: Via Adamello 16

country: Italy

institute: Istituto Europeo Oncologia

data_processing:
base-calling
WGS alignment
Methylation call: Bismark version 0.19.0
Genome_build: Quercus robur
Supplementary_files_format_and_content: WGBS Coverage file in .txt format

organism: Quercus robur

source_name: Heartwood

extract_protocol:
Extraction of DNA by lysis buffer, chloroform purification and ethanol precipitation
Meyer and Kircher 2010 (WGS), adaptation of Meyer and Kircher 2010 (WGBS)

value: Heartwood

tag: time period

tag: sequencing type

value: WGBS


title: Sample 10: 1401F2L


title: Sample 8: 1340F9L


title: GLOR07_1990-2014_WGBS

source_name: Sapwood

value: Sapwood


title: 1338.3 Sample 2

description:
Central; Disc 1
Z2111


title: GLOR03_1962-1972_WGBS


title: 1466.1 Sample 1

description:
Right; Disc 2
Z2112


title: Sample 7: 1340F8L


title: 11-RKn16-preLRA-012318-LNCD4

value: preLRA


title: 21-RFk16-dose3-022818-LNCD4


title: 1338.3 Sample 1

description:
Right; Disc 1
Z2110


title: GLOR03_1980-2013_WGBS


title: Sample 6: 1340F7L


title: GLOR07_1902-1915_WGS

data_processing:
Library strategy: DNA-seq
base-calling
WGS alignment
Methylation call: Bismark version 0.19.0
Genome_build: Quercus robur
Supplementary_files_format_and_content: WGBS Coverage file in .txt format

value: WGS


title: 10-RDl16-preLRA-012318-LNCD4


title: Sample 5: 1340F5L


title: 1466.3 Sample 2

description:
Right; Disc 1
Z2109


title: 1466.3 Sample 1

description:
Central; Disc 2
Z2108


title: Sample 4: 1338F6L


title: GLOR07_1934-1943_WGS


title: 1357.5 Sample 2

description:
Right; Disc 1
Z2107


title: 9-RLu16-preLRA-013118-LNCD4


title: 8-RNp16-preLRA-013118-LNCD4


title: Sample 3: 1338F4L


title: GLOR07_1990-2014_WGS


title: 7-RFk16-preLRA-013118-LNCD4


title: 12-RDm16-preLRA-012318-LNCD4


title: Sample 2: 1338F3L


title: 1322.2 Sample 2

description:
Right; Disc 1
Z2105


title: GLOR03_1962-1972_WGS


title: 26-RKn16-dose10-041818-pCD4

source_name: Sorted peripheral cells


title: 25-RDm16-dose10-041818-pCD4


title: 1322.2 Sample 1

description:
Central; Disc 1
Z2104


title: GLOR03_1980-2013_WGS


title: 24-RDl16-dose10-041818-pCD4


title: 1241.2 Sample 2

description:
Central; Disc 2
Z2103


title: GLOR02_1800-1805_WGS


title: Psojae_WT_MY_H3K4me2

city: Nanjing

first: Haidong

last: Shu

state: Jiangsu

address: Weigang NO.1

department: Department of Plant Pathology

institute: Nanjing Agricultural University

data_processing:
Clean reads were aligned to Psojae genome using bowtie2 v2.3.3.1 with parameter -N 1
Bigwig files were generated by DeepTools "bamCompare" using --normalizeUsing RPKM --scaleFactorsMethod None
Genome_build: Psojae2019.1
Supplementary_files_format_and_content: Bigwig files, scores represent enriched value(log2(fold-change))

organism: Phytophthora sojae

source_name: centromeres

growth_protocol: V8 medium

extract_protocol:
After antibody Immunoprecipitation, target DNA was eluted from Dynabeads and precipitated using ethanol followed by twice washes, finally the samples was dried and dissolved in 33 μl ddH2O
Qualified library for sequencing was prepared using the QIAquick PCR Purification Kit(Qiagen). Briefly, 10-300ng DNA was taken to do DNA-end repair(3'-dA overhang and ligation of methylated sequencing adaptors) followed by PCR amplication and size selection (usually 100-300bp, including adaptor sequencing).

tag: strain

value: mycelium

tag: chip antibody


title: 20-RLu16-dose3-022818-pCD4


title: 1241.2 Sample 1

description:
Right; Disc 1
Z2102


title: Psojae_WT_MY_H3K9me3_rep2

tag: tissue


title: Psojae_WT_MY_H3K9me3_rep1


title: GLOR02_1925-1940_WGS


title: 1261.3 Sample 2

description:
Right; Disc 1
Z2101


title: GLOR07_1964-1980_WGS


title: 1357.5 Sample 1

description:
Central; Disc 2
Z2106


title: GLOR01_1811-1815_WGS


title: 1333.4 Sample 2

description:
Right; Disc 1
Z2099


title: 1261.3 Sample 1

description:
Central; Disc 1
Z2100


title: Sample 1: 1338F2L


title: GLOR02_1996-2014_WGS


title: 6-RDm16-preLRA-012318-pCD4


title: Sample 25: 1412F5L


title: GLOR01_1816-1820_WGS


title: 5-RKn16-preLRA-012318-pCD4


title: Invivomyocardium_obesity_replicate 3

city: Shenyang

state: Liaoning

address: 155th North of Nanjing Street

institute: The first affiliated hospital of China Medical University

description: microRNA expression in myocardium of rat fed high-fat diet

hyb_protocol: Array hybridization was performed according to the Agilent miRNA Microarray Systemwith miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology). Briefly,55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent Microarray Scanner (part number 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 v14.9 software package (Agilent Technologies). After quantile normalization of the raw data, miRNAs that at least 3 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed miRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed miRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts.

organism: Rattus norvegicus

source_name: Invivo myocardium_obesity_replicate 3

label_protocol: Sample labeling was performed according to the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit protocol (Agilent Technology). Briefly, total miRNA from each sample was labeled with Cyanine 3-pCp under the action of T4 RNA ligase. The labeled cRNA over the procession of  inspissation and desiccation and then redissolved with water. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min.

extract_protocol: Total RNA was isolated with Trizolreagent(Takara) following the manufacturer's recommendations. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Wistar rats were randomly divided into two groups, which feed normal chow or high-fat diet for 20 weeks, respectively.

value: Wistar

value: Left ventricular myocardium

tag: gender

value: Male

tag: diet

value: high-fat diet


title: 1333.4 Sample 1

description:
Central; Disc 1
Z2098


title: 19-RNp16-dose3-022818-pCD4

tag: cell type


title: GLOR01_1950-1960_WGS


title: Invivomyocardium_obesity_replicate 1

source_name: Invivo myocardium_obesity_replicate 1


title: Invivomyocardium_normal_replicate 3

description: microRNA expression in myocardium of rat fed normal diet

source_name: Invivo myocardium_normal_replicate 3

value: normal chow


title: 3-RLu16-preLRA-013118-pCD4


title: GLOR01_1970-1980_WGS


title: GLOR01_1821-1830_WGS


title: 1261.1 Sample 2

description:
Central; Disc 1
Z2097


title: 4-RDl16-preLRA-012318-pCD4


title: GLOR01_2000-2014_WGS


title: 1333.5 Sample 2

description:
Right; Disc 2
Z2095


title: 1333.5 Sample 1

description:
Central; Disc 2
Z2094


title: Invivomyocardium_obesity_replicate 2

source_name: Invivo myocardium_obesity_replicate 2


title: Invivomyocardium_normal_replicate 2

source_name: Invivo myocardium_normal_replicate 2


title: Histone ChIP-seq from Peyer's patch (ENCLB427IMW)

status: Public on Jan 06 2020

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR998QKF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR998QKF
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR118FQN
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB427IMW
fragmentation methods: sonication (generic)
size range: 200-600

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

source_name: Homo sapiens male adult (54 years) Peyer's patch tissue

tag: antibody

value: Peyer's patch

value: tissue

tag: description

value: EnTEX:Small Intestine - Terminal Ileum

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

value: 54 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Kristin Ardlie

tag: link

value: ENCBS524MUK at ENCODE; https://www.encodeproject.org/ENCBS524MUK/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from tibial nerve (ENCLB509CNE)

description:
https://www.encodeproject.org/experiments/ENCSR992XOO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR992XOO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR059VTG
encode release date: 2019-02-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB509CNE
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) tibial nerve tissue

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: female

tag: age

value: 51 year

value: ENCBS925LQY at ENCODE; https://www.encodeproject.org/ENCBS925LQY/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Histone ChIP-seq from Peyer's patch (ENCLB510UFQ)

description:
https://www.encodeproject.org/experiments/ENCSR998QKF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR998QKF
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR118FQN
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB510UFQ
fragmentation methods: sonication (generic)
size range: 200-600


title: 18-RFk16-dose3-022818-pCD4

tag: subjectid

tag: sampletime


title: Histone ChIP-seq from tibial nerve (ENCLB668DFA)

description:
https://www.encodeproject.org/experiments/ENCSR992XOO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR992XOO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR059VTG
encode release date: 2019-02-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB668DFA
fragmentation methods: sonication (generic)
size range: 200-600


title: Control ChIP-seq from stomach (ENCLB182BCR)

description:
https://www.encodeproject.org/experiments/ENCSR962EJE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR962EJE
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB182BCR
size range: 200-600

source_name: Homo sapiens male adult (54 years) stomach tissue

value: stomach

value: ENCBS443LLE at ENCODE; https://www.encodeproject.org/ENCBS443LLE/


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB051VTH)

description:
https://www.encodeproject.org/experiments/ENCSR960UYN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR960UYN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR514EZP
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB051VTH
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: tissue

value: EnTEX:Esophagus - Mucosa

value: ENCBS467KQD at ENCODE; https://www.encodeproject.org/ENCBS467KQD/


title: Control ChIP-seq from stomach (ENCLB741WLI)

description:
https://www.encodeproject.org/experiments/ENCSR962EJE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR962EJE
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB741WLI
size range: 200-600

value: male

value: adult

value: 54 year


title: Hi-C seq

city: Bonn

first: Katrin

last: Paeschke

address: Sigmund Freud Str. 25

department: Department of Oncology, Hematology and Rheumatology

country: Germany

institute: University Hospital Bonn

description: crosslinked DpnII digested DNA

data_processing:
Paired-end sequencing reads were mapped independently to the genome of Saccharomyces cerevisiae S288C (NCBI Primary Assembly: GCF_000146055.2) using Bowtie 2.3.5 and an algorithm which iteratively increases truncation length to maximize yield of valid Hi-C interactions. Only read pairs with both reads uniquely aligned to the genome were considered for subsequent steps. The S. cerevisiae genome was then divided into restriction fragments produced by the restriction enzyme DpnII. Each read of a read pair was sorted into its corresponding restriction fragment. Read pairs were classified as valid Hi-C products, non-ligation, or self-ligation products; only valid Hi-C products were considered below.
To create interaction matrices, the S. cerevisiae genome was first divided into bins of length 10 kbp. We then assigned valid Hi-C products to the bins proportional to their overlap, i.e. each read contributes a count of one to the contact map, but it can be split between bins. As raw Hi-C contact frequency maps are biased due to the uneven distribution of restriction enzyme sites, differences in GC content and the mappability of individual reads, we normalized raw contact maps using the Sinkhorn-Knopp balancing algorithm [1]. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using Python and R scripts.
Genome_build: Saccharomyces cerevisiae S288C (NCBI Primary Assembly: GCF_000146055.2)

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: S. cerevisiae cells were grown in YPD (1% Yeast extract, 2% Peptone, 2% Glucose) to exponential phase at 30 °C, 250 rpm

extract_protocol:
Snap freezed cells were thawed, processed with the Hi-C protocol and the resulting DNA was extracted using phenol-chloroform extraction methods before sequencing
Biotinylated fragments were enriched using streptavidin magnetic beads (C1), DNA ends were A-tailed and NextFlex (Bioo Scientific) barcoded adapters were ligated while the DNA was on the beads. Resulting libraries were minimally amplified by PCR and sequenced using paired end 75 bp reads on a NextSeq550 (Illumina; Brighton Genomics).

treatment_protocol: untreated sample

tag: strain

tag: Stage

value: exponential


title: 1261.1 Sample 1

description:
Right; Disc 1
Z2096

source_name: placenta

tag: maternal weight day 60

tag: maternal weight day 90

tag: maternal weight day 120


title: Histone ChIP-seq from testis (ENCLB241RGN)

description:
https://www.encodeproject.org/experiments/ENCSR956VQB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR956VQB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR215WNN
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB241RGN
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) testis tissue

value: testis

value: 37 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS631HJF at ENCODE; https://www.encodeproject.org/ENCBS631HJF/

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


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB793FWQ)

description:
https://www.encodeproject.org/experiments/ENCSR960UYN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR960UYN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR514EZP
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB793FWQ
fragmentation methods: sonication (generic)
size range: 200-600

value: female

value: 51 year

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Histone ChIP-seq from testis (ENCLB423OLQ)

description:
https://www.encodeproject.org/experiments/ENCSR956VQB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR956VQB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR215WNN
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB423OLQ
fragmentation methods: sonication (generic)
size range: 200-600


title: Histone ChIP-seq from testis (ENCLB378KWP)

description:
https://www.encodeproject.org/experiments/ENCSR954IGQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR954IGQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR385ODY
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB378KWP
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) testis tissue

value: ENCBS849BBS at ENCODE; https://www.encodeproject.org/ENCBS849BBS/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from testis (ENCLB077BNF)

description:
https://www.encodeproject.org/experiments/ENCSR954IGQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR954IGQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR385ODY
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB077BNF
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: Histone ChIP-seq from upper lobe of left lung (ENCLB779TPX)

description:
https://www.encodeproject.org/experiments/ENCSR948TOS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR948TOS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR774MLK
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB779TPX
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) upper lobe of left lung tissue

value: upper lobe of left lung

value: ENCBS401SWW at ENCODE; https://www.encodeproject.org/ENCBS401SWW/


title: Control ChIP-seq from stomach (ENCLB901MAO)

description:
https://www.encodeproject.org/experiments/ENCSR948DNK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR948DNK
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB901MAO
size range: 200-600

source_name: Homo sapiens female adult (51 year) stomach tissue

value: stomach

value: adult

value: ENCBS633XWN at ENCODE; https://www.encodeproject.org/ENCBS633XWN/


title: Control ChIP-seq from stomach (ENCLB079JPN)

description:
https://www.encodeproject.org/experiments/ENCSR948DNK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR948DNK
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB079JPN
size range: 200-600


title: 2-RNp16-preLRA-013118-pCD4

source_name: Sorted peripheral cells

tag: cell type

value: preLRA


title: Invivomyocardium_normal_replicate 1

source_name: Invivo myocardium_normal_replicate 1

value: Wistar

tag: tissue

value: Left ventricular myocardium

tag: gender

value: Male

tag: diet

value: normal chow


title: Histone ChIP-seq from thyroid gland (ENCLB814UNT)

description:
https://www.encodeproject.org/experiments/ENCSR942UIL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR942UIL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR347VUG
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB814UNT
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) thyroid gland tissue

tag: antibody

value: thyroid gland

tag: description

tag: biosample encode accession

tag: Sex

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS541DMP at ENCODE; https://www.encodeproject.org/ENCBS541DMP/


title: Histone ChIP-seq from thyroid gland (ENCLB558BYX)

description:
https://www.encodeproject.org/experiments/ENCSR942UIL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR942UIL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR347VUG
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB558BYX
fragmentation methods: sonication (generic)
size range: 200-600

value: female

tag: dev stage

value: 51 year

tag: lab

tag: source

tag: link

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: 1-RFk16-preLRA-013118-pCD4

tag: subjectid

tag: sampletime


title: Histone ChIP-seq from sigmoid colon (ENCLB910KQF)

description:
https://www.encodeproject.org/experiments/ENCSR937EVN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR937EVN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR524NCH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB910KQF
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) sigmoid colon tissue

value: sigmoid colon

value: tissue

value: EnTEX:Colon - Sigmoid

value: male

tag: age

value: 54 year

value: ENCBS243UXH at ENCODE; https://www.encodeproject.org/ENCBS243UXH/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from upper lobe of left lung (ENCLB163YYP)

description:
https://www.encodeproject.org/experiments/ENCSR948TOS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR948TOS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR774MLK
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB163YYP
fragmentation methods: sonication (generic)
size range: 200-600

value: upper lobe of left lung

value: adult

value: ENCBS401SWW at ENCODE; https://www.encodeproject.org/ENCBS401SWW/


title: Histone ChIP-seq from sigmoid colon (ENCLB038ESU)

description:
https://www.encodeproject.org/experiments/ENCSR937EVN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR937EVN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR524NCH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB038ESU
fragmentation methods: none
size range: 200-600


title: Histone ChIP-seq from thyroid gland (ENCLB460FLA)

description:
https://www.encodeproject.org/experiments/ENCSR942UIL/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR942UIL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR347VUG
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB460FLA
fragmentation methods: sonication (generic)
size range: 200-600

value: thyroid gland


title: Histone ChIP-seq from Peyer's patch (ENCLB748AAL)

description:
https://www.encodeproject.org/experiments/ENCSR927PLE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR927PLE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR118FQN
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB748AAL
fragmentation methods: sonication (generic)
size range: 200-600

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum

value: Bradley Bernstein, Broad

value: ENCBS524MUK at ENCODE; https://www.encodeproject.org/ENCBS524MUK/


title: Histone ChIP-seq from Peyer's patch (ENCLB976IKV)

description:
https://www.encodeproject.org/experiments/ENCSR927PLE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR927PLE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR118FQN
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB976IKV
fragmentation methods: sonication (generic)
size range: 200-600

value: Kristin Ardlie


title: Histone ChIP-seq from tibial nerve (ENCLB971LWT)

description:
https://www.encodeproject.org/experiments/ENCSR925FSB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR925FSB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR152HLZ
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB971LWT
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) tibial nerve tissue

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: ENCBS952IFF at ENCODE; https://www.encodeproject.org/ENCBS952IFF/


title: Histone ChIP-seq from Peyer's patch (ENCLB056LAF)

description:
https://www.encodeproject.org/experiments/ENCSR912XAL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR912XAL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR118FQN
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB056LAF
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: Histone ChIP-seq from tibial nerve (ENCLB553FLQ)

description:
https://www.encodeproject.org/experiments/ENCSR925FSB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR925FSB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR152HLZ
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB553FLQ
fragmentation methods: sonication (generic)
size range: 200-600

value: male


title: Histone ChIP-seq from sigmoid colon (ENCLB450JWE)

description:
https://www.encodeproject.org/experiments/ENCSR860GPM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR860GPM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR524NCH
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB450JWE
fragmentation methods: none
size range: 200-600

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: 54 year


title: TF ChIP-seq from sigmoid colon (ENCLB065DVC)

description:
https://www.encodeproject.org/experiments/ENCSR857RJQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR857RJQ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR524NCH
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB065DVC
fragmentation methods: none
size range: 200-600

value: CTCF

value: ENCBS243UXH at ENCODE; https://www.encodeproject.org/ENCBS243UXH/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from Peyer's patch (ENCLB585EHV)

description:
https://www.encodeproject.org/experiments/ENCSR874HIG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR874HIG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773UBR
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB585EHV
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) Peyer's patch tissue

value: female

value: adult

value: 51 year

value: ENCBS654VYQ at ENCODE; https://www.encodeproject.org/ENCBS654VYQ/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Histone ChIP-seq from ovary (ENCLB788ZAR)

description:
https://www.encodeproject.org/experiments/ENCSR828CCQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR828CCQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR509SEX
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB788ZAR
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (53 years) ovary tissue

value: ovary

value: 53 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS760QKF at ENCODE; https://www.encodeproject.org/ENCBS760QKF/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: Histone ChIP-seq from ovary (ENCLB914WUS)

description:
https://www.encodeproject.org/experiments/ENCSR828CCQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR828CCQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR509SEX
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB914WUS
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: AK10_fibroblast_UT_2

source_name: fibroblast

tag: patient id

tag: condition

value: ASD +

value: fibroblast

tag: treatment

value: Untreated (UT)


title: Control ChIP-seq from stomach (ENCLB255DFS)

description:
https://www.encodeproject.org/experiments/ENCSR948DNK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR948DNK
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB255DFS
size range: 200-600

value: stomach

value: ENCBS728IMD at ENCODE; https://www.encodeproject.org/ENCBS728IMD/


title: TF ChIP-seq from sigmoid colon (ENCLB872PQX)

description:
https://www.encodeproject.org/experiments/ENCSR857RJQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR857RJQ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR524NCH
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB872PQX
fragmentation methods: none
size range: 200-600

value: CTCF

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: male

value: 54 year

value: ENCBS243UXH at ENCODE; https://www.encodeproject.org/ENCBS243UXH/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from transverse colon (ENCLB842MMP)

description:
https://www.encodeproject.org/experiments/ENCSR813ZEY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR813ZEY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB842MMP
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) transverse colon tissue

value: transverse colon

value: EnTEX:Colon - Transverse

value: adult

value: 37 year

value: Bradley Bernstein, Broad

value: ENCBS816BKF at ENCODE; https://www.encodeproject.org/ENCBS816BKF/

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


title: Control ChIP-seq from spleen (ENCLB712BAM)

description:
https://www.encodeproject.org/experiments/ENCSR803JPO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR803JPO
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB712BAM
size range: 200-600

source_name: Homo sapiens male adult (54 years) spleen tissue

value: spleen

value: tissue

value: Kristin Ardlie

value: ENCBS223WIE at ENCODE; https://www.encodeproject.org/ENCBS223WIE/


title: Histone ChIP-seq from transverse colon (ENCLB622VNP)

description:
https://www.encodeproject.org/experiments/ENCSR792VLP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR792VLP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR384KIB
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB622VNP
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) transverse colon tissue

value: female

value: 51 year

value: ENCBS555CAN at ENCODE; https://www.encodeproject.org/ENCBS555CAN/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: TF ChIP-seq from tibial nerve (ENCLB173UHP)

description:
https://www.encodeproject.org/experiments/ENCSR793YAD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR793YAD
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR059VTG
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB173UHP
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) tibial nerve tissue

value: CTCF

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: ENCBS925LQY at ENCODE; https://www.encodeproject.org/ENCBS925LQY/


title: Control ChIP-seq from spleen (ENCLB204BTF)

description:
https://www.encodeproject.org/experiments/ENCSR803JPO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR803JPO
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB204BTF
size range: 200-600

value: male

value: adult

value: 54 year

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from transverse colon (ENCLB516EST)

description:
https://www.encodeproject.org/experiments/ENCSR813ZEY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR813ZEY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB516EST
fragmentation methods: sonication (generic)
size range: 200-600

value: transverse colon

value: EnTEX:Colon - Transverse

value: 37 year

value: Bradley Bernstein, Broad

value: ENCBS816BKF at ENCODE; https://www.encodeproject.org/ENCBS816BKF/

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


title: Histone ChIP-seq from Peyer's patch (ENCLB089NVL)

description:
https://www.encodeproject.org/experiments/ENCSR912XAL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR912XAL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR118FQN
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB089NVL
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) Peyer's patch tissue

value: Peyer's patch

value: tissue

value: EnTEX:Small Intestine - Terminal Ileum

value: Kristin Ardlie

value: ENCBS524MUK at ENCODE; https://www.encodeproject.org/ENCBS524MUK/


title: Histone ChIP-seq from sigmoid colon (ENCLB316ILZ)

description:
https://www.encodeproject.org/experiments/ENCSR792EDG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR792EDG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR316ZPQ
encode release date: 2019-02-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB316ILZ
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) sigmoid colon tissue

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: female

value: 51 year

value: ENCBS474RXX at ENCODE; https://www.encodeproject.org/ENCBS474RXX/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Histone ChIP-seq from sigmoid colon (ENCLB686WHW)

description:
https://www.encodeproject.org/experiments/ENCSR792EDG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR792EDG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR316ZPQ
encode release date: 2019-02-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB686WHW
fragmentation methods: sonication (generic)
size range: 200-600

value: adult


title: TF ChIP-seq from gastroesophageal sphincter (ENCLB737WRB)

description:
https://www.encodeproject.org/experiments/ENCSR805YLE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR805YLE
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR728EIP
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB737WRB
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) gastroesophageal sphincter tissue

value: CTCF

value: gastroesophageal sphincter

value: EnTEX:Esophagus - Gastroesophageal Junction

value: male

value: 54 year

value: ENCBS542QYP at ENCODE; https://www.encodeproject.org/ENCBS542QYP/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from spleen (ENCLB551NYK)

description:
https://www.encodeproject.org/experiments/ENCSR787YHR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR787YHR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR803JPO
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB551NYK
fragmentation methods: none
size range: 200-600

value: spleen

value: tissue

value: Bradley Bernstein, Broad

value: ENCBS223WIE at ENCODE; https://www.encodeproject.org/ENCBS223WIE/


title: Histone ChIP-seq from sigmoid colon (ENCLB422EEX)

description:
https://www.encodeproject.org/experiments/ENCSR860GPM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR860GPM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR524NCH
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB422EEX
fragmentation methods: sonication (generic)
size range: 200-600

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: Kristin Ardlie

value: ENCBS243UXH at ENCODE; https://www.encodeproject.org/ENCBS243UXH/


title: Histone ChIP-seq from stomach (ENCLB050HCI)

description:
https://www.encodeproject.org/experiments/ENCSR787TQW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR787TQW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR948DNK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB050HCI
fragmentation methods: sonication (generic)
size range: 200-600

value: stomach

value: female

value: 51 year

value: ENCBS633XWN at ENCODE; https://www.encodeproject.org/ENCBS633XWN/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Histone ChIP-seq from tibial nerve (ENCLB088CVE)

description:
https://www.encodeproject.org/experiments/ENCSR778QHG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR778QHG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR059VTG
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB088CVE
fragmentation methods: sonication (generic)
size range: 200-600

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: adult

value: ENCBS925LQY at ENCODE; https://www.encodeproject.org/ENCBS925LQY/


title: Control ChIP-seq from esophagus muscularis mucosa (ENCLB508MVA)

description:
https://www.encodeproject.org/experiments/ENCSR777AJC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR777AJC
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB508MVA
size range: 200-600

source_name: Homo sapiens male adult (54 years) esophagus muscularis mucosa tissue

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis

value: male

value: 54 year

value: ENCBS390MKW at ENCODE; https://www.encodeproject.org/ENCBS390MKW/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from stomach (ENCLB673EZV)

description:
https://www.encodeproject.org/experiments/ENCSR787TQW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR787TQW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR948DNK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB673EZV
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) stomach tissue

value: tissue

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: Histone ChIP-seq from sigmoid colon (ENCLB322ESQ)

description:
https://www.encodeproject.org/experiments/ENCSR774NRD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR774NRD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR524NCH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB322ESQ
fragmentation methods: none
size range: 200-600

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: ENCBS243UXH at ENCODE; https://www.encodeproject.org/ENCBS243UXH/


title: Control ChIP-seq from upper lobe of left lung (ENCLB763VML)

description:
https://www.encodeproject.org/experiments/ENCSR774MLK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR774MLK
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB763VML
size range: 200-600

source_name: Homo sapiens male adult (54 years) upper lobe of left lung tissue

value: upper lobe of left lung

value: ENCBS401SWW at ENCODE; https://www.encodeproject.org/ENCBS401SWW/


title: Control ChIP-seq from upper lobe of left lung (ENCLB721DHS)

description:
https://www.encodeproject.org/experiments/ENCSR774MLK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR774MLK
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB721DHS
size range: 200-600


title: Histone ChIP-seq from sigmoid colon (ENCLB830VEE)

description:
https://www.encodeproject.org/experiments/ENCSR774NRD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR774NRD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR524NCH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB830VEE
fragmentation methods: sonication (generic)
size range: 200-600


title: Histone ChIP-seq from sigmoid colon (ENCLB696EYJ)

description:
https://www.encodeproject.org/experiments/ENCSR775LGE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR775LGE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR524NCH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB696EYJ
fragmentation methods: none
size range: 200-600


title: TF ChIP-seq from gastroesophageal sphincter (ENCLB141CAO)

description:
https://www.encodeproject.org/experiments/ENCSR805YLE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR805YLE
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR728EIP
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB141CAO
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: gastroesophageal sphincter

value: EnTEX:Esophagus - Gastroesophageal Junction

value: ENCBS542QYP at ENCODE; https://www.encodeproject.org/ENCBS542QYP/


title: Control ChIP-seq from Peyer's patch (ENCLB970KCB)

description:
https://www.encodeproject.org/experiments/ENCSR773UBR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR773UBR
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB970KCB
size range: 200-600

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum

value: female

value: adult

value: 51 year

value: ENCBS654VYQ at ENCODE; https://www.encodeproject.org/ENCBS654VYQ/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Histone ChIP-seq from Peyer's patch (ENCLB761SKM)

description:
https://www.encodeproject.org/experiments/ENCSR874HIG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR874HIG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773UBR
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB761SKM
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: TF ChIP-seq from tibial nerve (ENCLB977AZM)

description:
https://www.encodeproject.org/experiments/ENCSR793YAD/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR793YAD
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR059VTG
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB977AZM
fragmentation methods: sonication (generic)
size range: 200-600

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: ENCBS925LQY at ENCODE; https://www.encodeproject.org/ENCBS925LQY/


title: Control ChIP-seq from esophagus muscularis mucosa (ENCLB993GLS)

description:
https://www.encodeproject.org/experiments/ENCSR777AJC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR777AJC
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB993GLS
size range: 200-600

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis

value: male

value: 54 year

value: ENCBS390MKW at ENCODE; https://www.encodeproject.org/ENCBS390MKW/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Control ChIP-seq from Peyer's patch (ENCLB797UXD)

description:
https://www.encodeproject.org/experiments/ENCSR773UBR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR773UBR
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-07-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB797UXD
size range: 200-600

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum

value: female


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB744OYE)

description:
https://www.encodeproject.org/experiments/ENCSR773PIU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR773PIU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR514EZP
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB744OYE
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa

value: adult

value: 51 year

value: ENCBS821VGX at ENCODE; https://www.encodeproject.org/ENCBS821VGX/


title: Histone ChIP-seq from transverse colon (ENCLB932PHE)

description:
https://www.encodeproject.org/experiments/ENCSR792VLP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR792VLP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR384KIB
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB932PHE
fragmentation methods: sonication (generic)
size range: 200-600

value: transverse colon

value: tissue

value: EnTEX:Colon - Transverse

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS555CAN at ENCODE; https://www.encodeproject.org/ENCBS555CAN/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB181JVQ)

description:
https://www.encodeproject.org/experiments/ENCSR773PIU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR773PIU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR514EZP
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB181JVQ
fragmentation methods: none
size range: 200-600


title: Histone ChIP-seq from spleen (ENCLB756CFA)

description:
https://www.encodeproject.org/experiments/ENCSR787YHR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR787YHR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR803JPO
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB756CFA
fragmentation methods: sonication (generic)
size range: 200-600

value: spleen

value: male

value: 54 year

value: ENCBS223WIE at ENCODE; https://www.encodeproject.org/ENCBS223WIE/


title: Histone ChIP-seq from transverse colon (ENCLB886CSH)

description:
https://www.encodeproject.org/experiments/ENCSR813ZEY/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR813ZEY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB886CSH
fragmentation methods: sonication (generic)
size range: 200-600

extract_protocol: not provided

value: 37 year

value: ENCBS990XOM at ENCODE; https://www.encodeproject.org/ENCBS990XOM/

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


title: Histone ChIP-seq from Peyer's patch (ENCLB992IRA)

description:
https://www.encodeproject.org/experiments/ENCSR758KRK/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR758KRK
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR118FQN
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB992IRA
fragmentation methods: sonication (generic)
size range: 200-600

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum

value: adult

value: ENCBS524MUK at ENCODE; https://www.encodeproject.org/ENCBS524MUK/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: TF ChIP-seq from esophagus squamous epithelium (ENCLB714ISJ)

description:
https://www.encodeproject.org/experiments/ENCSR756URL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR756URL
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR652EPR
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB714ISJ
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens esophagus squamous epithelium tissue female adult (53 years)

value: CTCF

value: esophagus squamous epithelium

value: tissue

value: EnTEX:Esophagus - Mucosa

value: female

value: 53 year

value: ENCBS054JUC at ENCODE; https://www.encodeproject.org/ENCBS054JUC/

value: Derived from ENCODE donor ENCDO793LXB; https://www.encodeproject.org/ENCDO793LXB/


title: Histone ChIP-seq from tibial nerve (ENCLB669CWD)

description:
https://www.encodeproject.org/experiments/ENCSR778QHG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR778QHG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR059VTG
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB669CWD
fragmentation methods: sonication (generic)
size range: 200-600

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: 51 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS925LQY at ENCODE; https://www.encodeproject.org/ENCBS925LQY/

value: Derived from ENCODE donor ENCDO271OUW; https://www.encodeproject.org/ENCDO271OUW/


title: TF ChIP-seq from esophagus squamous epithelium (ENCLB500FGN)

description:
https://www.encodeproject.org/experiments/ENCSR756URL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR756URL
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR652EPR
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB500FGN
fragmentation methods: sonication (generic)
size range: 200-600

value: adult


title: Histone ChIP-seq from stomach (ENCLB015HXE)

description:
https://www.encodeproject.org/experiments/ENCSR751BHO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR751BHO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR948DNK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB015HXE
fragmentation methods: sonication (generic)
size range: 200-600

value: stomach

value: ENCBS633XWN at ENCODE; https://www.encodeproject.org/ENCBS633XWN/


title: TF ChIP-seq from testis (ENCLB557BPF)

description:
https://www.encodeproject.org/experiments/ENCSR753RME/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR753RME
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR215WNN
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB557BPF
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (37 years) testis tissue

value: CTCF

value: testis

value: male

value: 37 year

value: ENCBS631HJF at ENCODE; https://www.encodeproject.org/ENCBS631HJF/

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


title: TF ChIP-seq from testis (ENCLB572UIS)

description:
https://www.encodeproject.org/experiments/ENCSR753RME/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR753RME
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR215WNN
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB572UIS
fragmentation methods: none
size range: 200-600

value: tissue


title: Histone ChIP-seq from sigmoid colon (ENCLB214OYH)

description:
https://www.encodeproject.org/experiments/ENCSR775LGE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR775LGE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR524NCH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB214OYH
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) sigmoid colon tissue

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: 54 year

value: ENCBS243UXH at ENCODE; https://www.encodeproject.org/ENCBS243UXH/

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from stomach (ENCLB552OGG)

description:
https://www.encodeproject.org/experiments/ENCSR751BHO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR751BHO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR948DNK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB552OGG
fragmentation methods: sonication (generic)
size range: 200-600

value: female

value: 51 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: Histone ChIP-seq from transverse colon (ENCLB752BTM)

description:
https://www.encodeproject.org/experiments/ENCSR749ABB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR749ABB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB752BTM
fragmentation methods: sonication (generic)
size range: 200-600

value: transverse colon

value: EnTEX:Colon - Transverse

value: adult

value: ENCBS816BKF at ENCODE; https://www.encodeproject.org/ENCBS816BKF/


title: Histone ChIP-seq from Peyer's patch (ENCLB946JAO)

description:
https://www.encodeproject.org/experiments/ENCSR735VKO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR735VKO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR118FQN
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB946JAO
fragmentation methods: sonication (generic)
size range: 200-600

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum

value: male

value: ENCBS524MUK at ENCODE; https://www.encodeproject.org/ENCBS524MUK/


title: Histone ChIP-seq from transverse colon (ENCLB707WDM)

description:
https://www.encodeproject.org/experiments/ENCSR749ABB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR749ABB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB707WDM
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: 37 year

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


title: Control ChIP-seq from gastroesophageal sphincter (ENCLB282HQK)

description:
https://www.encodeproject.org/experiments/ENCSR728EIP/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR728EIP
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB282HQK
size range: 200-600

value: gastroesophageal sphincter

value: EnTEX:Esophagus - Gastroesophageal Junction

value: 54 year

value: ENCBS542QYP at ENCODE; https://www.encodeproject.org/ENCBS542QYP/


title: Control ChIP-seq from gastroesophageal sphincter (ENCLB846YFY)

description:
https://www.encodeproject.org/experiments/ENCSR728EIP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR728EIP
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB846YFY
size range: 200-600

value: Bradley Bernstein, Broad

value: Derived from ENCODE donor ENCDO451RUA; https://www.encodeproject.org/ENCDO451RUA/


title: Histone ChIP-seq from tibial nerve (ENCLB172KZR)

description:
https://www.encodeproject.org/experiments/ENCSR726EEM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR726EEM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR152HLZ
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB172KZR
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) tibial nerve tissue

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: Kristin Ardlie

value: ENCBS952IFF at ENCODE; https://www.encodeproject.org/ENCBS952IFF/


title: Histone ChIP-seq from tibial nerve (ENCLB829WNN)

description:
https://www.encodeproject.org/experiments/ENCSR726EEM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR726EEM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR152HLZ
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB829WNN
fragmentation methods: sonication (generic)
size range: 200-600

value: adult


title: Histone ChIP-seq from Peyer's patch (ENCLB706DPE)

description:
https://www.encodeproject.org/experiments/ENCSR718LSM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR718LSM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR118FQN
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB706DPE
fragmentation methods: sonication (generic)
size range: 200-600

value: Peyer's patch

value: EnTEX:Small Intestine - Terminal Ileum