title: Fall'13 Day 42 Control Illinois Heart Fat 1113


title: GFP-H3.Y replicate 1

status: Public on Mar 13 2017

type: SRA

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description:
GFP-H3.Y_rep_1
pIRESneo-EGFP (generated from pIRESneo (digested with EcoRV and BamHI) with the EGFP insert from pEGFP-C1 (digested with NheI followed by Klenow reaction and subsequently digested with BamHI)).

library_source: genomic

data_processing:
Quality control was done using FASTQC.
Removal of low quality reads and adapters was done by trim_galore.
Alignment was done with bowtie2-2.0.0-beta6 with parameters -p 6 -D 15 -R 2 -N 0 -L 32 -i S,1,0.75 -M 10000.
Duplicate reads were removed with Samtools' rmdup function.
Peak calling was performed with Macs2 callpeak function.
Coverage vectors were extracted with deeptools' bamCoverage function.
Additional processing was done in R/BioConductor. Peaks separated by less then 2 kb were stitched together.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Coverage vectors from bamCoverage are stored as bigwig files.
Supplementary_files_format_and_content: Genomic intervals of binding peaks are stored as BED format files.

molecule: genomic DNA

organism: Homo sapiens

source_name: HeLa (Kyoto), GFP-H3.Y ChIP

growth_protocol: Hela Kyoto (HK) cells were grown in DMEM (Sigma) supplemented with 10% fetal calf serum (FCS; Sigma) and 1% penicillin/streptomycin at 37°C and 5% CO2.

extract_protocol:
HeLa Kyoto cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Nuclear lysates were subjected to chromatin shearing to an average size of 150 bp. Histone-DNA complexes were isolated with GFP-antibody.
All libraries were prepared with the MicroPlex library preparation kit v2 (order no C05010012) following manufacturer's instructions.

tag: cell line

value: HeLa (Kyoto)

tag: transfected plasmid

value: pIRESneo-EGFP

tag: chip antibody

value: GFP (Abcam, ab290, lot GR278073-1)


title: Input replicate 2

description:
Input_rep_2
pIRESneo-EGFP (generated from pIRESneo (digested with EcoRV and BamHI) with the EGFP insert from pEGFP-C1 (digested with NheI followed by Klenow reaction and subsequently digested with BamHI)).

source_name: HeLa (Kyoto), Input


title: Fall'13 Day 42 Control Illinois Heart Fat 1111

city: Newark

first: Carl

last: Schmidt

state: DE

address: 601 Sincock Ln

country: USA

institute: University of Delaware

library_source: transcriptomic

data_processing:
Bowtie
TopHat
Cufflinks
Genome_build: Gallus gallus ver 4

molecule: polyA RNA

organism: Gallus gallus

source_name: Cardiac Adipose Tissue

growth_protocol: Birds were raised following grower standards outlined by our AACUC protocol (#(27)03-12-14R). Briefly, birds were raised on litter with ad libitum access to feed and water. First week house temperature: 35 degrees C with 5 degrees C decrease each week until 25 degrees celsius was reached. The house was maintained this temperature through completion of the trial at day 42 (typical market age). The house received 23 hours of light and 1 hour of dark for the entirety of the study. Necropsies were performed on Day 21, Day 22, Day 26, Day 32 and Day 42.

extract_protocol:
Birds were euthanized via cervical dislocation and necropsied on each day listed above. Abdominal adipose tissue and cardiac adipose tissue samples were collected and flash frozen with liquid nitrogen.
Libraries were constructed using the Illumina Stranded RNA-seq kit according to manufacturers instructions.

treatment_protocol: First week house temperature: 35 degrees C with 5 degrees C decrease each week until 25 degrees celsius was reached. The house maintained this temperature through completion of the trial at day 42 (typical market age).

tag: tissue

value: Cardiac Adipose

tag: breed/line

value: Illinois

tag: gender

value: male

tag: age of collection

value: Day 42 posthatch


title: Fall'13 Day 42 Control Illinois Heart Fat 1110


title: Fall'12 Day 42 Control Ross Ab Fat 1201

source_name: Abdominal Adipose Tissue

value: Abdominal Adipose

value: Ross


title: Fall'13 Day 42 Control Illinois Heart Fat 1107


title: GFP-Y_C3

description:
GFP_Y_C3
pIRESneo-EGFP (generated from pIRESneo (digested with EcoRV and BamHI) with the EGFP insert from pEGFP-C1 (digested with NheI followed by Klenow reaction and subsequently digested with BamHI)).

source_name: HeLa (Kyoto), GFP-Y_C3 ChIP


title: Fall'13 Day 42 Control Illinois Heart Fat 1108


title: Fall'13 Day 42 Control Illinois Heart Fat 1109


title: Fall'13 Day 42 Control Illinois Ab Fat 1099


title: GFP-NY_3

description:
GFP_NY_3
pIRESneo-EGFP (generated from pIRESneo (digested with EcoRV and BamHI) with the EGFP insert from pEGFP-C1 (digested with NheI followed by Klenow reaction and subsequently digested with BamHI)).

source_name: HeLa (Kyoto), GFP-NY_3 ChIP


title: Fall'13 Day 42 Control Illinois Ab Fat 1098


title: Fall'13 Day 42 Control Ross Ab Fat 1195


title: Fall'13 Day 42 Control Illinois Ab Fat 1097


title: Fall'13 Day 42 Control Illinois Ab Fat 1096


description:
GFP_H3Y_L46V_L62I_R53K_triple_H33C-terminus
pIRESneo-EGFP (generated from pIRESneo (digested with EcoRV and BamHI) with the EGFP insert from pEGFP-C1 (digested with NheI followed by Klenow reaction and subsequently digested with BamHI)).

source_name: HeLa (Kyoto), GFP-H3Y_L46V_L62I_R53K_triple_H33C-terminus ChIP


title: Fall'13 Day 42 Control Illinois Ab Fat 1092


title: Fall'13 Day 42 Control Illinois Ab Fat 1094


title: Fall'13 Day 42 Control Illinois Ab Fat 1093


title: AM_repC_run3

city: Denver

first: Claudia

last: Jakubzick

state: Colorado

address: 1400 Jackson St

department: Pediatrics

institute: National Jewish Health

data_processing:
Basecalling, barcode demultiplexing and adapter trimming was performed by Ion Torrent Suite 5.0.4.
Sequence reads of at least 30 nt length were mapped to the mm10 release of the mouse genome using STAR (version 2.5.1b) with splice site data from the Ensembl 78 annotation.
Reads mapping unambiguously to each gene in the Ensembl 78 annotation were quantified using the featureCounts program from the subread package (v1.5.0-p1).
Read counts from individual sequencing runs of the same sample were added together.
Statistical comparisons of the gene expression between the cell genotypes were performed with the DESeq2 package version 1.8.1 for the R statistical software version 3.2.0.
Genome_build: mm10
Supplementary_files_format_and_content: read counts assigned to each gene and sample, as tab-separated text tables: 1) output from subread featureCounts, 2) aggregated by adding different sequencing runs for each sample

molecule: total RNA

organism: Mus musculus

source_name: Pulmonary Alveolar macrophage

extract_protocol:
Mice were euthanized and lungs perfused with phosphate buffered saline, finely minced and digested by incubation in 0.5mg/ml Liberase enzyme mix for 30 minutes. Individual pulmonary macrophage populations were sorted using a FACS Aria cell sorter. RNA was extracted from approx 50000 cells using the Qiagen RNeasy Microkit as decsribed by manufacturer's protocols.
SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) followed by Covaris shearing and finished with Kapa Hyper prep kit using modified Life Technologies indexes.
All total RNA was run on a Bioanalyzer pico chip prior to library build with RIN scores from 9.2-10.0. All samples were started with 2ng of total RNA (based on the pico chip). After library build, samples were run on a High Sensitivity DNA quibit assay (measuring 2ul of library), diluted to ~1ng/ul and run on a High Sensitivity DNA bioanalyzer chip. All samples were pooled together and run on Ion Proton P1 chips.

treatment_protocol: Pulmonary single cell suspension from 8-10 week old naive mice was enriched for MerTK. Enriched MerTK+ cells were stained for FACS sorting to separate three interstitial macrophage populations. To sort IMs: Live cells were gated on CD64+, DAPI- Linage- (Lin: B220, CD3, NK1.1, Ly6G, Siglec F, CD43 and CD24) cells. Doublet excluded cells were then plotted as CD11c versus CD11b. CD11b+ cells were plotted as CD206 versus MHCII to identify IM1 (MHC II low, CD206 high), IM2 (MHCII high, CD206 high) and IM3 (MHCII high, CD206 low).   AM sorts: sorted on DAPI-Lin-( B220, CD3, NK1.1, Gr1, CD11b, and CD103) cells. Doublet excluded cells were then plotted as CD11c versus SiglecF+ to identify AMs as CD11c+SiglecF+.

tag: strain

value: Lung

tag: markers

value: MerTK+CD64+CD11b-CD11c+Siglec F+


title: AM_repC_run2


title: GFP replicate 2

description:
GFP-rep_2
pIRESneo-EGFP (generated from pIRESneo (digested with EcoRV and BamHI) with the EGFP insert from pEGFP-C1 (digested with NheI followed by Klenow reaction and subsequently digested with BamHI)).

source_name: HeLa (Kyoto), GFP ChIP


title: AM_repC_run1


title: GFP-H3.Y replicate 2

description:
GFP-H3.Y_rep_2
pIRESneo-EGFP (generated from pIRESneo (digested with EcoRV and BamHI) with the EGFP insert from pEGFP-C1 (digested with NheI followed by Klenow reaction and subsequently digested with BamHI)).


title: AM_repB_run1


title: AM_repB_run3


title: AM_repB_run2


title: GFP-H3.3 replicate 2

description:
GFP-H3.3_rep_2
pIRESneo-EGFP (generated from pIRESneo (digested with EcoRV and BamHI) with the EGFP insert from pEGFP-C1 (digested with NheI followed by Klenow reaction and subsequently digested with BamHI)).

source_name: HeLa (Kyoto), GFP-H3.3 ChIP


title: AM_repA_run3


title: DoxEtop_2 (FAIRE-Seq)

city: Tartu

first: Pärt

last: Peterson

address: Ravila 19

department: Department of Biomedicine

country: Estonia

institute: University of Tartu

data_processing:
Base calling was performed with the HiSeq Control Software in real time.
Prior to alignment, the reads were trimmed to remove adapter sequences and bases with a Phred score lower than 30 using Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Paired-end reads were mapped to the human genome (hg19) with bowtie2 in “local“ mode (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Aligned reads were processed with the csaw R/Bioconductor package (https://bioconductor.org/packages/release/bioc/html/csaw.html)
Differential FAIRE signal enrichment between the experimental samples was analysed with csaw (https://bioconductor.org/packages/release/bioc/html/csaw.html).
Genome_build: hg19
Supplementary_files_format_and_content: A text file containing the genomic coordinates of 150 bp windows together with the read count of the respective windows in all samples.

source_name: AIRE-Tet cell line, doxycycline induced, etoposide treated

growth_protocol: Cells were cultured in DMEM medium supplemented with 10% tetracycline-negative fetal calf serum, 100 U/ml penicillin/streptomycin and 0.15 mg/ml G418.

extract_protocol:
Genomic DNA was isolated from 10 million formaldehyde-fixed AIRE-Tet cells. 10% of the sample volume was used for input sample preparation. The input samples were first treated with RNase A and proteinase K and the crosslinks were reversed by incubating the samples at 65°C. Subsequently, phenol:chloroform extraction followed by PCR purification columns (Qiagen) were used to purify the input DNA. From the remaining sample volume, the genomic DNA was first isolated by two rounds of phenol:chloroform extraction and then followed by RNase A and proteinase K treatments and finally purified with PCR purification columns (Qiagen). Two independent biological replicates from each experimental condition were prepared.
The FAIRE-seq libraries were prepared following the Illumina Truseq ChIP Sample Preparation Guide and subjected to 100 bp paired-end sequencing on an Illumina HiSeq 2000. All libraries were sequenced twice.

treatment_protocol: Human AIRE expression was induced with 1.5 μM doxycycline (631311, Clontech) 20-24 h after plating (Dox). Untreated cells were used as negative controls (Control). Following 24 h of AIRE induction,  the cells were incubated with 2 µM etoposide (E1383,  Sigma) for 24 h (Dox+Etop). Similarly, negative control cells were treated with etoposide (Etop).

value: AIRE-Tet, Tet-On Advanced HEK293 (Clontech) with inducible AIRE expression

tag: aire expression

value: Induced

tag: etoposide treatment

value: Treated


title: GFP-3_CY

description:
GFP_3_CY
pIRESneo-EGFP (generated from pIRESneo (digested with EcoRV and BamHI) with the EGFP insert from pEGFP-C1 (digested with NheI followed by Klenow reaction and subsequently digested with BamHI)).

source_name: HeLa (Kyoto), GFP-3_CY ChIP


title: DoxEtop_1 (FAIRE-Seq)


title: IM3_repC_run3

source_name: Pulmonary Interstital macrophage


title: IM3_repC_run2


title: Etop_2 (FAIRE-Seq)

source_name: AIRE-Tet cell line, etopsoside treated

value: Uninduced


title: AM_repA_run1


title: IM3_repB_run3


title: IM3_repC_run1


title: GFP-N3_Y

description:
GFP_N3_Y
pIRESneo-EGFP (generated from pIRESneo (digested with EcoRV and BamHI) with the EGFP insert from pEGFP-C1 (digested with NheI followed by Klenow reaction and subsequently digested with BamHI)).

source_name: HeLa (Kyoto), GFP-N3_Y ChIP


title: IM3_repB_run2


title: Etop_1 (FAIRE-Seq)


title: IM3_repB_run1


title: A549_KD_n3

city: Cologne

first: Soyoung

last: Lim

address: Kerpener Str. 62

department: Institute of Pathology

institute: Cologne medical school

description: KDM1A shRNA rep3

data_processing:
Fastq files were obtained after demultiplexing using Illuminas CASAVA v1.8.2 pipeline (default parameters)
Reads were mapped against the human genome GRCh37/hg19 using bwa v0.5.9-r16 with default parameters
Exon read coverages were obtained with coverageBed v2.17.0 using exon coordinates from Ensembl database v73
Subsequent analyses were done using the edgeR package in R
Expression changes were calculated as log2 ratios and p values were adjusted for multiple testing by controlling the false discovery rate at 5% (Benjamini & Hochberg)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text file include log2 FC, p-value, cpm values and counts for all 6 samples

source_name: lung adenocarcinoma cell line

growth_protocol: A549 cells were cultivated in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum, L-glutamine and antibiotics.

extract_protocol:
Total RNA was isolated from cells using the RNeasyMini kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549 cells were transduced with vector control (GFP shRNA) and KDM1A shRNA using a retroviral system. For knockdown cells, monoclonal cell population (clon KD15) was used for RNA-Seq .

value: lung adenocarcinoma


title: A549_KD_n2

description: KDM1A shRNA rep2


title: IM3_repA_run3


title: IM3_repA_run2


title: Dox_1 (FAIRE-Seq)

source_name: AIRE-Tet cell line, doxycycline induced

value: Untreated


title: A549_KD_n1

description: KDM1A shRNA rep1


title: IM2_repC_run3


title: Control_2 (FAIRE-Seq)

source_name: AIRE-Tet cell line, untreated


title: IM3_repA_run1


title: IM2_repC_run1


title: IM2_repC_run2


title: AM_repA_run2


title: IM2_repB_run3


title: IM2_repB_run2


title: Control_1 (FAIRE-Seq)


title: A549_Ctrl_n2

description: shRNA ctrl rep2


title: A549_Ctrl_n1

description: shRNA ctrl rep1


title: Etop_2

data_processing:
Base calling was performed with the HiSeq Control Software in real time.
Prior to alignment, the reads were trimmed to remove adapter sequences and bases with a Phred score lower than 30 using Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Reads were mapped to the human reference genome GRCh37 (Ensembl release 75) using the STAR aligner version 2.4.2a with the 2-pass mode (https://github.com/alexdobin/STAR).
Read count tables were generated with the STAR aligner option --quantMode geneCounts. Strand-specific counts were used for further analyses.
Differential gene expression between the experimental samples was analysed with DESeq2 (http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html).
Read count tables and group comparisons for differential exon usage were performed with DEXSeq (http://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html).
Genome_build: Ensembl GRCh37.75 (ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/)
Supplementary_files_format_and_content: Matrix of read counts based on the Ensembl GRCh37.75 gene sets (ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/) as a csv file.

source_name: Total RNA, AIRE-Tet cell line, etopsoside treated

extract_protocol:
RNA was isolated with the miRNAeasy Mini Kit (Qiagen) using on-column DNase digestion from 106 AIRE-Tet cells. Two independent biological replicates from each treatment were prepared from 500 ng of RNA with RIN >9.
Sequencing libraries were generated with the TruSeq Stranded Total RNA LT (w/ Ribo Zero Gold) Sample Prep Kit (Illumina) according to the manufacturer’s instructions with the exception that 12 PCR cycles were used for the DNA enrichment step. Paired-end sequencing (2 x 100 bp) was performed with Illumina HiSeq 2000, which generated 80-100 x 10^6 sequenced fragments per sample.

treatment_protocol: Human AIRE expression was induced with 1.5 μM doxycycline (631311, Clontech) 20-24 h after plating (Aire+). Untreated cells were used as negative controls (Aire-). Following 24 h of AIRE induction,  the cells were incubated with 2 µM etoposide (E1383,  Sigma) for 24 h (Aire+Etop+). Similarly, negative control cells were treated with etoposide (Etop+).


title: IM2_repA_run3


title: Control_2

source_name: Total RNA, AIRE-Tet cell line, untreated


title: IM2_repA_run4


title: IM2_repB_run1


title: 2794_S6

city: Utrecht

first: Karen

last: Uhde

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

data_processing:
library generation using  3' and 5' RACE like protocols
adapter trimming and mapping of high quality data to the reference genome (bos taurus)
Genome_build: Bos_taurus_UMD_3.1.1

organism: Bos taurus

source_name: cumulus pieces surrounding oocytes that developed into blastocysts after fertilization

extract_protocol:
RNA of cumulus pieces was isoloated using the miCURY RNA isolation kit (Exiqon), according to the manufacturer’s protocol.
For sequencing library preparation the NEBNEXT kit (New England Biolabs, Ipswich, MA, USA) was used.

value: cumulus cells


title: IM2_repA_run5


title: Dox_2 (FAIRE-Seq)


title: IM2_repA_run1


title: Dox_2

source_name: Total RNA, AIRE-Tet cell line, doxycycline induced


title: IM2_repA_run2


title: DoxEtop_2

source_name: Total RNA, AIRE-Tet cell line, doxycycline induced, etoposide treated


title: 2794_S5


title: IM1_repC_run3


title: 2794_S4

source_name: cumulus pieces surrounding oocytes that not cleave after fertilization


title: IM1_repC_run2


title: A549_Ctrl_n3

description: shRNA ctrl rep3


title: 2794_S3


title: Control_1


title: IM1_repB_run3


title: IM1_repC_run1


title: Etop_1


title: IM1_repB_run2


title: IM1_repB_run1


title: 2794_S2


title: IM1_repA_run3


title: Dox_1


title: 2794_S1


title: IM1_repA_run1


title: IM1_repA_run2


title: DoxEtop_1


title: ChIP-seq from MCF-7 (ENCLB899CNW)

status: Public on Mar 12 2017

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR999WHE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR999WHE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2016-10-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB899CNW
size range: 200-600

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

source_name: Homo sapiens MCF-7 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/be2a0f12-af38-430c-8f2d-57953baab5f5/@@download/attachment/Epigenomics_Alternative_Mag_Bead_ChIP_Protocol_v1.1_exp.pdf

tag: antibody

tag: line

value: immortalized cell line

tag: description

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

tag: biosample encode accession

tag: age

value: 69 year

tag: dev stage

value: adult

tag: Sex

value: female

tag: health state

value: breast cancer (adenocarcinoma)

tag: passage number

tag: lab

value: Bradley Bernstein, Broad

tag: link

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

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

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

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


title: ChIP-seq from MCF-7 (ENCLB532OUZ)

description:
https://www.encodeproject.org/experiments/ENCSR999WHE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR999WHE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2016-10-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB532OUZ
size range: 200-600

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

value: ENCBS789UPK at ENCODE; https://www.encodeproject.org/ENCBS789UPK/


title: ChIP-seq from A673 (ENCLB302PXN)

description:
https://www.encodeproject.org/experiments/ENCSR988EGR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR988EGR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR196CXJ
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB302PXN
size range: 200-600

source_name: Homo sapiens A673 immortalized cell line

value: Cell line is A673; this is a purchasable public domain cell type per Miguel Rivera, M.D.

value: unknown

value: 15 year

value: ENCBS615MBV at ENCODE; https://www.encodeproject.org/ENCBS615MBV/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/

value: ENCODE dbxrefs Cellosaurus CVCL_0080; http://web.expasy.org/cellosaurus/CVCL_0080


title: ChIP-seq from cardiac muscle cell (ENCLB862KDH)

description:
https://www.encodeproject.org/experiments/ENCSR994NPK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR994NPK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR867SJE
encode release date: 2016-11-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB862KDH
size range: 200-600

source_name: Homo sapiens cardiac muscle in vitro differentiated cells fetal

value: cardiac muscle cell

value: in vitro differentiated cells

value: fetal

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS806KLM at ENCODE; https://www.encodeproject.org/ENCBS806KLM/

value: Derived from ENCODE donor ENCDO924HBJ; https://www.encodeproject.org/ENCDO924HBJ/


title: ChIP-seq from thoracic aorta (ENCLB819ZQQ)

description:
https://www.encodeproject.org/experiments/ENCSR988DFT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR988DFT
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR266XMB
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB819ZQQ
size range: 200-600
nucleic acid starting quantity: 72.82
nucleic acid starting quantity units: ng

source_name: Homo sapiens thoracic aorta tissue male adult (54 years)

value: thoracic aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult

value: male

value: 54 year

value: Bradley Bernstein, Broad

value: ENCBS294RTL at ENCODE; https://www.encodeproject.org/ENCBS294RTL/

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


title: ChIP-seq from cardiac muscle cell (ENCLB376NHI)

description:
https://www.encodeproject.org/experiments/ENCSR994NPK/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR994NPK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR867SJE
encode release date: 2016-11-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB376NHI
size range: 200-600

value: unknown


title: ChIP-seq from thoracic aorta (ENCLB323KIY)

description:
https://www.encodeproject.org/experiments/ENCSR988DFT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR988DFT
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR266XMB
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB323KIY
size range: 200-600
nucleic acid starting quantity: 72.82
nucleic acid starting quantity units: ng


title: ChIP-seq from cardiac muscle cell (ENCLB481SFE)

description:
https://www.encodeproject.org/experiments/ENCSR994NPK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR994NPK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR867SJE
encode release date: 2016-11-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB481SFE
size range: 200-600

value: cardiac muscle cell

value: ENCBS343AKO at ENCODE; https://www.encodeproject.org/ENCBS343AKO/


title: ChIP-seq from OCI-LY3 (ENCLB054JQP)

description:
https://www.encodeproject.org/experiments/ENCSR996GHD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR996GHD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB054JQP
size range: 300-600
nucleic acid starting quantity: 5.848
nucleic acid starting quantity units: ng

source_name: Homo sapiens OCI-LY3 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/18f0d330-5799-45f7-babe-7728dfbd1103/@@download/attachment/Epigenomics_Mag%20Bead_ChIP_Protocol_v01.4_exp.pdf

value: immortalized cell line

value: Oci-Ly-3- Immortalized diffuse large B cell lymphoma cell line developed at the Ontario Cancer Institute

value: 52 year

value: B cell lymphoma

value: ENCBS757GPD at ENCODE; https://www.encodeproject.org/ENCBS757GPD/

value: Derived from ENCODE donor ENCDO355AAA; https://www.encodeproject.org/ENCDO355AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_8800; http://web.expasy.org/cellosaurus/CVCL_8800


title: ChIP-seq from OCI-LY3 (ENCLB679MCX)

description:
https://www.encodeproject.org/experiments/ENCSR996GHD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR996GHD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB679MCX
size range: 200-600

value: ENCBS018GXW at ENCODE; https://www.encodeproject.org/ENCBS018GXW/


title: ChIP-seq from bipolar spindle neuron (ENCLB564WHV)

description:
https://www.encodeproject.org/experiments/ENCSR983CSB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR983CSB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR001KCX
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB564WHV
size range: 200-600

source_name: Homo sapiens bipolar spindle neuron in vitro differentiated cells male adult (53 years) derived from induced pluripotent stem cell

value: bipolar spindle neuron

value: in vitro differentiated cells

value: These are bipolar neurons created from iPSC from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: adult

value: Thomas Gingeras, CSHL

value: ENCBS369AAA at ENCODE; https://www.encodeproject.org/ENCBS369AAA/

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


title: ChIP-seq from bipolar spindle neuron (ENCLB147HYH)

description:
https://www.encodeproject.org/experiments/ENCSR983CSB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR983CSB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR001KCX
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB147HYH
size range: 200-600

value: male

value: ENCBS374AAA at ENCODE; https://www.encodeproject.org/ENCBS374AAA/


title: ChIP-seq from right lobe of liver (ENCLB177YYO)

description:
https://www.encodeproject.org/experiments/ENCSR981UJA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR981UJA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR276SJT
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB177YYO
size range: 200-600

source_name: Homo sapiens right lobe of liver tissue female adult (53 years)

value: right lobe of liver

value: tissue

value: i.e. REMC 2,3,4,5 and 16; EnTEX:Liver

value: female

value: Bradley Bernstein, Broad

value: ENCBS536THV at ENCODE; https://www.encodeproject.org/ENCBS536THV/

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


title: ChIP-seq from SK-N-SH (ENCLB471YFP)

description:
https://www.encodeproject.org/experiments/ENCSR978CNH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR978CNH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2016-11-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB471YFP
size range: 200-600

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

value: SK-N-SH

value: immortalized cell line

value: 4 year

value: child

value: ENCBS324TZB at ENCODE; https://www.encodeproject.org/ENCBS324TZB/

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

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


title: ChIP-seq from thyroid gland (ENCLB435ERT)

description:
https://www.encodeproject.org/experiments/ENCSR975NOU/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR975NOU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR164POT
encode release date: 2016-10-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB435ERT
size range: 200-600
nucleic acid starting quantity: 548
nucleic acid starting quantity units: ng

source_name: Homo sapiens thyroid gland tissue male adult (54 years)

value: thyroid gland

value: adult

value: 54 year

value: ENCBS050AKF at ENCODE; https://www.encodeproject.org/ENCBS050AKF/

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


title: ChIP-seq from KMS-11 (ENCLB424YQO)

description:
https://www.encodeproject.org/experiments/ENCSR976JHS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR976JHS
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR720GSE
encode release date: 2016-11-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB424YQO
size range: 200-600

source_name: Homo sapiens KMS-11 immortalized cell line

value: multiple myeloma

value: 67 year

value: ENCBS682HMC at ENCODE; https://www.encodeproject.org/ENCBS682HMC/

value: Derived from ENCODE donor ENCDO133EXU; https://www.encodeproject.org/ENCDO133EXU/

value: ENCODE dbxrefs Cellosaurus CVCL_2989; http://web.expasy.org/cellosaurus/CVCL_2989


title: ChIP-seq from thyroid gland (ENCLB145KVC)

description:
https://www.encodeproject.org/experiments/ENCSR975NOU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR975NOU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR164POT
encode release date: 2016-10-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB145KVC
size range: 200-600
nucleic acid starting quantity: 416.5
nucleic acid starting quantity units: ng

value: tissue

value: male

value: Bradley Bernstein, Broad


title: ChIP-seq from thyroid gland (ENCLB670LYT)

description:
https://www.encodeproject.org/experiments/ENCSR975NOU/
***************
biological replicate number: 2
technical replicate number: 3
description:
experiment encode accession: ENCSR975NOU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR164POT
encode release date: 2016-10-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB670LYT
size range: 200-600
nucleic acid starting quantity: 416.5
nucleic acid starting quantity units: ng


title: ChIP-seq from SK-N-SH (ENCLB257LFP)

description:
https://www.encodeproject.org/experiments/ENCSR975GZA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR975GZA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2016-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB257LFP
size range: 200-600

value: SK-N-SH

value: immortalized cell line

value: 4 year

value: child

value: female

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


title: ChIP-seq from gastrocnemius medialis (ENCLB772GCV)

description:
https://www.encodeproject.org/experiments/ENCSR972ETR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR972ETR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR897RRA
encode release date: 2016-06-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB772GCV
size range: 200-600

source_name: Homo sapiens gastrocnemius medialis tissue male adult (54 years)

value: gastrocnemius medialis

value: i.e. REMC 6, 13, 14 and 15; EnTEX:Muscle - Skeletal

value: adult

value: 54 year

value: ENCBS693QTT at ENCODE; https://www.encodeproject.org/ENCBS693QTT/


title: ChIP-seq from gastrocnemius medialis (ENCLB492EUL)

description:
https://www.encodeproject.org/experiments/ENCSR972ETR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR972ETR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR897RRA
encode release date: 2016-06-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB492EUL
size range: 200-600

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


title: ChIP-seq from H9 (ENCLB264PLF)

description:
https://www.encodeproject.org/experiments/ENCSR967HXD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR967HXD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR625CEM
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB264PLF
size range: 200-600
nucleic acid starting quantity: 179
nucleic acid starting quantity units: ng

source_name: Homo sapiens H9 stem cell female embryo (5 days) stably expressing C-terminal eGFP-HES5 fusion protein

value: stem cell

value: HES5::eGFP BAC transgenic human ES cells (H9; WA-09; Wicell) expressing GFP under the HES5 promoter

value: embryonic

value: 5 day

value: healthy

value: ENCBS769EPD at ENCODE; https://www.encodeproject.org/ENCBS769EPD/

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

value: ENCODE dbxrefs Cellosaurus CVCL_9773; http://web.expasy.org/cellosaurus/CVCL_9773


title: ChIP-seq from SK-N-SH (ENCLB810UPC)

description:
https://www.encodeproject.org/experiments/ENCSR975GZA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR975GZA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2016-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB810UPC
size range: 200-600

value: SK-N-SH

value: immortalized cell line

value: 4 year

value: child

value: Bradley Bernstein, Broad

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

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

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


title: ChIP-seq from MCF-7 (ENCLB268FCU)

description:
https://www.encodeproject.org/experiments/ENCSR985MIB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR985MIB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2016-08-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB268FCU
size range: 200-600

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

value: 69 year

value: adult

value: female

value: breast cancer (adenocarcinoma)

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

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

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

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


title: ChIP-seq from DOHH2 (ENCLB017AOE)

description:
https://www.encodeproject.org/experiments/ENCSR966HBM/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR966HBM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2016-10-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB017AOE
size range: 200-600
nucleic acid starting quantity: 13.2
nucleic acid starting quantity units: ng

source_name: Homo sapiens DOHH2 immortalized cell line

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: male

value: 60 year

value: ENCBS898JGF at ENCODE; https://www.encodeproject.org/ENCBS898JGF/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: ChIP-seq from right lobe of liver (ENCLB754JNQ)

description:
https://www.encodeproject.org/experiments/ENCSR981UJA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR981UJA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR276SJT
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB754JNQ
size range: 200-600

value: right lobe of liver

value: tissue

value: i.e. REMC 2,3,4,5 and 16; EnTEX:Liver

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS536THV at ENCODE; https://www.encodeproject.org/ENCBS536THV/

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


title: ChIP-seq from OCI-LY1 (ENCLB285DPI)

description:
https://www.encodeproject.org/experiments/ENCSR960ZMM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR960ZMM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2016-10-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB285DPI
size range: 200-600

source_name: Homo sapiens OCI-LY1 immortalized cell line

value: immortalized cell line

value: established from the bone marrow of a 44-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL; diffuse large cell), stage 4B at relapse in 1983

value: 44 year

value: adult

value: B cell lymphoma

value: ENCBS899DSB at ENCODE; https://www.encodeproject.org/ENCBS899DSB/

value: Derived from ENCODE donor ENCDO350AAA; https://www.encodeproject.org/ENCDO350AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1879; http://web.expasy.org/cellosaurus/CVCL_1879


title: ChIP-seq from K562 (ENCLB241HGY)

description:
https://www.encodeproject.org/experiments/ENCSR996HUG/
***************
biological replicate number: 13
technical replicate number: 2
description: Reverse Crosslink Control ChIP-seq on human K562 (fragmentation date 11-13-13)
experiment encode accession: ENCSR996HUG
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB241HGY

source_name: Homo sapiens K562 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/6ecd8240-a351-479b-9de6-f09ca3702ac3/@@download/attachment/ChIP-seq_Protocol_v011014.pdf

value: Control

value: K562, myelogenous leukemia

value: female

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

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

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

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

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


title: ChIP-seq from OCI-LY1 (ENCLB139SLR)

description:
https://www.encodeproject.org/experiments/ENCSR960ZMM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR960ZMM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2016-10-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB139SLR
size range: 200-600

value: immortalized cell line

value: male

value: Bradley Bernstein, Broad


title: ChIP-seq from KMS-11 (ENCLB901WMW)

description:
https://www.encodeproject.org/experiments/ENCSR976JHS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR976JHS
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR720GSE
encode release date: 2016-11-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB901WMW
size range: 200-600
nucleic acid starting quantity: 101
nucleic acid starting quantity units: ng

value: multiple myeloma

value: adult

value: 67 year

value: ENCBS987CHP at ENCODE; https://www.encodeproject.org/ENCBS987CHP/

value: Derived from ENCODE donor ENCDO133EXU; https://www.encodeproject.org/ENCDO133EXU/

value: ENCODE dbxrefs Cellosaurus CVCL_2989; http://web.expasy.org/cellosaurus/CVCL_2989


title: ChIP-seq from neural cell (ENCLB064FOH)

description:
https://www.encodeproject.org/experiments/ENCSR958ZMM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR958ZMM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR308JFE
encode release date: 2016-10-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB064FOH
size range: 200-600

source_name: Homo sapiens neural in vitro differentiated cells male embryo

value: neural cell

value: in vitro differentiated cells

value: embryonic

value: unknown

value: healthy

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

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


title: ChIP-seq from liver (ENCLB997DAV)

description:
https://www.encodeproject.org/experiments/ENCSR994YLZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on YY1-human
experiment encode accession: ENCSR994YLZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR849OTN, ENCSR769JUI
encode release date: 2016-03-31
lab: Richard Myers, HAIB
library encode accession: ENCLB997DAV

source_name: Homo sapiens liver tissue female child (4 years)

value: liver

value: tissue

value: Human liver tissue obtained from a healthy, 4 year old female donor

value: 4 year

value: child

value: female

value: Michael Snyder, Stanford

value: ENCBS401URL at ENCODE; https://www.encodeproject.org/ENCBS401URL/

value: Derived from ENCODE donor ENCDO882MMZ; https://www.encodeproject.org/ENCDO882MMZ/


title: ChIP-seq from OCI-LY3 (ENCLB995ZQU)

description:
https://www.encodeproject.org/experiments/ENCSR957CQH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR957CQH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB995ZQU
size range: 300-600
nucleic acid starting quantity: 20.298
nucleic acid starting quantity units: ng

value: immortalized cell line

value: Oci-Ly-3- Immortalized diffuse large B cell lymphoma cell line developed at the Ontario Cancer Institute

value: 52 year

value: adult

value: male

value: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS757GPD at ENCODE; https://www.encodeproject.org/ENCBS757GPD/

value: Derived from ENCODE donor ENCDO355AAA; https://www.encodeproject.org/ENCDO355AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_8800; http://web.expasy.org/cellosaurus/CVCL_8800


title: ChIP-seq from OCI-LY3 (ENCLB963NFX)

description:
https://www.encodeproject.org/experiments/ENCSR957CQH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR957CQH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR361GKY
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB963NFX
size range: 200-600

value: ENCBS018GXW at ENCODE; https://www.encodeproject.org/ENCBS018GXW/


title: ChIP-seq from KMS-11 (ENCLB562GLZ)

description:
https://www.encodeproject.org/experiments/ENCSR955IXZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR955IXZ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR720GSE
encode release date: 2016-11-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB562GLZ
size range: 200-600
nucleic acid starting quantity: 20
nucleic acid starting quantity units: ng

value: multiple myeloma

value: 67 year

value: ENCBS987CHP at ENCODE; https://www.encodeproject.org/ENCBS987CHP/

value: Derived from ENCODE donor ENCDO133EXU; https://www.encodeproject.org/ENCDO133EXU/

value: ENCODE dbxrefs Cellosaurus CVCL_2989; http://web.expasy.org/cellosaurus/CVCL_2989


title: ChIP-seq from gastrocnemius medialis (ENCLB295VCL)

description:
https://www.encodeproject.org/experiments/ENCSR948YYZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR948YYZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR897RRA
encode release date: 2016-06-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB295VCL
size range: 200-600

value: gastrocnemius medialis

value: tissue

value: i.e. REMC 6, 13, 14 and 15; EnTEX:Muscle - Skeletal

value: 54 year

value: ENCBS693QTT at ENCODE; https://www.encodeproject.org/ENCBS693QTT/

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


title: ChIP-seq from HepG2 (ENCLB430OCV)

description:
https://www.encodeproject.org/experiments/ENCSR993LMB/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR993LMB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR346XJA
encode release date: 2016-06-14
lab: Richard Myers, HAIB
library encode accession: ENCLB430OCV

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-TGIF2 fusion protein

value: immortalized cell line

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS595FPT at ENCODE; https://www.encodeproject.org/ENCBS595FPT/

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

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


title: ChIP-seq from gastrocnemius medialis (ENCLB721GZX)

description:
https://www.encodeproject.org/experiments/ENCSR948YYZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR948YYZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR897RRA
encode release date: 2016-06-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB721GZX
size range: 200-600

value: adult

value: Bradley Bernstein, Broad


title: ChIP-seq from keratinocyte (ENCLB550PWQ)

description:
https://www.encodeproject.org/experiments/ENCSR970FPM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR970FPM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000ALS
encode release date: 2016-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB550PWQ
size range: 200-600

source_name: Homo sapiens keratinocyte primary cell female

value: keratinocyte

value: primary cell

value: unknown

value: female

value: ENCBS574ILP at ENCODE; https://www.encodeproject.org/ENCBS574ILP/

value: Derived from ENCODE donor ENCDO268AAA; https://www.encodeproject.org/ENCDO268AAA/


title: ChIP-seq from HepG2 (ENCLB438OUO)

description:
https://www.encodeproject.org/experiments/ENCSR993LMB/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR993LMB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR346XJA
encode release date: 2016-06-14
lab: Richard Myers, HAIB
library encode accession: ENCLB438OUO

value: immortalized cell line

value: ENCBS246HTK at ENCODE; https://www.encodeproject.org/ENCBS246HTK/


title: ChIP-seq from PC-3 (ENCLB935KUR)

description:
https://www.encodeproject.org/experiments/ENCSR946QFD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR946QFD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2016-11-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB935KUR
size range: 300-600
nucleic acid starting quantity: 40.12
nucleic acid starting quantity units: ng

source_name: Homo sapiens PC-3 immortalized cell line

value: prostate cancer cell line

value: male

value: 62 year

value: grade IV, adenocarcinoma

value: ENCBS596CTT at ENCODE; https://www.encodeproject.org/ENCBS596CTT/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: ChIP-seq from PC-3 (ENCLB019XUS)

description:
https://www.encodeproject.org/experiments/ENCSR943LZX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR943LZX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2016-11-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB019XUS
size range: 300-600
nucleic acid starting quantity: 23.222
nucleic acid starting quantity units: ng

value: adult

value: Bradley Bernstein, Broad


title: ChIP-seq from PC-9 (ENCLB630BXV)

description:
https://www.encodeproject.org/experiments/ENCSR945KBK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR945KBK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2017-01-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB630BXV
size range: 200-600

source_name: Homo sapiens PC-9 immortalized cell line

value: PC-14 was originally deposited with the Riken BioResource Center as a cell line derived from human lung adenocarcinoma (undifferentiated type) in 1989. The RIKEN BioResource Center subsequently informed the European Collection of Cell Cultures (ECACC) that short tandem repeat (STR) DNA profile analysis, undertaken in collaboration Immuno-Biological Laboratories Co., Ltd Japan, has shown this cell line to be identical to PC-9 a cell line derived from human lung adenocarcinoma (differentiated type). The misidentification occurred prior to the cell line being deposited at the RIKEN BioResource Center. The name of the cell line has been changed to PC-9 to reflect this finding

value: not collected

value: ENCBS987JQH at ENCODE; https://www.encodeproject.org/ENCBS987JQH/

value: Derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/

value: ENCODE dbxrefs Cellosaurus CVCL_B260; http://web.expasy.org/cellosaurus/CVCL_B260


title: ChIP-seq from OCI-LY1 (ENCLB342YXO)

description:
https://www.encodeproject.org/experiments/ENCSR960ZMM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR960ZMM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2016-10-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB342YXO
size range: 200-600

value: immortalized cell line

value: established from the bone marrow of a 44-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL; diffuse large cell), stage 4B at relapse in 1983

value: 44 year

value: B cell lymphoma

value: ENCBS729LWO at ENCODE; https://www.encodeproject.org/ENCBS729LWO/

value: Derived from ENCODE donor ENCDO350AAA; https://www.encodeproject.org/ENCDO350AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1879; http://web.expasy.org/cellosaurus/CVCL_1879


title: ChIP-seq from DOHH2 (ENCLB056ILV)

description:
https://www.encodeproject.org/experiments/ENCSR992YSL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR992YSL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB056ILV
size range: 200-600

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: 60 year

value: male

value: ENCBS662OGM at ENCODE; https://www.encodeproject.org/ENCBS662OGM/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: ChIP-seq from HepG2 (ENCLB443GCQ)

description:
https://www.encodeproject.org/experiments/ENCSR988ZSI/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR988ZSI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB443GCQ

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-RERE fusion protein

value: FLAG-RERE

value: child

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS364WYE at ENCODE; https://www.encodeproject.org/ENCBS364WYE/

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


title: ChIP-seq from thoracic aorta (ENCLB668IZW)

description:
https://www.encodeproject.org/experiments/ENCSR939RLS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR939RLS
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR158PLZ
encode release date: 2016-10-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB668IZW
size range: 200-600

source_name: Homo sapiens thoracic aorta tissue male adult (37 years)

value: thoracic aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult

value: 37 year

value: Bradley Bernstein, Broad

value: ENCBS882JUX at ENCODE; https://www.encodeproject.org/ENCBS882JUX/

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


title: ChIP-seq from thoracic aorta (ENCLB372DRU)

description:
https://www.encodeproject.org/experiments/ENCSR939RLS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR939RLS
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR158PLZ
encode release date: 2016-10-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB372DRU
size range: 200-600

value: male


title: ChIP-seq from KMS-11 (ENCLB067SIE)

description:
https://www.encodeproject.org/experiments/ENCSR955IXZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR955IXZ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR720GSE
encode release date: 2016-11-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB067SIE
size range: 200-600

value: immortalized cell line

value: multiple myeloma

value: female

value: 67 year

value: ENCBS682HMC at ENCODE; https://www.encodeproject.org/ENCBS682HMC/

value: Derived from ENCODE donor ENCDO133EXU; https://www.encodeproject.org/ENCDO133EXU/

value: ENCODE dbxrefs Cellosaurus CVCL_2989; http://web.expasy.org/cellosaurus/CVCL_2989


title: ChIP-seq from HepG2 (ENCLB536XKW)

description:
https://www.encodeproject.org/experiments/ENCSR988ZSI/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR988ZSI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB536XKW

value: FLAG-RERE

value: child

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS362YKU at ENCODE; https://www.encodeproject.org/ENCBS362YKU/

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


title: ChIP-seq from thoracic aorta (ENCLB815EFY)

description:
https://www.encodeproject.org/experiments/ENCSR930HLX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR930HLX
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR266XMB
encode release date: 2016-10-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB815EFY
size range: 200-600
nucleic acid starting quantity: 36.74
nucleic acid starting quantity units: ng

source_name: Homo sapiens thoracic aorta tissue male adult (54 years)

value: thoracic aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult

value: 54 year

value: Bradley Bernstein, Broad

value: ENCBS294RTL at ENCODE; https://www.encodeproject.org/ENCBS294RTL/

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


title: ChIP-seq from thoracic aorta (ENCLB636CFZ)

description:
https://www.encodeproject.org/experiments/ENCSR930HLX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR930HLX
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR266XMB
encode release date: 2016-10-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB636CFZ
size range: 200-600
nucleic acid starting quantity: 42.46
nucleic acid starting quantity units: ng

value: male

value: ENCBS703OTV at ENCODE; https://www.encodeproject.org/ENCBS703OTV/


title: ChIP-seq from liver (ENCLB638SGS)

description:
https://www.encodeproject.org/experiments/ENCSR994YLZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on YY1-human
experiment encode accession: ENCSR994YLZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR849OTN, ENCSR769JUI
encode release date: 2016-03-31
lab: Richard Myers, HAIB
library encode accession: ENCLB638SGS

value: liver

value: Human liver tissue obtained from a healthy, 4 year old female donor

value: 4 year

value: female

value: healthy

value: Michael Snyder, Stanford

value: ENCBS401URL at ENCODE; https://www.encodeproject.org/ENCBS401URL/

value: Derived from ENCODE donor ENCDO882MMZ; https://www.encodeproject.org/ENCDO882MMZ/


title: ChIP-seq from thoracic aorta (ENCLB591CJJ)

description:
https://www.encodeproject.org/experiments/ENCSR930HLX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR930HLX
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR266XMB
encode release date: 2016-10-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB591CJJ
size range: 200-600
nucleic acid starting quantity: 36.74
nucleic acid starting quantity units: ng

value: thoracic aorta

value: tissue


title: ChIP-seq from thoracic aorta (ENCLB135ZPG)

description:
https://www.encodeproject.org/experiments/ENCSR930HLX/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR930HLX
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR266XMB
encode release date: 2016-10-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB135ZPG
size range: 200-600
nucleic acid starting quantity: 42.46
nucleic acid starting quantity units: ng

value: EnTEX:Artery- Aorta

value: adult


title: ChIP-seq from HepG2 (ENCLB800OKW)

description:
https://www.encodeproject.org/experiments/ENCSR988LZG/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR988LZG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB800OKW

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-ARID4B fusion protein

value: immortalized cell line

value: child

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS957XVL at ENCODE; https://www.encodeproject.org/ENCBS957XVL/

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


title: ChIP-seq from HepG2 (ENCLB861TCE)

description:
https://www.encodeproject.org/experiments/ENCSR988LZG/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR988LZG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB861TCE

value: male

value: ENCBS777QYW at ENCODE; https://www.encodeproject.org/ENCBS777QYW/


title: ChIP-seq from A673 (ENCLB883UWA)

description:
https://www.encodeproject.org/experiments/ENCSR988EGR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR988EGR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR196CXJ
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB883UWA
size range: 200-600
nucleic acid starting quantity: 1.8
nucleic acid starting quantity units: ng

source_name: Homo sapiens A673 immortalized cell line

value: Cell line is A673; this is a purchasable public domain cell type per Miguel Rivera, M.D.

value: unknown

value: female

value: Bradley Bernstein, Broad

value: ENCBS385OLC at ENCODE; https://www.encodeproject.org/ENCBS385OLC/

value: Derived from ENCODE donor ENCDO027VXA; https://www.encodeproject.org/ENCDO027VXA/

value: ENCODE dbxrefs Cellosaurus CVCL_0080; http://web.expasy.org/cellosaurus/CVCL_0080


title: ChIP-seq from gastrocnemius medialis (ENCLB119QUF)

description:
https://www.encodeproject.org/experiments/ENCSR922OXX/
***************
biological replicate number: 2
technical replicate number: 4
description:
experiment encode accession: ENCSR922OXX
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR775IMI
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB119QUF
size range: 200-600
nucleic acid starting quantity: 228.8
nucleic acid starting quantity units: ng

source_name: Homo sapiens gastrocnemius medialis tissue male adult (37 years)

value: gastrocnemius medialis

value: tissue

value: i.e. REMC 6, 13, 14 and 15; EnTEX:Muscle - Skeletal

value: adult

value: 37 year

value: ENCBS861DVK at ENCODE; https://www.encodeproject.org/ENCBS861DVK/

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


title: ChIP-seq from gastrocnemius medialis (ENCLB219HOL)

description:
https://www.encodeproject.org/experiments/ENCSR922OXX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR922OXX
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR775IMI
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB219HOL
size range: 200-600
nucleic acid starting quantity: 228.8
nucleic acid starting quantity units: ng


title: ChIP-seq from gastrocnemius medialis (ENCLB227PJN)

description:
https://www.encodeproject.org/experiments/ENCSR922OXX/
***************
biological replicate number: 2
technical replicate number: 3
description:
experiment encode accession: ENCSR922OXX
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR775IMI
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB227PJN
size range: 200-600
nucleic acid starting quantity: 136.84
nucleic acid starting quantity units: ng


title: ChIP-seq from gastrocnemius medialis (ENCLB280AXZ)

description:
https://www.encodeproject.org/experiments/ENCSR922OXX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR922OXX
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR775IMI
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB280AXZ
size range: 200-600
nucleic acid starting quantity: 136.84
nucleic acid starting quantity units: ng


title: ChIP-seq from DOHH2 (ENCLB024MRY)

description:
https://www.encodeproject.org/experiments/ENCSR992YSL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR992YSL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB024MRY
size range: 200-600

value: immortalized cell line

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: 60 year

value: ENCBS100ZVH at ENCODE; https://www.encodeproject.org/ENCBS100ZVH/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: ChIP-seq from MCF-7 (ENCLB480UNK)

description:
https://www.encodeproject.org/experiments/ENCSR985MIB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR985MIB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2016-08-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB480UNK
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens MCF-7 immortalized cell line

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

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

value: Bradley Bernstein, Broad

value: ENCBS789UPK at ENCODE; https://www.encodeproject.org/ENCBS789UPK/

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

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

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


title: ChIP-seq from SK-N-SH (ENCLB691SDO)

description:
https://www.encodeproject.org/experiments/ENCSR978CNH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR978CNH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2016-11-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB691SDO
size range: 200-600

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

value: SK-N-SH

value: 4 year

value: child

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

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

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


title: ChIP-seq from mid-neurogenesis radial glial cells (ENCLB595GMR)

description:
https://www.encodeproject.org/experiments/ENCSR922CAT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR922CAT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR287XMW
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB595GMR
size range: 200-600

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

value: mid-neurogenesis radial glial cells

value: in vitro differentiated cells

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

value: embryonic

value: 5 day

value: healthy

value: ENCBS355KGI at ENCODE; https://www.encodeproject.org/ENCBS355KGI/

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


title: ChIP-seq from HepG2 (ENCLB128AOL)

description:
https://www.encodeproject.org/experiments/ENCSR966PJY/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR966PJY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB128AOL

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-MIXL1 fusion protein, N-terminal FLAG-MIXL1 fusion protein

value: immortalized cell line

value: male

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS335HAM at ENCODE; https://www.encodeproject.org/ENCBS335HAM/

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


title: ChIP-seq from DOHH2 (ENCLB412ARC)

description:
https://www.encodeproject.org/experiments/ENCSR966HBM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR966HBM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2016-10-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB412ARC
size range: 200-600

source_name: Homo sapiens DOHH2 immortalized cell line

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: adult

value: 60 year

value: Bradley Bernstein, Broad

value: ENCBS898JGF at ENCODE; https://www.encodeproject.org/ENCBS898JGF/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: ChIP-seq from H9 (ENCLB803FLC)

description:
https://www.encodeproject.org/experiments/ENCSR967HXD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR967HXD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR625CEM
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB803FLC
size range: 300-1000

source_name: Homo sapiens H9 stem cell female embryo (5 days) stably expressing C-terminal eGFP-HES5 fusion protein

value: stem cell

value: HES5::eGFP BAC transgenic human ES cells (H9; WA-09; Wicell) expressing GFP under the HES5 promoter, Cells were cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs) (Globalstem). Undifferentiated ES cells were maintained in medium containing DMEM/F12, 20% KSR, 1mM Glutamine, 1% Penicillin/Streptomycin, non essential amino acids and beta-mercaptoethanol. Undifferentiated ES cells were purified with pluripotency markers Tra-1-60 and PE-conjugated SSEA-3 (BD Pharmingen).

value: embryonic

value: female

value: 5 day

value: healthy

value: ENCBS703ZDS at ENCODE; https://www.encodeproject.org/ENCBS703ZDS/

value: ENCODE dbxrefs Cellosaurus CVCL_9773; http://web.expasy.org/cellosaurus/CVCL_9773


title: ChIP-seq from HepG2 (ENCLB275ULF)

description:
https://www.encodeproject.org/experiments/ENCSR966PJY/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR966PJY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB275ULF

value: immortalized cell line

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS051XDO at ENCODE; https://www.encodeproject.org/ENCBS051XDO/


title: ChIP-seq from PC-9 (ENCLB208TNP)

description:
https://www.encodeproject.org/experiments/ENCSR913MGR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR913MGR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB208TNP
size range: 200-600

value: PC-14 was originally deposited with the Riken BioResource Center as a cell line derived from human lung adenocarcinoma (undifferentiated type) in 1989. The RIKEN BioResource Center subsequently informed the European Collection of Cell Cultures (ECACC) that short tandem repeat (STR) DNA profile analysis, undertaken in collaboration Immuno-Biological Laboratories Co., Ltd Japan, has shown this cell line to be identical to PC-9 a cell line derived from human lung adenocarcinoma (differentiated type). The misidentification occurred prior to the cell line being deposited at the RIKEN BioResource Center. The name of the cell line has been changed to PC-9 to reflect this finding

value: unknown

value: not collected

value: Bradley Bernstein, Broad

value: ENCBS177ANS at ENCODE; https://www.encodeproject.org/ENCBS177ANS/

value: Derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/

value: ENCODE dbxrefs Cellosaurus CVCL_B260; http://web.expasy.org/cellosaurus/CVCL_B260


title: ChIP-seq from thoracic aorta (ENCLB047SNF)

description:
https://www.encodeproject.org/experiments/ENCSR909VUB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR909VUB
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR266XMB
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB047SNF
size range: 200-600
nucleic acid starting quantity: 26.18
nucleic acid starting quantity units: ng

value: thoracic aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult

value: 54 year

value: ENCBS294RTL at ENCODE; https://www.encodeproject.org/ENCBS294RTL/

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


title: ChIP-seq from DOHH2 (ENCLB190ZRM)

description:
https://www.encodeproject.org/experiments/ENCSR966HBM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR966HBM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR742WWB
encode release date: 2016-10-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB190ZRM
size range: 200-600

value: immortalized cell line

value: established from the pleural effusion of a 60-year-old man with refractory immunoblastic B cell lymphoma progressed from follicular centroblastic/centrocytic lymphoma in 1990

value: 60 year

value: male

value: ENCBS662OGM at ENCODE; https://www.encodeproject.org/ENCBS662OGM/

value: Derived from ENCODE donor ENCDO352AAA; https://www.encodeproject.org/ENCDO352AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1179; http://web.expasy.org/cellosaurus/CVCL_1179


title: ChIP-seq from thoracic aorta (ENCLB042WGU)

description:
https://www.encodeproject.org/experiments/ENCSR909VUB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR909VUB
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR266XMB
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB042WGU
size range: 200-600
nucleic acid starting quantity: 26.18
nucleic acid starting quantity units: ng

value: Bradley Bernstein, Broad


title: ChIP-seq from K562 (ENCLB663FAC)

description:
https://www.encodeproject.org/experiments/ENCSR962APM/
***************
biological replicate number: 14
technical replicate number: 2
description: Reverse Crosslink Control ChIP-seq on human K562 (fragmentation date 02-26-14)
experiment encode accession: ENCSR962APM
assay title: ChIP-seq
encode release date: 2015-11-13
lab: Richard Myers, HAIB
library encode accession: ENCLB663FAC
size range: 100-500

source_name: Homo sapiens K562 immortalized cell line

value: Control

value: K562, myelogenous leukemia

value: 53 year

value: female

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: ENCBS316CKF at ENCODE; https://www.encodeproject.org/ENCBS316CKF/

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

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

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


title: ChIP-seq from thoracic aorta (ENCLB361IHP)

description:
https://www.encodeproject.org/experiments/ENCSR909VUB/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR909VUB
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR266XMB
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB361IHP
size range: 200-600
nucleic acid starting quantity: 53.02
nucleic acid starting quantity units: ng

value: thoracic aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult

value: 54 year

value: ENCBS703OTV at ENCODE; https://www.encodeproject.org/ENCBS703OTV/

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


title: ChIP-seq from thoracic aorta (ENCLB345YOF)

description:
https://www.encodeproject.org/experiments/ENCSR909VUB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR909VUB
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR266XMB
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB345YOF
size range: 200-600
nucleic acid starting quantity: 53.02
nucleic acid starting quantity units: ng

value: male

value: Bradley Bernstein, Broad


title: ChIP-seq from HepG2 (ENCLB338FNZ)

description:
https://www.encodeproject.org/experiments/ENCSR961WLZ/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR961WLZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB338FNZ

source_name: Homo sapiens HepG2 immortalized cell line stably expressing N-terminal FLAG-SOX5 fusion protein, C-terminal FLAG-SOX5 fusion protein

value: immortalized cell line

value: child

value: 15 year

value: hepatocellular carcinoma

value: ENCBS809XQW at ENCODE; https://www.encodeproject.org/ENCBS809XQW/

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


title: ChIP-seq from HepG2 (ENCLB322KTI)

description:
https://www.encodeproject.org/experiments/ENCSR961WLZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR961WLZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB322KTI

value: Richard Myers, HAIB

value: ENCBS837RPL at ENCODE; https://www.encodeproject.org/ENCBS837RPL/


title: ChIP-seq from induced pluripotent stem cell (ENCLB271JAZ)

description:
https://www.encodeproject.org/experiments/ENCSR908FQA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR908FQA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2016-11-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB271JAZ
size range: 200-600

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

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

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

value: 53 year

value: Thomas Gingeras, CSHL

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

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

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

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


title: ChIP-seq from HepG2 (ENCLB751ZCQ)

description:
https://www.encodeproject.org/experiments/ENCSR959OMS/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR959OMS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB751ZCQ

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-SAP130 fusion protein

value: immortalized cell line

value: male

value: ENCBS579GLC at ENCODE; https://www.encodeproject.org/ENCBS579GLC/


title: ChIP-seq from induced pluripotent stem cell (ENCLB312OGJ)

description:
https://www.encodeproject.org/experiments/ENCSR908FQA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR908FQA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2016-11-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB312OGJ
size range: 200-600

value: adult


title: ChIP-seq from keratinocyte (ENCLB883AHC)

description:
https://www.encodeproject.org/experiments/ENCSR970FPM/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR970FPM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000ALS
encode release date: 2016-11-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB883AHC
size range: 200-600
nucleic acid starting quantity: 12.0
nucleic acid starting quantity units: ng

source_name: Homo sapiens keratinocyte primary cell female

value: keratinocyte

value: primary cell

value: unknown

value: female

value: Bradley Bernstein, Broad

value: ENCBS935RSN at ENCODE; https://www.encodeproject.org/ENCBS935RSN/

value: Derived from ENCODE donor ENCDO268AAA; https://www.encodeproject.org/ENCDO268AAA/


title: ChIP-seq from neural cell (ENCLB191WDP)

description:
https://www.encodeproject.org/experiments/ENCSR958ZMM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR958ZMM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR308JFE
encode release date: 2016-10-25
lab: Bradley Bernstein, Broad
library encode accession: ENCLB191WDP
size range: 200-600

source_name: Homo sapiens neural in vitro differentiated cells male embryo

value: neural cell

value: in vitro differentiated cells

value: embryonic

value: healthy

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

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


title: ChIP-seq from thyroid gland (ENCLB138IVW)

description:
https://www.encodeproject.org/experiments/ENCSR906YES/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR906YES
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR777VQP
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB138IVW
size range: 200-600

source_name: Homo sapiens thyroid gland tissue male adult (37 years)

value: thyroid gland

value: tissue

value: 37 year

value: ENCBS522TJW at ENCODE; https://www.encodeproject.org/ENCBS522TJW/

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


title: ChIP-seq from thyroid gland (ENCLB831YCC)

description:
https://www.encodeproject.org/experiments/ENCSR906YES/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR906YES
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR777VQP
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB831YCC
size range: 200-600

value: adult

value: male


title: ChIP-seq from HepG2 (ENCLB436MYU)

description:
https://www.encodeproject.org/experiments/ENCSR954KIC/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR954KIC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB436MYU

source_name: Homo sapiens HepG2 immortalized cell line stably expressing N-terminal FLAG-KAT8 fusion protein, C-terminal FLAG-KAT8 fusion protein

value: immortalized cell line

value: child

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS174NQD at ENCODE; https://www.encodeproject.org/ENCBS174NQD/

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


title: ChIP-seq from PC-9 (ENCLB807AVU)

description:
https://www.encodeproject.org/experiments/ENCSR913MGR/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR913MGR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB807AVU
size range: 200-600

source_name: Homo sapiens PC-9 immortalized cell line

value: PC-14 was originally deposited with the Riken BioResource Center as a cell line derived from human lung adenocarcinoma (undifferentiated type) in 1989. The RIKEN BioResource Center subsequently informed the European Collection of Cell Cultures (ECACC) that short tandem repeat (STR) DNA profile analysis, undertaken in collaboration Immuno-Biological Laboratories Co., Ltd Japan, has shown this cell line to be identical to PC-9 a cell line derived from human lung adenocarcinoma (differentiated type). The misidentification occurred prior to the cell line being deposited at the RIKEN BioResource Center. The name of the cell line has been changed to PC-9 to reflect this finding

value: unknown

value: not collected

value: Bradley Bernstein, Broad

value: ENCBS177ANS at ENCODE; https://www.encodeproject.org/ENCBS177ANS/

value: Derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/

value: ENCODE dbxrefs Cellosaurus CVCL_B260; http://web.expasy.org/cellosaurus/CVCL_B260


title: ChIP-seq from HepG2 (ENCLB797RKD)

description:
https://www.encodeproject.org/experiments/ENCSR954KIC/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR954KIC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB797RKD

value: ENCBS020UGF at ENCODE; https://www.encodeproject.org/ENCBS020UGF/


title: ChIP-seq from PC-9 (ENCLB350BAB)

description:
https://www.encodeproject.org/experiments/ENCSR913MGR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR913MGR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB350BAB
size range: 200-600

value: ENCBS987JQH at ENCODE; https://www.encodeproject.org/ENCBS987JQH/


title: ChIP-seq from K562 (ENCLB916OLW)

description:
https://www.encodeproject.org/experiments/ENCSR948QLZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562-human
experiment encode accession: ENCSR948QLZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000FCA, ENCSR962APM
encode release date: 2016-02-05
lab: Richard Myers, HAIB
library encode accession: ENCLB916OLW

value: K562, myelogenous leukemia

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

value: ENCBS316CKF at ENCODE; https://www.encodeproject.org/ENCBS316CKF/

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

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

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


title: ChIP-seq from bipolar spindle neuron (ENCLB695WYQ)

description:
https://www.encodeproject.org/experiments/ENCSR905TYC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR905TYC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR001KCX
encode release date: 2016-05-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695WYQ
size range: 200-600

source_name: Homo sapiens bipolar spindle neuron in vitro differentiated cells male adult (53 years) derived from induced pluripotent stem cell

value: bipolar spindle neuron

value: in vitro differentiated cells

value: These are bipolar neurons created from iPSC from the PGP1 donor from the Personal Genome Project (PGP).

value: male

value: Thomas Gingeras, CSHL

value: ENCBS374AAA at ENCODE; https://www.encodeproject.org/ENCBS374AAA/

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


title: ChIP-seq from PC-3 (ENCLB018JTO)

description:
https://www.encodeproject.org/experiments/ENCSR946QFD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR946QFD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2016-11-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB018JTO
size range: 300-600
nucleic acid starting quantity: 21.726
nucleic acid starting quantity units: ng

source_name: Homo sapiens PC-3 immortalized cell line

extract_protocol: extraction method: see document

value: immortalized cell line

value: prostate cancer cell line

value: 62 year

value: grade IV, adenocarcinoma

value: Bradley Bernstein, Broad

value: ENCBS451OVM at ENCODE; https://www.encodeproject.org/ENCBS451OVM/

value: Derived from ENCODE donor ENCDO349AAA; https://www.encodeproject.org/ENCDO349AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: ChIP-seq from KMS-11 (ENCLB156PCC)

description:
https://www.encodeproject.org/experiments/ENCSR900DFO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR900DFO
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR720GSE
encode release date: 2017-01-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB156PCC
size range: 200-600
nucleic acid starting quantity: 57
nucleic acid starting quantity units: ng

source_name: Homo sapiens KMS-11 immortalized cell line

value: multiple myeloma

value: adult

value: female

value: 67 year

value: ENCBS987CHP at ENCODE; https://www.encodeproject.org/ENCBS987CHP/

value: Derived from ENCODE donor ENCDO133EXU; https://www.encodeproject.org/ENCDO133EXU/

value: ENCODE dbxrefs Cellosaurus CVCL_2989; http://web.expasy.org/cellosaurus/CVCL_2989


title: ChIP-seq from bipolar spindle neuron (ENCLB946YYC)

description:
https://www.encodeproject.org/experiments/ENCSR905TYC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR905TYC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR001KCX
encode release date: 2016-05-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB946YYC
size range: 200-600

value: bipolar spindle neuron

value: in vitro differentiated cells

value: These are bipolar neurons created from iPSC from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS369AAA at ENCODE; https://www.encodeproject.org/ENCBS369AAA/

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


title: ChIP-seq from PC-9 (ENCLB237KVV)

description:
https://www.encodeproject.org/experiments/ENCSR945KBK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR945KBK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2017-01-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB237KVV
size range: 200-600

value: immortalized cell line

value: PC-14 was originally deposited with the Riken BioResource Center as a cell line derived from human lung adenocarcinoma (undifferentiated type) in 1989. The RIKEN BioResource Center subsequently informed the European Collection of Cell Cultures (ECACC) that short tandem repeat (STR) DNA profile analysis, undertaken in collaboration Immuno-Biological Laboratories Co., Ltd Japan, has shown this cell line to be identical to PC-9 a cell line derived from human lung adenocarcinoma (differentiated type). The misidentification occurred prior to the cell line being deposited at the RIKEN BioResource Center. The name of the cell line has been changed to PC-9 to reflect this finding

value: unknown

value: not collected

value: Bradley Bernstein, Broad

value: ENCBS177ANS at ENCODE; https://www.encodeproject.org/ENCBS177ANS/

value: Derived from ENCODE donor ENCDO647UHQ; https://www.encodeproject.org/ENCDO647UHQ/

value: ENCODE dbxrefs Cellosaurus CVCL_B260; http://web.expasy.org/cellosaurus/CVCL_B260


title: ChIP-seq from KMS-11 (ENCLB503ZEM)

description:
https://www.encodeproject.org/experiments/ENCSR900DFO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR900DFO
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR720GSE
encode release date: 2017-01-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB503ZEM
size range: 200-600
nucleic acid starting quantity: 57
nucleic acid starting quantity units: ng

value: multiple myeloma

value: adult

value: female

value: 67 year

value: ENCBS987CHP at ENCODE; https://www.encodeproject.org/ENCBS987CHP/

value: Derived from ENCODE donor ENCDO133EXU; https://www.encodeproject.org/ENCDO133EXU/

value: ENCODE dbxrefs Cellosaurus CVCL_2989; http://web.expasy.org/cellosaurus/CVCL_2989


title: ChIP-seq from fibroblast of arm (ENCLB412CNU)

description:
https://www.encodeproject.org/experiments/ENCSR900AQX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR900AQX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR922FLS
encode release date: 2016-11-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB412CNU
size range: 200-600
nucleic acid starting quantity: 281.6
nucleic acid starting quantity units: ng

source_name: Homo sapiens fibroblast of arm primary cell male adult (53 years)

value: fibroblast of arm

value: primary cell

value: These are primary fibroblasts taken from the PGP1 donor from the Personal Genome Project (PGP).

value: 53 year

value: male

value: Thomas Gingeras, CSHL

value: ENCBS372AAA at ENCODE; https://www.encodeproject.org/ENCBS372AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_F183; http://web.expasy.org/cellosaurus/CVCL_F183

value: Coriell sample source; http://www.ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23248&PgId=166