title: CSC10MEZH2_R1

data_processing:
Illumina's CASAVA 1.8.2 was used to convert BCL files to FASTQ files. Default parameters were used.
bowtie1.0.0 was used for running the alignments. Default parameters were used. The data was aligned to HG19 reference genome.
Data was filtered using samtools to remove duplicates and create bam file (-b) of only mapped reads (-F 4) with mapping quality (MAPQ) better than 20 (-q 20), and not more than 1 mismatches (NM is 0 or 1). This bam file was then converted to bed file using bamToBed (bedtools). The coverage data (normalized to total read counts ) in 200 bp windows was generated using BedTools function coverageBed
Genome_build: Hg19
Supplementary_files_format_and_content: Bed files normalized to total read counts in each sample

source_name: Human bronchial epithelial cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed according to the Illumina’s TruSeq DNA Sample Preparation v2 Kit protocol and sequenced on an Illumina HiSeq 2500 for 50 cycles

treatment_protocol: cells were treated with 10 ug/ml CSC or DMSO (con cells) for upto 10 months. Cell were harvested at 10 Days and 10 months

tag: agent

value: CSC

tag: treatment time

value: 10 Months

value: EZH2 (Cell signaling, 5246)


title: CSC10MInput_R1

status: Public on Oct 21 2017

type: SRA

city: Baltimore

first: Hariharan

last: Easwaran

state: Maryland

address: 1650 Orleans St #544, Baltimore, MD 21205

department: SOM Onc Cancer Biology

country: USA

institute: Johns Hopkins Medicine

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Cells were maintained in keratinocyte serum-free medium (KSFM; Life Technologies Inc.) media containing 50mg/mL of bovine pituitary extract (BPE; Life Technologies Inc.) and 5 ng/mL of EGF (Life Technologies Inc.)

tag: cell line

tag: chip antibody


title: CSC10MH3K4_R1

value: H3K4me3 (Millipore, 07-473)


title: C10MInput_R1

value: DMSO


title: C155-GFP [IL7017-709-505]

city: Stanford

first: Felix

last: Horns

state: CA

address: Clark Center E300, Quake Lab

department: Bioengineering

institute: Stanford University

description:
Single cell
processed data files: df_libs.csv, htseq.tab, STAR.tab

library_source: transcriptomic

data_processing:
Library strategy: 5’ RACE RNA-seq
alignment (STAR 2.4.2a, ENCODE standard options, except --outFilterScoreMinOverLread 0.4 --outFilterMatchNminOverLread 0.4 --  outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04)
gene count (HTSeq-count 0.7.1, default options, except -m intersection-strict)
Genome_build: Dmel r6.10
Supplementary_files_format_and_content: htseq.tab (gene counts), STAR.tab (summary of mapping results), df_libs.csv (sample information)

molecule: total RNA

organism: Drosophila melanogaster

source_name: neuron

extract_protocol: Modified SMART-seq2 (Li et al. 2017)

tag: genotype

tag: cell type

value: neuron

tag: number of cells


title: CSC10MDNMT1_R1

value: DNMT1 (Sigma-Aldrich, D4692)


title: C10MH3K4_R1


title: C10MDNMT1_R1


title: C155-GFP [IL7017-709-502]


title: C155-GFP [IL7017-709-503]


title: C10MH3K27_R1

value: H3K27me3 (Millipore, 07-449)


title: CSC10DH3K27_R1

value: 10 Days


title: CSC10DH3K4_R1


title: CSC10DInput_R1


title: CSC10DEZH2_R1


title: CSC10DDNMT1_R1


title: LIVER2

first: Ming

last: Zheng

address: Room L212, Lane Bldg

description: Processed data file: log2CPM.csv

data_processing:
Adapter sequences and low-quality bases at the end of the reads were then removed using the Cutadapt software.
The reads were then aligned to human exon sequences (Build GRCh38) using STAR.
The expression level of each gene for each cell were then quantified using the FeatureCounts tool.
The counts-per-million (CPM) values were generated using scater package in R.
Genome_build: GRCh38
Supplementary_files_format_and_content: log2CPM.csv: Comma-delimited file containing the log2-transformed CPM values.

source_name: normal liver tissue

growth_protocol: Differentiation protocol details described in manuscript. Briefly, we collected samples from different stages during iPSC toward hepatic organoids.

extract_protocol:
SMART-SEQ2
Nextera XT DNA Sample Preparation kit.

tag: tissue

value: normal liver


title: LIVER1

description: Processed data file: log2CPM.csv


title: C10DInput_R1


title: C10DH3K27_R1


title: C10DH3K4_R1


title: C10DEZH2_R1


title: DM

description: Processed data file: log2CPM.csv

source_name: secondary hepatic organoids in differentiation medium

value: secondary hepatic organoids

tag: day

value: > day 62


title: t_PGDX4579X3_Ex

data_processing:
Before mutation calling, primary processing of sequence data both the sample and for control was performed using Illumina CASAVA software (version 1.8), including masking of adaptor sequences
Sequence reads were aligned against the human reference genome (version hg19) using ELAND with additional realignment of select regions using the Needleman-Wunsch method.
Candidate mutations, consisting of point mutations, insertions, and deletions, were then identified using VariantDx across the whole exome. VariantDx examines sequence alignments of samples against a control while applying filters to exclude alignment and sequencing artifacts
Potential alterations were compared with mouse sequences from experimentally obtained mouse whole-exome and targeted sequence data as well as the reference mouse genome (mm9) to remove mouse-specific variants.
Amplification analyses were performed using the digital karyotyping approach by comparing the number of reads mapping to a particular gene with the average number of reads mapping to each gene in the panel, along with a minor allele fraction analysis of heterozygous single nucleotide polymorphisms contained within each gene. Candidate somatic mutations were further filtered on the basis of gene annotation to identify those occurring in protein coding regions. Functional consequences were predicted using snpEff and a custom database of CCDS, RefSeq and Ensembl annotations using the latest transcript versions available on hg19 from UCSC (https://genome.ucsc.edu/). Predictions were ordered to prefer transcripts with canonical start and stop codons and CCDS or Refseq transcripts over Ensembl when available.
Genome_build: hg19

source_name: xenograft from CSC treated HBEC cells with KRASV12

extract_protocol:
DNA was extracted from cells and xenograft tissues using the Qiagen DNeasy blood and tissue mini kit
Fragmented genomic DNA was used for Illumina TruSeq library construction.  Paired-end sequencing, resulting in 100 or 150 bases from each end of the DNA fragments for the exome or targeted sequencing libraries, respectively, was performed using Illumina HiSeq 2000/2500 instrumentation

treatment_protocol: cells were treated with 10 ug/ml CSC or DMSO (con cells) for 15 months. Xenografts were obtained by injecting 15 month CSC treated cells with KRASV12 in NSG mice.

tag: sequencing technique

value: Exome

tag: treatment

value: xenograft from 15M CSC treated HBEC cells with KRASV12


title: C10DDNMT1_R1


title: CSC10MH3K27_R1


title: t_PGDX4579X1_Ex


title: t_PGDX4579X2_Ex


title: t_PGDX4580T_Ex

source_name: HBEC cells

value: CSC for 15 months


title: C10MEZH2_R1


title: n_PGDX4580N_Ex

value: DMSO for 15 months


title: n_PGDX4579N_Ex

value: untreated


title: LD-32

city: Orlando

first: Charissa

last: de Bekker

state: FL

address: UCF Biology Dept, 4110 Libra Dr

department: Biology

institute: UCF

description: organism name: Ophiocordyceps kimflemingiae

data_processing:
RNA reads were mapped to the latest version of the O. kimflemingiae genome with CLC Genomics Workbench 9. Reads were also mapped to inter-genic regions and other parameters were kept at default settings. Expression levels were calculated for all genes in the genome and normalized to Reads Per Kilobase of exon model per Million mapped reads (RPKM).
Genome_build: LAZP02000000. This genome accession includes the gene IDs used in the processed data files.
Supplementary_files_format_and_content: text files containing the normalized gene expression values RPKM of all genes under cycling light conditions (samples LD-4 to LD-48) and under constant darkness conditions (samples DD-4 to DD-48)

molecule: polyA RNA

organism: Ophiocordyceps kimflemingiae

source_name: Fungal culture grown in Grace's insect cell culture media wit 10% FBS

growth_protocol: fungal cultures were grown in 25cm2 culture flasks holding 20 mL supplemented insect medium shaken at 60 rpm at 28C

extract_protocol:
Fungal blastospores were spun down and pellets were flash frozen in liquid nitrogen.The RNA was extracted using TRIzol reagent and subsequently cleaned up with RNAeasy MinElute columns (Qiagen).
mRNA-Seq libraries were constructed with a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs)

value: fungal mycelium

tag: strain

tag: photoperiod

value: light cycling (LD)

tag: sampling time point


title: LD-44


title: LD-36


title: LD-40


title: LD-12


title: LD-20


title: LD-8


title: LD-4


title: LD-16


title: DD-48

value: constant darkness (DD)


title: DD-36


title: LD-48


title: DD-32


title: DD-40


title: DD-28


title: LD-24


title: DD-44


title: DD-24


title: T08

city: Nanjing

first: Xiangyang

last: Yu

state: Jiangsu

address: 50 Zhongling Road

country: China

institute: Jiangsu Academy of Agricultural Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase Million was the value of expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced.TPM means transcripts per million,using the formula of R1*1000*1000000/(L1*Rtoatl),R1: The count value of the gene;L1: The length of the gene;Rtotal: the sum value of all the corrected count value .
Genome_build: Genome of Fusarium oxysporum f. sp. lycopersici 4287 was used for alignment.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Fusarium oxysporum

source_name: Fungus

growth_protocol: F. oxysporum was cultured in PDB under the condition of 150 rpm at 28 ℃ for 72 h.

extract_protocol:
The medium was removed,F. oxysporum was collected and ground to powder, and RNA was extracted using Trizol reagent. 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: F. oxysporum was cultured in PDB or PDB contained 80 μg/mL of thymol.

value: Fusarium oxysporum f.sp. niveum

value: Fusarium oxysporum cultured in PDB media with 80 μg/mL of thymol

tag: incubation time

value: 72 hours

tag: incubation conditions

value: 150 rpm at 28 °C in dark


title: T07


title: DD-20


title: T06


title: LD-28


title: DD-16


title: T03

value: Fusarium oxysporum cultured in PDB media


title: CTL H3K79me3_ChIPSeq

city: Seoul

first: Joo-Young

last: Kang

address: Heukseok-dong, Dongjak-gu

country: South Korea

institute: Chung-Ang University

description:
CTL-K79me3
Control

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2.
Peak callings were performed using MACS.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *peaks.txt: Tab-delimited text files include read count values for each Sample.

source_name: shCTL stable cells, H3K79me3 ChIP

extract_protocol:
DNA fragment was obtained from IP. 1ug DNA was used for the construction of sequencing libraries.
The construction of library was performed using NEBNext®UltraTM DNA Library Prep Kit for Illumina (New England Biolabs, UK) according to the manufacturer's instructions.

tag: stable shrna

value: shCTL


title: KDM2B-KD input DNA

description:
KD-Input 1/10
KDM2B knockdown

source_name: shKDM2B stable cells, input


title: DD-12


title: KDM2B-KD H3K79me2_ChIPSeq

description:
KD-K79me2
KDM2B knockdown

source_name: shKDM2B stable cells, H3K79me2 ChIP


title: KDM2B-KD H3K79me3_ChIPSeq

description:
KD-K79me3
KDM2B knockdown

source_name: shKDM2B stable cells, H3K79me3 ChIP


title: CTL H3K79me2_ChIPSeq

description:
CTL-K79me2
Control

source_name: shCTL stable cells, H3K79me2 ChIP


title: T02


title: DD-8


title: CTL input DNA

description:
CTL-Input 1/10
Control

source_name: shCTL stable cells, input


title: T01


title: DD-4


title: WT_gp33+ CD8+ T cells_5826

status: Public on Oct 20 2017

city: Ann Arbor

first: Shannon

last: Carty

state: MI

address: 109 Zina Pitcher Place

institute: University of Michigan

data_processing:
Basecalls generated using Illumina CASAVA . Sequence data generated converted to FASTQ files using Illumina bcl2fastq software
Sequence data generated converted to FASTQ files using Illumina bcl2fastq software and adaptor reads trimmed
Bismark used to align the filtered, adapter trimmed sequence reads to the bisulfite converted reference mus musculus genome mm9 and determine the methylation context for each cytosine.
Raw data processed via ERRBS pipeline (Garrett-bakelman et al., 2015)
Genome_build: mm9

organism: Mus musculus

source_name: WT_gp33+ CD8+ T cells

extract_protocol:
gp33+CD44+ CD8+TCRb+ cells were sorted using flow cytometric sorting. Genomic DNA was generated using Qiagen AllPrep DNA/RNA kit as per manufacturer's protocol. Genomic DNA was bisulfite converted using the EZ DNA Methylation kit (Zymo Research). Base-pair resolution DNA Methylation was performed on control and TET2-deficient gp33+CD8+ T cells (n=4/genotype) as described in Akalin et al., PLoS Genet, 2012.
Library was constructed as per protocol at Cornell Epigenomics Core

tag: strain background

tag: genotype/variation

value: WT

tag: sample id

tag: time point

value: day 8 of LCMV-Armstrong infection

value: gp33+ CD8+ T cells


title: WT_gp33+ CD8+ T cells_5858


title: TET2cKO_gp33+ CD8+ T cells_5856

source_name: TET2cKO_gp33+ CD8+ T cells

value: TET2cKO; TET2fl/flCD4Cre+


title: WT_gp33+ CD8+ T cells_5763


title: WT_gp33+ CD8+ T cells_5824


title: TET2cKO_gp33+ CD8+ T cells_5765


title: TET2cKO_gp33+ CD8+ T cells_5767


title: TET2cKO_gp33+ CD8+ T cells_5819


title: ChIP-seq from liver (ENCLB418CNI)

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR297GII/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HNF4G-human
experiment encode accession: ENCSR297GII
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR904IXG, ENCSR849OTN
encode release date: 2016-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB418CNI

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

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

extract_protocol: not provided

tag: antibody

value: liver

value: tissue

tag: description

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

tag: biosample encode accession

tag: age

value: 4 year

tag: dev stage

value: child

tag: Sex

value: female

tag: health state

value: healthy

tag: lab

value: Michael Snyder, Stanford

tag: link

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

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


title: ChIP-seq from HEK293 (ENCLB109VHQ)

description:
https://www.encodeproject.org/experiments/ENCSR295BIP/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF777 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR295BIP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR468NLK, ENCSR110ZVM, ENCSR260MAS, ENCSR873PPH, ENCSR851FFP, ENCSR523KUQ, ENCSR236FPN, ENCSR860UAT, ENCSR398UVH, ENCSR840JVQ, ENCSR499QIO, ENCSR679WSJ, ENCSR736BTL, ENCSR537CWQ, ENCSR316OQD, ENCSR278MZO, ENCSR603CJM, ENCSR361UQO, ENCSR499OOH, ENCSR123TVS, ENCSR049NDP, ENCSR311DYU, ENCSR782QKO
encode release date: 2017-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB109VHQ
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF777 fusion protein

tag: line

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF777 under the control of a CMV promoter.

value: unknown

value: embryonic

value: ENCBS900QTF at ENCODE; https://www.encodeproject.org/ENCBS900QTF/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from transverse colon (ENCLB111FWP)

description:
https://www.encodeproject.org/experiments/ENCSR293DLP/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Wed Aug 24 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR293DLP
assay title: ChIP-seq
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB111FWP

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

extract_protocol: extraction method: see document

value: Control

value: transverse colon

value: male

value: Richard Myers, HAIB

value: 37 year

value: adult

value: ENCBS272LPG at ENCODE; https://www.encodeproject.org/ENCBS272LPG/

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


title: ChIP-seq from liver (ENCLB995PTO)

description:
https://www.encodeproject.org/experiments/ENCSR297GII/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HNF4G-human
experiment encode accession: ENCSR297GII
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR904IXG, ENCSR849OTN
encode release date: 2016-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB995PTO

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: healthy

value: Michael Snyder, Stanford


title: ChIP-seq from HEK293 (ENCLB644HCK)

description:
https://www.encodeproject.org/experiments/ENCSR283MWQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF133 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR283MWQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB644HCK
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF133 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF133 under the control of a CMV promoter.

value: unknown

value: embryonic

value: ENCBS431ZNZ at ENCODE; https://www.encodeproject.org/ENCBS431ZNZ/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from upper lobe of left lung (ENCLB572PFM)

description:
https://www.encodeproject.org/experiments/ENCSR290QBB/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on upper lobe of left lung
experiment encode accession: ENCSR290QBB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR949XFR
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB572PFM

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

value: upper lobe of left lung

value: male

value: Richard Myers, HAIB

value: 54 year

value: adult

value: ENCBS708WNV at ENCODE; https://www.encodeproject.org/ENCBS708WNV/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/632f8c04-c6ae-4a33-b452-2fcbeff100f3/@@download/attachment/82358.svs


title: ChIP-seq from subcutaneous adipose tissue (ENCLB870THR)

description:
https://www.encodeproject.org/experiments/ENCSR281NCY/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Tue Aug 30 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR281NCY
assay title: ChIP-seq
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB870THR

source_name: Homo sapiens subcutaneous adipose tissue female adult (53 years)

value: Control

value: subcutaneous adipose tissue

value: tissue

value: female

value: 53 year

value: ENCBS740VLK at ENCODE; https://www.encodeproject.org/ENCBS740VLK/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/3c95a385-bcab-41e5-a486-468e71e759b1/@@download/attachment/83396.svs


title: ChIP-seq from HEK293 (ENCLB606UHT)

description:
https://www.encodeproject.org/experiments/ENCSR295BIP/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF777 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR295BIP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR468NLK, ENCSR110ZVM, ENCSR260MAS, ENCSR873PPH, ENCSR851FFP, ENCSR523KUQ, ENCSR236FPN, ENCSR860UAT, ENCSR398UVH, ENCSR840JVQ, ENCSR499QIO, ENCSR679WSJ, ENCSR736BTL, ENCSR537CWQ, ENCSR316OQD, ENCSR278MZO, ENCSR603CJM, ENCSR361UQO, ENCSR499OOH, ENCSR123TVS, ENCSR049NDP, ENCSR311DYU, ENCSR782QKO
encode release date: 2017-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB606UHT
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF777 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: unknown

value: embryonic

value: ENCBS434EGA at ENCODE; https://www.encodeproject.org/ENCBS434EGA/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from HEK293 (ENCLB107WQC)

description:
https://www.encodeproject.org/experiments/ENCSR283MWQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF133 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR283MWQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB107WQC
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF133 under the control of a CMV promoter.

value: ENCBS669LUY at ENCODE; https://www.encodeproject.org/ENCBS669LUY/


title: ChIP-seq from C4-2B (ENCLB205HAN)

description:
https://www.encodeproject.org/experiments/ENCSR279KIX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on human C4-2B
experiment encode accession: ENCSR279KIX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR585FQO
encode release date: 2017-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB205HAN
size range: 450-650

source_name: Homo sapiens C4-2B immortalized cell line

value: male

value: prostate adenocarcinoma

value: 50 year

value: adult

value: ENCBS109FVF at ENCODE; https://www.encodeproject.org/ENCBS109FVF/

value: derived from ENCODE donor ENCDO000ACX; https://www.encodeproject.org/ENCDO000ACX/


title: ChIP-seq from C4-2B (ENCLB151CZX)

description:
https://www.encodeproject.org/experiments/ENCSR279KIX/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on human C4-2B
experiment encode accession: ENCSR279KIX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR585FQO
encode release date: 2017-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB151CZX
size range: 450-650

value: ENCBS728XMM at ENCODE; https://www.encodeproject.org/ENCBS728XMM/


title: ChIP-seq from suprapubic skin (ENCLB656YOW)

description:
https://www.encodeproject.org/experiments/ENCSR277LNZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human suprapubic skin
experiment encode accession: ENCSR277LNZ
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB656YOW
size range: 450-650

source_name: Homo sapiens suprapubic skin tissue male adult (54 years)

value: Control

value: suprapubic skin

value: tissue

value: 54 year

value: ENCBS134OKV at ENCODE; https://www.encodeproject.org/ENCBS134OKV/

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


title: ChIP-seq from MCF-7 (ENCLB509HTQ)

description:
https://www.encodeproject.org/experiments/ENCSR265WJC/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-KLF4 ChIP-seq on human MCF-7
experiment encode accession: ENCSR265WJC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR167UME
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB509HTQ
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens MCF-7 immortalized cell line stably expressing C-terminal eGFP-KLF4 fusion protein

value: immortalized cell line

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to KLF4

value: female

value: Kevin White, UChicago

tag: passage number

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS984RGW at ENCODE; https://www.encodeproject.org/ENCBS984RGW/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA17; http://web.expasy.org/cellosaurus/CVCL_HA17


title: ChIP-seq from suprapubic skin (ENCLB571XIR)

description:
https://www.encodeproject.org/experiments/ENCSR270TYZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on suprapubic skin
experiment encode accession: ENCSR270TYZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR213GWR
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB571XIR

source_name: Homo sapiens suprapubic skin tissue male adult (37 years)

value: male

value: Richard Myers, HAIB

value: 37 year

value: adult

value: ENCBS090NNK at ENCODE; https://www.encodeproject.org/ENCBS090NNK/

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


title: ChIP-seq from MCF-7 (ENCLB135RYA)

description:
https://www.encodeproject.org/experiments/ENCSR265WJC/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-KLF4 ChIP-seq on human MCF-7
experiment encode accession: ENCSR265WJC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR167UME
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB135RYA
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: ENCBS949BEW at ENCODE; https://www.encodeproject.org/ENCBS949BEW/


title: ChIP-seq from body of pancreas (ENCLB993ADU)

description:
https://www.encodeproject.org/experiments/ENCSR265PFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human body of pancreas
experiment encode accession: ENCSR265PFQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR676WCI
encode release date: 2016-11-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB993ADU
size range: 450-650

source_name: Homo sapiens body of pancreas tissue male adult (54 years)

value: CTCF

value: body of pancreas

value: tissue

value: Michael Snyder, Stanford

value: 54 year

value: ENCBS867VCV at ENCODE; https://www.encodeproject.org/ENCBS867VCV/

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


title: ChIP-seq from VCaP (ENCLB352TMT)

description:
https://www.encodeproject.org/experiments/ENCSR265ARE/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on human VCaP
experiment encode accession: ENCSR265ARE
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR716BTZ
encode release date: 2017-07-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB352TMT
size range: 450-650

source_name: Homo sapiens VCaP immortalized cell line

value: VCaP

value: immortalized cell line

value: prostate adenocarcinoma

value: 50 year

value: ENCBS626UQL at ENCODE; https://www.encodeproject.org/ENCBS626UQL/

value: derived from ENCODE donor ENCDO000ACX; https://www.encodeproject.org/ENCDO000ACX/


title: ChIP-seq from MCF-7 (ENCLB425YMK)

description:
https://www.encodeproject.org/experiments/ENCSR277BXW/
***************
biological replicate number: 2
technical replicate number: 1
description: ZBTB7B ChIP-seq on human MCF-7
experiment encode accession: ENCSR277BXW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB425YMK
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

value: adult

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

value: ENCBS488MMM at ENCODE; https://www.encodeproject.org/ENCBS488MMM/

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

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


title: ChIP-seq from A549 (ENCLB034KPQ)

description:
https://www.encodeproject.org/experiments/ENCSR277OOQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ZC3H11A ChIP-seq on human A549
experiment encode accession: ENCSR277OOQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR610YRT, ENCSR871XML
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB034KPQ
size range: 450-650

source_name: Homo sapiens A549 immortalized cell line

value: epithelial cell line derived from a 58 year old caucasian male lung carcinoma.

value: 58 year

value: male

value: Michael Snyder, Stanford

value: ENCBS848SUF at ENCODE; https://www.encodeproject.org/ENCBS848SUF/

value: Derived from ENCODE donor ENCDO000AAZ; https://www.encodeproject.org/ENCDO000AAZ/

value: ENCODE dbxrefs Cellosaurus CVCL_0023; http://web.expasy.org/cellosaurus/CVCL_0023

value: ATCC sample source; http://www.atcc.org/Products/All/CCL-185.aspx


title: ChIP-seq from MCF-7 (ENCLB310LPG)

description:
https://www.encodeproject.org/experiments/ENCSR277BXW/
***************
biological replicate number: 1
technical replicate number: 1
description: ZBTB7B ChIP-seq on human MCF-7
experiment encode accession: ENCSR277BXW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB310LPG
size range: 450-650

value: immortalized cell line

value: ENCBS158RRU at ENCODE; https://www.encodeproject.org/ENCBS158RRU/


title: ChIP-seq from A549 (ENCLB070PKR)

description:
https://www.encodeproject.org/experiments/ENCSR277OOQ/
***************
biological replicate number: 3
technical replicate number: 1
description: ZC3H11A ChIP-seq on human A549
experiment encode accession: ENCSR277OOQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR610YRT, ENCSR871XML
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB070PKR
size range: 450-650

value: adult

value: ENCBS611JSC at ENCODE; https://www.encodeproject.org/ENCBS611JSC/


title: ChIP-seq from VCaP (ENCLB697NZR)

description:
https://www.encodeproject.org/experiments/ENCSR265ARE/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human VCaP
experiment encode accession: ENCSR265ARE
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR716BTZ
encode release date: 2017-07-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB697NZR
size range: 450-650

value: CTCF

value: VCaP

value: prostate adenocarcinoma

value: 50 year

value: ENCBS316RCQ at ENCODE; https://www.encodeproject.org/ENCBS316RCQ/

value: derived from ENCODE donor ENCDO000ACX; https://www.encodeproject.org/ENCDO000ACX/


title: ChIP-seq from ovary (ENCLB341QWK)

description:
https://www.encodeproject.org/experiments/ENCSR255HLM/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Thu Nov 03 2016 23:00:00 GMT-0600 (CST)
experiment encode accession: ENCSR255HLM
assay title: ChIP-seq
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB341QWK

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

value: Control

value: ovary

value: tissue

value: female

value: Richard Myers, HAIB

value: 53 year

value: ENCBS874ZKQ at ENCODE; https://www.encodeproject.org/ENCBS874ZKQ/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/76117c8f-427c-46a3-83e7-06a793af0684/@@download/attachment/83379.svs


title: ChIP-seq from HEK293 (ENCLB272QRO)

description:
https://www.encodeproject.org/experiments/ENCSR253CKN/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZSCAN21 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR253CKN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2017-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB272QRO
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZSCAN21 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZSCAN21 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: unknown

value: embryonic

value: ENCBS686CCI at ENCODE; https://www.encodeproject.org/ENCBS686CCI/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from HepG2 (ENCLB306RKG)

description:
https://www.encodeproject.org/experiments/ENCSR258SXK/
***************
biological replicate number: 1
technical replicate number: 1
description: SFPQ ChIP-seq in HepG2
experiment encode accession: ENCSR258SXK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR735QJO
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB306RKG
size range: 200-400

source_name: Homo sapiens HepG2 immortalized cell line

value: SFPQ

value: SFPQ ChIP-seq in HepG2

value: male

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS267AEP at ENCODE; https://www.encodeproject.org/ENCBS267AEP/

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


title: ChIP-seq from neural cell (ENCLB175URE)

description:
https://www.encodeproject.org/experiments/ENCSR198ZYJ/
***************
biological replicate number: 1
technical replicate number: 1
description: RAD21 ChIP-seq on human neural cell
experiment encode accession: ENCSR198ZYJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR634PYN
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB175URE
size range: 450-650

source_name: Homo sapiens neural in vitro differentiated cells male embryo originated from H1-hESC

value: neural cell

value: in vitro differentiated cells

value: Neurons derived from H1 embryonic stem cells

value: healthy

value: ENCBS980OYK at ENCODE; https://www.encodeproject.org/ENCBS980OYK/

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

value: ENCODE dbxrefs H1-neurons; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=H1-neurons


title: ChIP-seq from esophagus muscularis mucosa (ENCLB945FGG)

description:
https://www.encodeproject.org/experiments/ENCSR249UPE/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Wed Sep 07 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR249UPE
assay title: ChIP-seq
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB945FGG

source_name: Homo sapiens esophagus muscularis mucosa tissue female adult (53 years)

value: Control

value: esophagus muscularis mucosa

value: tissue

value: female

value: Richard Myers, HAIB

value: 53 year

value: adult

value: ENCBS078KRE at ENCODE; https://www.encodeproject.org/ENCBS078KRE/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/cfd92841-5b08-4c14-8e0b-4d4f6420f799/@@download/attachment/83388.svs


title: ChIP-seq from HEK293 (ENCLB007TUM)

description:
https://www.encodeproject.org/experiments/ENCSR253CKN/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZSCAN21 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR253CKN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2017-04-05
lab: Michael Snyder, Stanford
library encode accession: ENCLB007TUM
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZSCAN21 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: unknown

value: embryonic

value: ENCBS685DHF at ENCODE; https://www.encodeproject.org/ENCBS685DHF/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from HepG2 (ENCLB764ORA)

description:
https://www.encodeproject.org/experiments/ENCSR258SXK/
***************
biological replicate number: 2
technical replicate number: 1
description: SFPQ ChIP-seq in HepG2
experiment encode accession: ENCSR258SXK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR735QJO
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB764ORA
size range: 200-400

value: SFPQ

value: SFPQ ChIP-seq in HepG2

value: male

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS950TLN at ENCODE; https://www.encodeproject.org/ENCBS950TLN/

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


title: ChIP-seq from sigmoid colon (ENCLB160EUD)

description:
https://www.encodeproject.org/experiments/ENCSR244ZAO/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on sigmoid colon
experiment encode accession: ENCSR244ZAO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR509RYG
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB160EUD

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

value: sigmoid colon

value: tissue

value: female

value: Richard Myers, HAIB

value: 51 year

value: adult

value: ENCBS538MFJ at ENCODE; https://www.encodeproject.org/ENCBS538MFJ/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/76821021-0729-4f4a-8283-353359136254/@@download/attachment/84281.svs


title: Hi-C from HepG2 (ENCLB625TGE)

description:
https://www.encodeproject.org/experiments/ENCSR194SRI/
***************
biological replicate number: 2
technical replicate number: 1
description: HiC experiment done on HepG2
experiment encode accession: ENCSR194SRI
assay title: Hi-C
encode release date: 2017-09-28
lab: Job Dekker, UMass
library encode accession: ENCLB625TGE

value: immortalized cell line

value: John Stamatoyannopoulos, UW

value: ENCBS232MEB at ENCODE; https://www.encodeproject.org/ENCBS232MEB/


title: ChIP-seq from 22Rv1 (ENCLB516BSK)

description:
https://www.encodeproject.org/experiments/ENCSR246MLJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ZFX ChIP-seq on human 22Rv1
experiment encode accession: ENCSR246MLJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR933UGQ
encode release date: 2017-06-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB516BSK
size range: 450-650

source_name: Homo sapiens 22Rv1 immortalized cell line

value: ZFX

value: not collected

value: Michael Snyder, Stanford

value: carcinoma (prostate)

value: unknown

value: ENCBS383WOY at ENCODE; https://www.encodeproject.org/ENCBS383WOY/

value: derived from ENCODE donor ENCDO719HIY; https://www.encodeproject.org/ENCDO719HIY/


title: Hi-C from HepG2 (ENCLB022KPF)

description:
https://www.encodeproject.org/experiments/ENCSR194SRI/
***************
biological replicate number: 1
technical replicate number: 1
description: HiC experiment done on HepG2
experiment encode accession: ENCSR194SRI
assay title: Hi-C
encode release date: 2017-09-28
lab: Job Dekker, UMass
library encode accession: ENCLB022KPF

value: male

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS061GMD at ENCODE; https://www.encodeproject.org/ENCBS061GMD/

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


title: ChIP-seq from epithelial cell of prostate (ENCLB046TKT)

description:
https://www.encodeproject.org/experiments/ENCSR196HOM/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human epithelial cell of prostate
experiment encode accession: ENCSR196HOM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR131SEB
encode release date: 2017-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB046TKT
size range: 450-650

source_name: Homo sapiens epithelial of prostate primary cell male

value: CTCF

value: epithelial cell of prostate

value: primary cell

value: ENCBS706NVS at ENCODE; https://www.encodeproject.org/ENCBS706NVS/

value: derived from ENCODE donor ENCDO569WSJ; https://www.encodeproject.org/ENCDO569WSJ/


title: ChIP-seq from neural cell (ENCLB038MYD)

description:
https://www.encodeproject.org/experiments/ENCSR198ZYJ/
***************
biological replicate number: 2
technical replicate number: 1
description: RAD21 ChIP-seq on human neural cell
experiment encode accession: ENCSR198ZYJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR634PYN
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB038MYD
size range: 450-650

value: neural cell

value: in vitro differentiated cells

value: Neurons derived from H1 embryonic stem cells

value: healthy

value: embryonic

value: ENCBS163EMU at ENCODE; https://www.encodeproject.org/ENCBS163EMU/

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

value: ENCODE dbxrefs H1-neurons; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=H1-neurons


title: ChIP-seq from epithelial cell of prostate (ENCLB116DCU)

description:
https://www.encodeproject.org/experiments/ENCSR196HOM/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on human epithelial cell of prostate
experiment encode accession: ENCSR196HOM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR131SEB
encode release date: 2017-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB116DCU
size range: 450-650

value: male

value: Michael Snyder, Stanford

value: unknown

value: ENCBS143IKI at ENCODE; https://www.encodeproject.org/ENCBS143IKI/


title: ChIP-seq from neural cell (ENCLB092FSB)

description:
https://www.encodeproject.org/experiments/ENCSR198ZYJ/
***************
biological replicate number: 1
technical replicate number: 2
description: RAD21 ChIP-seq on human neural cell
experiment encode accession: ENCSR198ZYJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR634PYN
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB092FSB

value: ENCBS980OYK at ENCODE; https://www.encodeproject.org/ENCBS980OYK/


title: ChIP-seq from HEK293 (ENCLB589ZPX)

description:
https://www.encodeproject.org/experiments/ENCSR194KWL/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF704 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR194KWL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB589ZPX
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF704 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF704 under the control of a CMV promoter.

value: female

value: ENCBS514PWP at ENCODE; https://www.encodeproject.org/ENCBS514PWP/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from 22Rv1 (ENCLB133TRK)

description:
https://www.encodeproject.org/experiments/ENCSR246MLJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ZFX ChIP-seq on human 22Rv1
experiment encode accession: ENCSR246MLJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR933UGQ
encode release date: 2017-06-15
lab: Michael Snyder, Stanford
library encode accession: ENCLB133TRK
size range: 450-650

value: ZFX

value: not collected

value: carcinoma (prostate)

value: ENCBS596KKM at ENCODE; https://www.encodeproject.org/ENCBS596KKM/

value: derived from ENCODE donor ENCDO719HIY; https://www.encodeproject.org/ENCDO719HIY/


title: ChIP-seq from MCF-7 (ENCLB602OOL)

description:
https://www.encodeproject.org/experiments/ENCSR239POD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human MCF-7
experiment encode accession: ENCSR239POD
assay title: ChIP-seq
encode release date: 2017-07-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB602OOL
size range: 450-650

value: Control

value: breast cancer (adenocarcinoma)

value: 69 year

value: adult

value: ENCBS968SNH at ENCODE; https://www.encodeproject.org/ENCBS968SNH/

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


title: ChIP-seq from MCF-7 (ENCLB201ELE)

description:
https://www.encodeproject.org/experiments/ENCSR239POD/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human MCF-7
experiment encode accession: ENCSR239POD
assay title: ChIP-seq
encode release date: 2017-07-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB201ELE
size range: 450-650

value: Michael Snyder, Stanford

value: ENCBS573TKZ at ENCODE; https://www.encodeproject.org/ENCBS573TKZ/


title: ChIP-seq from K562 (ENCLB547ZUO)

description:
https://www.encodeproject.org/experiments/ENCSR189TRZ/
***************
biological replicate number: 2
technical replicate number: 1
description: TCF12 ChIP-seq on human K562
experiment encode accession: ENCSR189TRZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-07-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB547ZUO
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS320BUL at ENCODE; https://www.encodeproject.org/ENCBS320BUL/

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

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


title: ChIP-seq from K562 (ENCLB152PAW)

description:
https://www.encodeproject.org/experiments/ENCSR239ZLZ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-FOSL1 ChIP-seq on human K562
experiment encode accession: ENCSR239ZLZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR039ZBB
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB152PAW
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-FOSL1 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to FOSL1

value: female

value: Kevin White, UChicago

value: ENCBS894HTX at ENCODE; https://www.encodeproject.org/ENCBS894HTX/

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

value: ENCODE dbxrefs Cellosaurus CVCL_GZ84; http://web.expasy.org/cellosaurus/CVCL_GZ84


title: ChIP-seq from K562 (ENCLB402PWC)

description:
https://www.encodeproject.org/experiments/ENCSR239ZLZ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-FOSL1 ChIP-seq on human K562
experiment encode accession: ENCSR239ZLZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR039ZBB
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB402PWC
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: adult

value: ENCBS129EER at ENCODE; https://www.encodeproject.org/ENCBS129EER/


title: ChIP-seq from K562 (ENCLB631MXP)

description:
https://www.encodeproject.org/experiments/ENCSR189TRZ/
***************
biological replicate number: 1
technical replicate number: 1
description: TCF12 ChIP-seq on human K562
experiment encode accession: ENCSR189TRZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-07-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB631MXP
size range: 450-650

value: ENCBS783WYV at ENCODE; https://www.encodeproject.org/ENCBS783WYV/


title: ChIP-seq from sigmoid colon (ENCLB381HOH)

description:
https://www.encodeproject.org/experiments/ENCSR185GDB/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Mon Sep 19 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR185GDB
assay title: ChIP-seq
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB381HOH

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

value: Control

value: sigmoid colon

value: tissue

value: male

value: Richard Myers, HAIB

value: 37 year

value: ENCBS806WZK at ENCODE; https://www.encodeproject.org/ENCBS806WZK/

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


title: ChIP-seq from K562 (ENCLB234YCU)

description:
https://www.encodeproject.org/experiments/ENCSR290MUH/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-GABPA ChIP-seq on human K562
experiment encode accession: ENCSR290MUH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR311ULL
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB234YCU
size range: 200-800

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-GABPA fusion protein

value: eGFP-GABPA

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to GABPA

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS084QBR at ENCODE; https://www.encodeproject.org/ENCBS084QBR/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ86; http://web.expasy.org/cellosaurus/CVCL_GZ86


title: ChIP-seq from K562 (ENCLB950PVQ)

description:
https://www.encodeproject.org/experiments/ENCSR296MXW/
***************
biological replicate number: 1
technical replicate number: 1
description: HNRNPUL1 ChIP-seq in K562
experiment encode accession: ENCSR296MXW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR966DOU
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB950PVQ
size range: 200-400

value: HNRNPUL1 ChIP-seq in K562

value: female

value: Xiang-Dong Fu, UCSD

value: adult

value: ENCBS379OMY at ENCODE; https://www.encodeproject.org/ENCBS379OMY/

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


title: ChIP-seq from sigmoid colon (ENCLB802CDJ)

description:
https://www.encodeproject.org/experiments/ENCSR236MWZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human sigmoid colon
experiment encode accession: ENCSR236MWZ
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB802CDJ
size range: 450-650

source_name: Homo sapiens sigmoid colon tissue female adult (53 years)

value: Control

value: sigmoid colon

value: tissue

value: Michael Snyder, Stanford

value: ENCBS835BNK at ENCODE; https://www.encodeproject.org/ENCBS835BNK/

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


title: ChIP-seq from HepG2 (ENCLB791GPL)

description:
https://www.encodeproject.org/experiments/ENCSR182QWU/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR182QWU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2017-03-16
lab: Richard Myers, HAIB
library encode accession: ENCLB791GPL

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-ZNF3 fusion protein

value: immortalized cell line

value: male

value: Richard Myers, HAIB

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS531RMF at ENCODE; https://www.encodeproject.org/ENCBS531RMF/

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 HEK293 (ENCLB198FZC)

description:
https://www.encodeproject.org/experiments/ENCSR178QVJ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF274 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR178QVJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB198FZC
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF274 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF274 under the control of a CMV promoter.

value: female

value: unknown

value: embryonic

value: ENCBS224QCU at ENCODE; https://www.encodeproject.org/ENCBS224QCU/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from K562 (ENCLB080BTA)

description:
https://www.encodeproject.org/experiments/ENCSR296MXW/
***************
biological replicate number: 2
technical replicate number: 1
description: HNRNPUL1 ChIP-seq in K562
experiment encode accession: ENCSR296MXW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR966DOU
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB080BTA
size range: 200-400

value: HNRNPUL1 ChIP-seq in K562

value: Xiang-Dong Fu, UCSD

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

value: ENCBS012WJD at ENCODE; https://www.encodeproject.org/ENCBS012WJD/

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


title: ChIP-seq from HEK293 (ENCLB249UQG)

description:
https://www.encodeproject.org/experiments/ENCSR178QVJ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF274 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR178QVJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB249UQG
size range: 450-650

value: immortalized cell line

value: Michael Snyder, Stanford

value: ENCBS755LQF at ENCODE; https://www.encodeproject.org/ENCBS755LQF/


title: ChIP-seq from HEK293 (ENCLB744KZY)

description:
https://www.encodeproject.org/experiments/ENCSR194KWL/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF704 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR194KWL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB744KZY
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF704 under the control of a CMV promoter.

value: ENCBS953VTG at ENCODE; https://www.encodeproject.org/ENCBS953VTG/


title: ChIP-seq from K562 (ENCLB467KUL)

description:
https://www.encodeproject.org/experiments/ENCSR257XVY/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF83 ChIP-seq on human K562
experiment encode accession: ENCSR257XVY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR414HEF
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB467KUL
size range: 200-800

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ZNF83 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF83

value: female

value: Kevin White, UChicago

value: ENCBS949ZPT at ENCODE; https://www.encodeproject.org/ENCBS949ZPT/

value: ENCODE dbxrefs Cellosaurus CVCL_HA10; http://web.expasy.org/cellosaurus/CVCL_HA10


title: ChIP-seq from K562 (ENCLB323JXY)

description:
https://www.encodeproject.org/experiments/ENCSR257TKE/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-CUX1 tagged K562 cell line.
experiment encode accession: ENCSR257TKE
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB323JXY
size range: 200-800

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-CUX1 fusion protein

value: Control

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to CUX1

value: ENCBS846OZP at ENCODE; https://www.encodeproject.org/ENCBS846OZP/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ78; http://web.expasy.org/cellosaurus/CVCL_GZ78


title: ChIP-seq from spleen (ENCLB641TAW)

description:
https://www.encodeproject.org/experiments/ENCSR234HEM/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human spleen
experiment encode accession: ENCSR234HEM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR376QKK
encode release date: 2016-07-11
lab: Michael Snyder, Stanford
library encode accession: ENCLB641TAW
size range: 450-650

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

value: CTCF

value: spleen

value: tissue

value: male

value: 37 year

value: adult

value: ENCBS780KFJ at ENCODE; https://www.encodeproject.org/ENCBS780KFJ/

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


title: ChIP-seq from HEK293 (ENCLB110VUQ)

description:
https://www.encodeproject.org/experiments/ENCSR233MWH/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-ZNF670 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR233MWH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB110VUQ
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF670 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF670 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: unknown

value: embryonic

value: ENCBS743ZXV at ENCODE; https://www.encodeproject.org/ENCBS743ZXV/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from K562 (ENCLB027BBG)

description:
https://www.encodeproject.org/experiments/ENCSR194IJN/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF766 ChIP-seq on human K562
experiment encode accession: ENCSR194IJN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR829NNQ
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB027BBG
size range: 200-800
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ZNF766 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF766

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS605NSN at ENCODE; https://www.encodeproject.org/ENCBS605NSN/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA09; http://web.expasy.org/cellosaurus/CVCL_HA09


title: ChIP-seq from K562 (ENCLB151ITS)

description:
https://www.encodeproject.org/experiments/ENCSR194IJN/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF766 ChIP-seq on human K562
experiment encode accession: ENCSR194IJN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR829NNQ
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB151ITS
size range: 200-800
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

value: adult

value: ENCBS105ZBV at ENCODE; https://www.encodeproject.org/ENCBS105ZBV/


title: ChIP-seq from HEK293 (ENCLB643TBI)

description:
https://www.encodeproject.org/experiments/ENCSR233MWH/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF670 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR233MWH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR007GUS, ENCSR049NDP, ENCSR110ZVM, ENCSR123TVS, ENCSR236FPN, ENCSR260MAS, ENCSR278MZO, ENCSR311DYU, ENCSR316OQD, ENCSR361UQO, ENCSR398UVH, ENCSR468NLK, ENCSR499OOH, ENCSR499QIO, ENCSR523KUQ, ENCSR537CWQ, ENCSR603CJM, ENCSR679WSJ, ENCSR736BTL, ENCSR782QKO, ENCSR840JVQ, ENCSR851FFP, ENCSR860UAT, ENCSR873PPH
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB643TBI
size range: 450-650

value: immortalized cell line

value: ENCBS698KCZ at ENCODE; https://www.encodeproject.org/ENCBS698KCZ/


title: ChIP-seq from K562 (ENCLB118KZH)

description:
https://www.encodeproject.org/experiments/ENCSR257XVY/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF83 ChIP-seq on human K562
experiment encode accession: ENCSR257XVY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR414HEF
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB118KZH
size range: 200-800

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF83

value: ENCBS340DSB at ENCODE; https://www.encodeproject.org/ENCBS340DSB/

value: ENCODE dbxrefs Cellosaurus CVCL_HA10; http://web.expasy.org/cellosaurus/CVCL_HA10


title: ChIP-seq from K562 (ENCLB314ILV)

description:
https://www.encodeproject.org/experiments/ENCSR230PTV/
***************
biological replicate number: 2
technical replicate number: 1
description: ZBTB2 ChIP-seq on human K562
experiment encode accession: ENCSR230PTV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB314ILV
size range: 450-650

value: Michael Snyder, Stanford

value: ENCBS389PVA at ENCODE; https://www.encodeproject.org/ENCBS389PVA/


title: ChIP-seq from HepG2 (ENCLB749VQV)

description:
https://www.encodeproject.org/experiments/ENCSR182QWU/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR182QWU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2017-03-16
lab: Richard Myers, HAIB
library encode accession: ENCLB749VQV

value: male

value: Richard Myers, HAIB

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS867TFR at ENCODE; https://www.encodeproject.org/ENCBS867TFR/

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


title: ChIP-seq from K562 (ENCLB637IGI)

description:
https://www.encodeproject.org/experiments/ENCSR178NTX/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-CUX1 ChIP-seq on human K562
experiment encode accession: ENCSR178NTX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR257TKE
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB637IGI
size range: 200-800

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to CUX1

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS544POC at ENCODE; https://www.encodeproject.org/ENCBS544POC/

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

value: ENCODE dbxrefs Cellosaurus CVCL_GZ78; http://web.expasy.org/cellosaurus/CVCL_GZ78


title: ChIP-seq from HepG2 (ENCLB907RSX)

description:
https://www.encodeproject.org/experiments/ENCSR183AXJ/
***************
biological replicate number: 1
technical replicate number: 1
description: HNRNPUL1 ChIP-seq in HepG2
experiment encode accession: ENCSR183AXJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR735QJO
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB907RSX
size range: 200-400

source_name: Homo sapiens HepG2 immortalized cell line

value: immortalized cell line

value: HNRNPUL1 ChIP-seq in HepG2

value: Xiang-Dong Fu, UCSD

value: ENCBS662TZZ at ENCODE; https://www.encodeproject.org/ENCBS662TZZ/


title: ChIP-seq from HepG2 (ENCLB108WWE)

description:
https://www.encodeproject.org/experiments/ENCSR183AXJ/
***************
biological replicate number: 2
technical replicate number: 1
description: HNRNPUL1 ChIP-seq in HepG2
experiment encode accession: ENCSR183AXJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR735QJO
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB108WWE
size range: 200-400

value: male

value: hepatocellular carcinoma

value: ENCBS747MTP at ENCODE; https://www.encodeproject.org/ENCBS747MTP/


title: ChIP-seq from K562 (ENCLB530CXT)

description:
https://www.encodeproject.org/experiments/ENCSR290MUH/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-GABPA ChIP-seq on human K562
experiment encode accession: ENCSR290MUH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR311ULL
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB530CXT
size range: 200-800

value: eGFP-GABPA

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to GABPA

value: adult

value: ENCBS021UXC at ENCODE; https://www.encodeproject.org/ENCBS021UXC/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ86; http://web.expasy.org/cellosaurus/CVCL_GZ86


title: ChIP-seq from subcutaneous adipose tissue (ENCLB805PVL)

description:
https://www.encodeproject.org/experiments/ENCSR176BAH/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on adipose tissue
experiment encode accession: ENCSR176BAH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR622ZDY
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB805PVL

source_name: Homo sapiens subcutaneous adipose tissue male adult (37 years)

value: subcutaneous adipose tissue

value: tissue

value: Richard Myers, HAIB

value: 37 year

value: ENCBS096VAL at ENCODE; https://www.encodeproject.org/ENCBS096VAL/

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


title: ChIP-seq from K562 (ENCLB516VHP)

description:
https://www.encodeproject.org/experiments/ENCSR178NTX/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-CUX1 ChIP-seq on human K562
experiment encode accession: ENCSR178NTX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR257TKE
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB516VHP
size range: 200-800

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to CUX1

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS613PZU at ENCODE; https://www.encodeproject.org/ENCBS613PZU/

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

value: ENCODE dbxrefs Cellosaurus CVCL_GZ78; http://web.expasy.org/cellosaurus/CVCL_GZ78


title: ChIP-seq from stomach (ENCLB351NXB)

description:
https://www.encodeproject.org/experiments/ENCSR228ZPZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on stomach
experiment encode accession: ENCSR228ZPZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR637MGJ
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB351NXB

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

value: stomach

value: male

value: adult

value: ENCBS555DNU at ENCODE; https://www.encodeproject.org/ENCBS555DNU/


title: ChIP-seq from K562 (ENCLB499FII)

description:
https://www.encodeproject.org/experiments/ENCSR171CAY/
***************
biological replicate number: 2
technical replicate number: 1
description: E2F7 ChIP-seq on human K562
experiment encode accession: ENCSR171CAY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR658AGP
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB499FII
size range: 450-650

value: Michael Snyder, Stanford

value: ENCBS187ZIN at ENCODE; https://www.encodeproject.org/ENCBS187ZIN/

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


title: ChIP-seq from stomach (ENCLB584SNT)

description:
https://www.encodeproject.org/experiments/ENCSR173AIR/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human stomach
experiment encode accession: ENCSR173AIR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR955OCL
encode release date: 2016-07-11
lab: Michael Snyder, Stanford
library encode accession: ENCLB584SNT
size range: 450-650

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

value: CTCF

value: tissue

value: 51 year

value: ENCBS314VNR at ENCODE; https://www.encodeproject.org/ENCBS314VNR/

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


title: ChIP-seq from suprapubic skin (ENCLB682HSP)

description:
https://www.encodeproject.org/experiments/ENCSR225UUX/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Mon Sep 12 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR225UUX
assay title: ChIP-seq
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB682HSP

source_name: Homo sapiens suprapubic skin tissue male adult (54 years)

value: Control

value: suprapubic skin

value: Richard Myers, HAIB

value: 54 year

value: ENCBS471QWL at ENCODE; https://www.encodeproject.org/ENCBS471QWL/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/f5435929-2851-47b5-adeb-b58261a3b1e7/@@download/attachment/82377.svs


title: Input DNA for samples diff20_APAneg

city: Neuherberg

first: Dmitry

last: Shaposhnikov

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Center Munich

data_processing:
FASTQ files were aligned to hg19(UCSC) using bowtie (default parameters but -m 1).
Calculation of genomic coverage vectors was performed for each sample after 200 bp read extension.
Coverages were exported in BEDGRAPH format.
Genome_build: hg19
Supplementary_files_format_and_content: BEDGRAPH

source_name: progenitors at day 2.5

growth_protocol: hESC cells were maintained in KSR-bFGF growth medium on irradiated MEF feeders. Differentiation was done in Matrigel-coated dishes using KSR medium without bFGF and 50 ng/ml BMP4 for 2.5 days

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using NEBNext® ChIP-Seq Library Prep kit for Illumina (New England Biolabs, #E6200) according to manufacturer's instructions

treatment_protocol: Differentiation was done in Matrigel-coated dishes using KSR medium without bFGF and 50 ng/ml BMP4 for 2.5 days. Cells were collected using Versene solution and subjected to FACS sorting using anti-APA and anti-SSEA5

tag: chip antibody

tag: cell line


title: ChIP-seq from breast epithelium (ENCLB185UXE)

description:
https://www.encodeproject.org/experiments/ENCSR226SNN/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Fri Nov 11 2016 00:00:00 GMT-0600 (CST)
experiment encode accession: ENCSR226SNN
assay title: ChIP-seq
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB185UXE

source_name: Homo sapiens breast epithelium tissue male adult (54 years)

value: breast epithelium

value: male

value: adult

value: ENCBS173VHR at ENCODE; https://www.encodeproject.org/ENCBS173VHR/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/3a8c7636-3c0d-4a8c-b793-17502ed1acc2/@@download/attachment/82375.svs


title: ChIP-seq from K562 (ENCLB673VPK)

description:
https://www.encodeproject.org/experiments/ENCSR171CAY/
***************
biological replicate number: 1
technical replicate number: 1
description: E2F7 ChIP-seq on human K562
experiment encode accession: ENCSR171CAY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR658AGP
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB673VPK
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: 53 year

value: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS727RLP at ENCODE; https://www.encodeproject.org/ENCBS727RLP/

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


title: ChIP-seq from sigmoid colon (ENCLB965GUX)

description:
https://www.encodeproject.org/experiments/ENCSR225KOT/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human sigmoid colon
experiment encode accession: ENCSR225KOT
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB965GUX
size range: 450-650

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

value: Control

value: sigmoid colon

value: tissue

value: 37 year

value: ENCBS919RQL at ENCODE; https://www.encodeproject.org/ENCBS919RQL/

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


title: Input DNA for samples diff20_APApos

source_name: trophoblast progenitors at day 2.5


title: Input DNA for samples diff19_APApos


title: Hi-C from SK-N-DZ (ENCLB524GGK)

description:
https://www.encodeproject.org/experiments/ENCSR105KFX/
***************
biological replicate number: 1
technical replicate number: 1
description: HiC experiment done on SK-N-DZ
experiment encode accession: ENCSR105KFX
assay title: Hi-C
assembly: hg19
encode release date: 2016-05-13
lab: Job Dekker, UMass
library encode accession: ENCLB524GGK

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

value: SK-N-DZ

value: John Stamatoyannopoulos, UW

value: neuroblastoma

value: 2 year

value: child

value: ENCBS373BOT at ENCODE; https://www.encodeproject.org/ENCBS373BOT/

value: derived from ENCODE donor ENCDO340AAA; https://www.encodeproject.org/ENCDO340AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1701; http://web.expasy.org/cellosaurus/CVCL_1701


title: ChIP-seq from HepG2 (ENCLB200JXD)

description:
https://www.encodeproject.org/experiments/ENCSR128IYN/
***************
biological replicate number: 2
technical replicate number: 1
description: SNRNP70 ChIP-seq in HepG2
experiment encode accession: ENCSR128IYN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR735QJO
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB200JXD
size range: 200-400

value: immortalized cell line

value: SNRNP70 ChIP-seq in HepG2

value: male

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: 15 year

value: ENCBS294TYB at ENCODE; https://www.encodeproject.org/ENCBS294TYB/

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


title: ChIP-seq from transverse colon (ENCLB597RVK)

description:
https://www.encodeproject.org/experiments/ENCSR170NMC/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on transverse colon
experiment encode accession: ENCSR170NMC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR602GPF
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB597RVK

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

value: transverse colon

value: tissue

value: female

value: Richard Myers, HAIB

value: 51 year

value: adult

value: ENCBS767MTN at ENCODE; https://www.encodeproject.org/ENCBS767MTN/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/7b223824-1a15-4554-b9a1-88b1d9060190/@@download/attachment/84280.svs


title: ChIP-seq from HepG2 (ENCLB412OGX)

description:
https://www.encodeproject.org/experiments/ENCSR128IYN/
***************
biological replicate number: 1
technical replicate number: 1
description: SNRNP70 ChIP-seq in HepG2
experiment encode accession: ENCSR128IYN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR735QJO
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB412OGX
size range: 200-400

value: immortalized cell line

value: child

value: ENCBS581REI at ENCODE; https://www.encodeproject.org/ENCBS581REI/


title: ChIP-seq from HepG2 (ENCLB822AWT)

description:
https://www.encodeproject.org/experiments/ENCSR115BLD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR115BLD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR055XHN
encode release date: 2017-08-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB822AWT
size range: 200-600
nucleic acid starting quantity: 8.24
nucleic acid starting quantity units: ng

value: Hep G2 (Hepatocellular carcinoma, human) Hep G2 is a perpetual cell line which was derived from the liver tissue of a 15-year-old Caucasian American male with a well-differentiated hepatocellular carcinoma. These cells are epithelial in morphology, have a model chromosome number of 55, and are not tumorigenic in nude mice.

value: male

value: Bradley Bernstein, Broad

value: ENCBS011BYX at ENCODE; https://www.encodeproject.org/ENCBS011BYX/


title: Input DNA for samples diff19_APAneg


title: ChIP-seq from transverse colon (ENCLB697NTM)

description:
https://www.encodeproject.org/experiments/ENCSR170BPY/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Wed Aug 24 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR170BPY
assay title: ChIP-seq
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB697NTM

source_name: Homo sapiens transverse colon tissue female adult (53 years)

value: Control

value: 53 year

value: ENCBS022PBN at ENCODE; https://www.encodeproject.org/ENCBS022PBN/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/01a2c769-a3d7-421f-8905-77082e5a5a7a/@@download/attachment/83389.svs


title: ChIP-seq from MCF-7 (ENCLB129NGR)

description:
https://www.encodeproject.org/experiments/ENCSR167UME/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-KLF4 tagged MCF7 cell line.
experiment encode accession: ENCSR167UME
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB129NGR
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens MCF-7 immortalized cell line stably expressing C-terminal eGFP-KLF4 fusion protein

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to KLF4

value: female

value: Kevin White, UChicago

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS033ECJ at ENCODE; https://www.encodeproject.org/ENCBS033ECJ/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA17; http://web.expasy.org/cellosaurus/CVCL_HA17


title: ChIP-seq from K562 (ENCLB585GFN)

description:
https://www.encodeproject.org/experiments/ENCSR230PTV/
***************
biological replicate number: 1
technical replicate number: 1
description: ZBTB2 ChIP-seq on human K562
experiment encode accession: ENCSR230PTV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-12-19
lab: Michael Snyder, Stanford
library encode accession: ENCLB585GFN
size range: 450-650

value: immortalized cell line

value: adult

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS783WYV at ENCODE; https://www.encodeproject.org/ENCBS783WYV/

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

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


title: Input DNA for samples diff18_APApos


title: ChIP-seq from K562 (ENCLB715DBM)

description:
https://www.encodeproject.org/experiments/ENCSR150XYW/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ZNF197 tagged K562 cell line.
experiment encode accession: ENCSR150XYW
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB715DBM
size range: 200-800

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ZNF197 fusion protein

value: Control

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF197

value: 53 year

value: ENCBS309IBB at ENCODE; https://www.encodeproject.org/ENCBS309IBB/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA01; http://web.expasy.org/cellosaurus/CVCL_HA01


title: Input DNA for samples p87

source_name: undifferentiated hESC


title: ChIP-seq from K562 (ENCLB792HDG)

description:
https://www.encodeproject.org/experiments/ENCSR222MYK/
***************
biological replicate number: 1
technical replicate number: 1
description: SRSF7 ChIP-seq in K562
experiment encode accession: ENCSR222MYK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR457PLC
encode release date: 2017-08-17
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB792HDG
size range: 200-400

value: SRSF7 ChIP-seq in K562

value: female

value: Xiang-Dong Fu, UCSD

value: ENCBS617ILH at ENCODE; https://www.encodeproject.org/ENCBS617ILH/


title: Input DNA for samples p84


title: microRNA-seq from adrenal gland (ENCLB699ZOZ)

description:
https://www.encodeproject.org/experiments/ENCSR160XYB/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human adrenal gland
experiment encode accession: ENCSR160XYB
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB699ZOZ
size range: <30

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

value: adrenal gland

value: tissue

value: Adrenal Gland

value: male

value: Barbara Wold, Caltech

value: 54 year

value: ENCBS719AMH at ENCODE; https://www.encodeproject.org/ENCBS719AMH/

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


title: ChIP-seq from K562 (ENCLB259WVW)

description:
https://www.encodeproject.org/experiments/ENCSR222MYK/
***************
biological replicate number: 2
technical replicate number: 1
description: SRSF7 ChIP-seq in K562
experiment encode accession: ENCSR222MYK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR457PLC
encode release date: 2017-08-17
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB259WVW
size range: 200-400

value: immortalized cell line

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS887FSB at ENCODE; https://www.encodeproject.org/ENCBS887FSB/


title: H3K27me3 ChIP from APA-negative progenitors, biological replicate 2

value: anti-H3K27me3 (C15410069; LotNr:A1821D; Diagenode)


title: ChIP-seq from K562 (ENCLB725GOW)

description:
https://www.encodeproject.org/experiments/ENCSR160QYK/
***************
biological replicate number: 1
technical replicate number: 1
description: GATAD2A ChIP-seq on human K562
experiment encode accession: ENCSR160QYK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR658AGP
encode release date: 2017-09-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB725GOW
size range: 450-650

value: 53 year

value: Michael Snyder, Stanford

value: ENCBS352MRW at ENCODE; https://www.encodeproject.org/ENCBS352MRW/

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


title: H3K4me3 ChIP from APA-negative progenitors, biological replicate 2


title: H3K27me3 ChIP from APA-positive trophoblast progenitors, biological replicate 3


title: ChIP-seq from HEK293T (ENCLB463YWV)

description:
https://www.encodeproject.org/experiments/ENCSR218GSN/
***************
biological replicate number: 1
technical replicate number: 1
description: ZFX ChIP-seq on human HEK293T
experiment encode accession: ENCSR218GSN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR821YOI
encode release date: 2017-07-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB463YWV
size range: 450-650

source_name: Homo sapiens HEK293T immortalized cell line

value: ZFX

value: female

value: unknown

value: embryonic

value: ENCBS319KKV at ENCODE; https://www.encodeproject.org/ENCBS319KKV/

value: derived from ENCODE donor ENCDO000ABF; https://www.encodeproject.org/ENCDO000ABF/


title: ChIP-seq from HEK293T (ENCLB413YGP)

description:
https://www.encodeproject.org/experiments/ENCSR218GSN/
***************
biological replicate number: 2
technical replicate number: 1
description: ZFX ChIP-seq on human HEK293T
experiment encode accession: ENCSR218GSN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR821YOI
encode release date: 2017-07-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB413YGP
size range: 450-650

value: ENCBS986WKD at ENCODE; https://www.encodeproject.org/ENCBS986WKD/


title: H3K4me3 ChIP from APA-positive trophoblast progenitors, biological replicate 3


title: ChIP-seq from K562 (ENCLB080KZF)

description:
https://www.encodeproject.org/experiments/ENCSR159MTA/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-CEBPG tagged K562 cell line.
experiment encode accession: ENCSR159MTA
assay title: ChIP-seq
encode release date: 2016-08-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB080KZF

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-CEBPG fusion protein

value: Control

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to CEBPG

value: Kevin White, UChicago

value: ENCBS476TFU at ENCODE; https://www.encodeproject.org/ENCBS476TFU/

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

value: ENCODE dbxrefs Cellosaurus CVCL_GZ77; http://web.expasy.org/cellosaurus/CVCL_GZ77


title: ChIP-seq from sigmoid colon (ENCLB970ODC)

description:
https://www.encodeproject.org/experiments/ENCSR190PGI/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Mon Sep 19 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR190PGI
assay title: ChIP-seq
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB970ODC

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

value: sigmoid colon

value: tissue

value: male

value: Richard Myers, HAIB

value: 54 year

value: adult

value: ENCBS089VLX at ENCODE; https://www.encodeproject.org/ENCBS089VLX/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/f08e09e8-d571-4a80-b574-da7e167668d5/@@download/attachment/82367.svs


title: H3K4me3 ChIP from APA-negative progenitors, biological replicate 1


title: H3K27me3 ChIP from APA-positive trophoblast progenitors, biological replicate 1

value: anti-H3K27me3 (C15410069; LotNr:A1821D; Diagenode)


title: H3K4me3 ChIP from APA-positive trophoblast progenitors, biological replicate 2


title: H3K27me3 ChIP from APA-positive trophoblast progenitors, biological replicate 2


title: H3K4me3 ChIP from APA-positive trophoblast progenitors, biological replicate 1


title: H3K27me3 ChIP from APA-negative progenitors, biological replicate 1


title: ChIP-seq from K562 (ENCLB623CNB)

description:
https://www.encodeproject.org/experiments/ENCSR149ZBI/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF584 ChIP-seq on human K562
experiment encode accession: ENCSR149ZBI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR212RMP
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB623CNB
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-ZNF584 fusion protein

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF584

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS922MVL at ENCODE; https://www.encodeproject.org/ENCBS922MVL/

value: ENCODE dbxrefs Cellosaurus CVCL_HA04; http://web.expasy.org/cellosaurus/CVCL_HA04


title: H3K27me3 ChIP from SSEA5-positive hESC, biological replicate 2


title: ChIP-seq from ovary (ENCLB831MSC)

description:
https://www.encodeproject.org/experiments/ENCSR158TRP/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on female gonad
experiment encode accession: ENCSR158TRP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594DIR
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB831MSC

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

value: ovary

value: 51 year

value: ENCBS751KZH at ENCODE; https://www.encodeproject.org/ENCBS751KZH/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/de0a6308-2256-4adc-b87d-dc9b32c8f938/@@download/attachment/84282.svs


title: ChIP-seq from MCF-7 (ENCLB331YDY)

description:
https://www.encodeproject.org/experiments/ENCSR158PLQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ELF1 tagged MCF7 cell line.
experiment encode accession: ENCSR158PLQ
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB331YDY
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens MCF-7 immortalized cell line stably expressing C-terminal eGFP-ELF1 fusion protein

value: Control

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ELF1

value: Kevin White, UChicago

value: breast cancer (adenocarcinoma)

value: 69 year

value: adult

value: ENCBS370XRA at ENCODE; https://www.encodeproject.org/ENCBS370XRA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA13; http://web.expasy.org/cellosaurus/CVCL_HA13


title: ChIP-seq from transverse colon (ENCLB154GSO)

description:
https://www.encodeproject.org/experiments/ENCSR147NJH/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Wed Aug 24 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR147NJH
assay title: ChIP-seq
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB154GSO

value: transverse colon

value: tissue

value: female

value: Richard Myers, HAIB

value: ENCBS767MTN at ENCODE; https://www.encodeproject.org/ENCBS767MTN/

value: high resolution pathology slide image; https://www.encodeproject.org/documents/7b223824-1a15-4554-b9a1-88b1d9060190/@@download/attachment/84280.svs


title: H3K27me3 ChIP from SSEA5-positive hESC, biological replicate 1

value: anti-H3K27me3 (C15410069; LotNr:A1821D; Diagenode)