title: ChIP-seq from subcutaneous adipose tissue (ENCLB189ZJZ)

description:
https://www.encodeproject.org/experiments/ENCSR147VKD/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on adipose tissue
experiment encode accession: ENCSR147VKD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR281NCY
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB189ZJZ

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

value: subcutaneous adipose tissue

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: H3K4me3 ChIP from SSEA5-positive hESC, biological replicate 1

status: Public on Oct 20 2017

type: SRA

city: Neuherberg

first: Dmitry

last: Shaposhnikov

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Center Munich

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: undifferentiated hESC

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 HepG2 (ENCLB615KYN)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR145BHD/
***************
biological replicate number: 4
technical replicate number: 1
description: NFRKB ChIP-seq on human HepG2
experiment encode accession: ENCSR145BHD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV
encode release date: 2017-06-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB615KYN
size range: 450-650

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

source_name: Homo sapiens HepG2 immortalized cell line

extract_protocol: not provided

tag: antibody

value: NFRKB

tag: line

value: immortalized cell line

tag: biosample encode accession

tag: dev stage

value: child

tag: Sex

value: male

tag: age

value: 15 year

tag: health state

value: hepatocellular carcinoma

tag: lab

value: Michael Snyder, Stanford

tag: link

value: ENCBS225ERF at ENCODE; https://www.encodeproject.org/ENCBS225ERF/

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: H3K4me3 ChIP from SSEA5-positive hESC, biological replicate 2


title: ChIP-seq from HepG2 (ENCLB896JFB)

description:
https://www.encodeproject.org/experiments/ENCSR145BHD/
***************
biological replicate number: 3
technical replicate number: 1
description: NFRKB ChIP-seq on human HepG2
experiment encode accession: ENCSR145BHD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV
encode release date: 2017-06-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB896JFB
size range: 450-650

value: ENCBS541YFT at ENCODE; https://www.encodeproject.org/ENCBS541YFT/


title: ChIP-seq from K562 (ENCLB137BSE)

description:
https://www.encodeproject.org/experiments/ENCSR160QYK/
***************
biological replicate number: 2
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: ENCLB137BSE
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: ENCBS185MQS at ENCODE; https://www.encodeproject.org/ENCBS185MQS/

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


title: ChIP-seq from HEK293 (ENCLB662BXB)

description:
https://www.encodeproject.org/experiments/ENCSR217QCK/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF697 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR217QCK
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: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB662BXB
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF697 fusion protein

tag: description

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF697 under the control of a CMV promoter.

value: unknown

value: embryonic

value: ENCBS879FIM at ENCODE; https://www.encodeproject.org/ENCBS879FIM/

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


title: ChIP-seq from MCF-7 (ENCLB195BWC)

description:
https://www.encodeproject.org/experiments/ENCSR094ZCF/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-CEBPG ChIP-seq on human MCF-7
experiment encode accession: ENCSR094ZCF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR965XFJ
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB195BWC
size range: 200-800

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

value: eGFP-CEBPG

value: immortalized cell line

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

value: Kevin White, UChicago

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS787WNX at ENCODE; https://www.encodeproject.org/ENCBS787WNX/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA11; http://web.expasy.org/cellosaurus/CVCL_HA11


title: ChIP-seq from K562 (ENCLB049SKA)

description:
https://www.encodeproject.org/experiments/ENCSR143CEO/
***************
biological replicate number: 2
technical replicate number: 1
description: ZC3H8 ChIP-seq on human K562
experiment encode accession: ENCSR143CEO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2017-06-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB049SKA
size range: 450-650

value: adult

value: 53 year

value: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS406RFF at ENCODE; https://www.encodeproject.org/ENCBS406RFF/

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 MCF-7 (ENCLB016TDO)

description:
https://www.encodeproject.org/experiments/ENCSR094ZCF/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-CEBPG ChIP-seq on human MCF-7
experiment encode accession: ENCSR094ZCF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR965XFJ
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB016TDO
size range: 200-800

value: eGFP-CEBPG

value: ENCBS948XBF at ENCODE; https://www.encodeproject.org/ENCBS948XBF/


title: ChIP-seq from HEK293 (ENCLB933NVZ)

description:
https://www.encodeproject.org/experiments/ENCSR217QCK/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-ZNF697 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR217QCK
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: 2016-10-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB933NVZ
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF697 under the control of a CMV promoter.

value: unknown

value: embryonic

value: ENCBS676HTV at ENCODE; https://www.encodeproject.org/ENCBS676HTV/

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


title: ChIP-seq from K562 (ENCLB742NAO)

description:
https://www.encodeproject.org/experiments/ENCSR149ZBI/
***************
biological replicate number: 1
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: ENCLB742NAO
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: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF584

value: Kevin White, UChicago

tag: passage number

value: ENCBS101CXP at ENCODE; https://www.encodeproject.org/ENCBS101CXP/

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

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


title: ChIP-seq from K562 (ENCLB438MYG)

description:
https://www.encodeproject.org/experiments/ENCSR021JFW/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-GTF2E2 tagged K562 cell line.
experiment encode accession: ENCSR021JFW
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB438MYG
size range: 200-800

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-GTF2E2 fusion protein

value: Control

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to GTF2E2

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

value: ENCBS231GMV at ENCODE; https://www.encodeproject.org/ENCBS231GMV/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ88; http://web.expasy.org/cellosaurus/CVCL_GZ88


title: ChIP-seq from K562 (ENCLB393QPV)

description:
https://www.encodeproject.org/experiments/ENCSR143CEO/
***************
biological replicate number: 1
technical replicate number: 1
description: ZC3H8 ChIP-seq on human K562
experiment encode accession: ENCSR143CEO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2017-06-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB393QPV
size range: 450-650

value: immortalized cell line

value: Michael Snyder, Stanford

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: Hi-C from DLD1 (ENCLB400YLP)

description:
https://www.encodeproject.org/experiments/ENCSR213DHH/
***************
biological replicate number: 2
technical replicate number: 1
description: HiC experiment done on DLD1
experiment encode accession: ENCSR213DHH
assay title: Hi-C
assembly: hg19
encode release date: 2017-08-15
lab: Job Dekker, UMass
library encode accession: ENCLB400YLP

source_name: Homo sapiens DLD1 immortalized cell line

value: male

value: John Stamatoyannopoulos, UW

value: unknown

value: ENCBS621AWM at ENCODE; https://www.encodeproject.org/ENCBS621AWM/

value: derived from ENCODE donor ENCDO649LMW; https://www.encodeproject.org/ENCDO649LMW/


title: ChIP-seq from suprapubic skin (ENCLB809XDJ)

description:
https://www.encodeproject.org/experiments/ENCSR213GWR/
***************
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: ENCSR213GWR
assay title: ChIP-seq
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB809XDJ

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

extract_protocol: extraction method: see document

value: Control

value: suprapubic skin

value: tissue

value: Richard Myers, HAIB

value: 37 year

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

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


title: ChIP-seq from K562 (ENCLB890OGJ)

description:
https://www.encodeproject.org/experiments/ENCSR017CYU/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-NR2C2 tagged K562 cell line.
experiment encode accession: ENCSR017CYU
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB890OGJ
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-NR2C2 fusion protein

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to NR2C2

value: female

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

value: ENCBS923ZGZ at ENCODE; https://www.encodeproject.org/ENCBS923ZGZ/

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

value: ENCODE dbxrefs Cellosaurus CVCL_GZ91; http://web.expasy.org/cellosaurus/CVCL_GZ91


title: Hi-C from DLD1 (ENCLB236LJZ)

description:
https://www.encodeproject.org/experiments/ENCSR213DHH/
***************
biological replicate number: 1
technical replicate number: 1
description: HiC experiment done on DLD1
experiment encode accession: ENCSR213DHH
assay title: Hi-C
assembly: hg19
encode release date: 2017-08-15
lab: Job Dekker, UMass
library encode accession: ENCLB236LJZ

value: male

value: John Stamatoyannopoulos, UW

value: unknown

value: ENCBS580BTU at ENCODE; https://www.encodeproject.org/ENCBS580BTU/

value: derived from ENCODE donor ENCDO649LMW; https://www.encodeproject.org/ENCDO649LMW/


title: ChIP-seq from K562 (ENCLB860TNQ)

description:
https://www.encodeproject.org/experiments/ENCSR212RMP/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ZNF584 tagged K562 cell line.
experiment encode accession: ENCSR212RMP
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB860TNQ
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: Control

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

value: ENCBS027DJL at ENCODE; https://www.encodeproject.org/ENCBS027DJL/

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


title: ChIP-seq from K562 (ENCLB069CDH)

description:
https://www.encodeproject.org/experiments/ENCSR017GBO/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-TFDP1 ChIP-seq on human K562
experiment encode accession: ENCSR017GBO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR556FBD
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB069CDH
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-TFDP1 fusion protein

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to TFDP1

value: female

value: ENCBS546RMD at ENCODE; https://www.encodeproject.org/ENCBS546RMD/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ94; http://web.expasy.org/cellosaurus/CVCL_GZ94


title: ChIP-seq from K562 (ENCLB979GRO)

description:
https://www.encodeproject.org/experiments/ENCSR051DXE/
***************
biological replicate number: 2
technical replicate number: 1
description: FUS ChIP-seq in K562
experiment encode accession: ENCSR051DXE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR932KYH
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB979GRO
size range: 200-400

value: FUS

value: FUS ChIP-seq in K562

value: Xiang-Dong Fu, UCSD

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

value: ENCBS425QDI at ENCODE; https://www.encodeproject.org/ENCBS425QDI/


title: ChIP-seq from Panc1 (ENCLB816FMP)

description:
https://www.encodeproject.org/experiments/ENCSR141ITZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human Panc1
experiment encode accession: ENCSR141ITZ
assay title: ChIP-seq
encode release date: 2017-07-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB816FMP
size range: 450-650

source_name: Homo sapiens Panc1 immortalized cell line

value: male

value: Michael Snyder, Stanford

value: pancreatic carcinoma

value: 56 year

value: unknown

value: ENCBS314FVF at ENCODE; https://www.encodeproject.org/ENCBS314FVF/

value: derived from ENCODE donor ENCDO000ABB; https://www.encodeproject.org/ENCDO000ABB/


title: ChIP-seq from K562 (ENCLB999MQA)

description:
https://www.encodeproject.org/experiments/ENCSR211LTF/
***************
biological replicate number: 1
technical replicate number: 1
description: EGR1 ChIP-seq on human K562
experiment encode accession: ENCSR211LTF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB999MQA
size range: 450-650

value: immortalized cell line

value: female

value: ENCBS357NWO at ENCODE; https://www.encodeproject.org/ENCBS357NWO/

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


title: ChIP-seq from K562 (ENCLB120KNR)

description:
https://www.encodeproject.org/experiments/ENCSR017GBO/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-TFDP1 ChIP-seq on human K562
experiment encode accession: ENCSR017GBO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR556FBD
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB120KNR
size range: 200-800

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to TFDP1

value: Kevin White, UChicago

value: ENCBS931GIA at ENCODE; https://www.encodeproject.org/ENCBS931GIA/

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

value: ENCODE dbxrefs Cellosaurus CVCL_GZ94; http://web.expasy.org/cellosaurus/CVCL_GZ94


title: ChIP-seq from Panc1 (ENCLB819OUB)

description:
https://www.encodeproject.org/experiments/ENCSR141ITZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human Panc1
experiment encode accession: ENCSR141ITZ
assay title: ChIP-seq
encode release date: 2017-07-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB819OUB
size range: 450-650

value: Control

value: ENCBS101NPD at ENCODE; https://www.encodeproject.org/ENCBS101NPD/


title: ChIP-seq from K562 (ENCLB012WJS)

description:
https://www.encodeproject.org/experiments/ENCSR211LTF/
***************
biological replicate number: 2
technical replicate number: 1
description: EGR1 ChIP-seq on human K562
experiment encode accession: ENCSR211LTF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB012WJS
size range: 450-650

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS538DYC at ENCODE; https://www.encodeproject.org/ENCBS538DYC/


title: ChIP-seq from K562 (ENCLB965PNJ)

description:
https://www.encodeproject.org/experiments/ENCSR047LSJ/
***************
biological replicate number: 1
technical replicate number: 1
description: TAF15 ChIP-seq in K562
experiment encode accession: ENCSR047LSJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR436OZQ
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB965PNJ
size range: 200-400

value: TAF15 ChIP-seq in K562

value: Xiang-Dong Fu, UCSD

value: ENCBS051ABU at ENCODE; https://www.encodeproject.org/ENCBS051ABU/


title: ChIP-seq from K562 (ENCLB059NBV)

description:
https://www.encodeproject.org/experiments/ENCSR047LSJ/
***************
biological replicate number: 2
technical replicate number: 1
description: TAF15 ChIP-seq in K562
experiment encode accession: ENCSR047LSJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR436OZQ
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB059NBV
size range: 200-400

value: immortalized cell line

value: female

value: ENCBS292UVA at ENCODE; https://www.encodeproject.org/ENCBS292UVA/


title: ChIP-seq from K562 (ENCLB073NUM)

description:
https://www.encodeproject.org/experiments/ENCSR051DXE/
***************
biological replicate number: 1
technical replicate number: 1
description: FUS ChIP-seq in K562
experiment encode accession: ENCSR051DXE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR932KYH
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB073NUM
size range: 200-400

value: FUS

value: FUS ChIP-seq in K562

value: ENCBS754HFN at ENCODE; https://www.encodeproject.org/ENCBS754HFN/


title: ChIP-seq from K562 (ENCLB821RYB)

description:
https://www.encodeproject.org/experiments/ENCSR039ZBB/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-FOSL1 tagged K562 cell line.
experiment encode accession: ENCSR039ZBB
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB821RYB
size range: 200-800

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: Kevin White, UChicago

value: ENCBS392SQX at ENCODE; https://www.encodeproject.org/ENCBS392SQX/

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 breast epithelium (ENCLB899SMJ)

description:
https://www.encodeproject.org/experiments/ENCSR299CAV/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human breast epithelium
experiment encode accession: ENCSR299CAV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR366VWM
encode release date: 2016-10-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB899SMJ
size range: 450-650

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

value: breast epithelium

value: tissue

value: Michael Snyder, Stanford

value: 53 year

value: adult

value: ENCBS114DQJ at ENCODE; https://www.encodeproject.org/ENCBS114DQJ/

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


title: ChIP-seq from HEK293 (ENCLB607FQK)

description:
https://www.encodeproject.org/experiments/ENCSR138RCE/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF132 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR138RCE
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: ENCLB607FQK
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF132 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF132 under the control of a CMV promoter.

value: female

value: unknown

value: embryonic

value: ENCBS478IQA at ENCODE; https://www.encodeproject.org/ENCBS478IQA/

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


title: ChIP-seq from lower leg skin (ENCLB888EYI)

description:
https://www.encodeproject.org/experiments/ENCSR287HAL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human lower leg skin
experiment encode accession: ENCSR287HAL
assay title: ChIP-seq
encode release date: 2016-11-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB888EYI
size range: 450-650

source_name: Homo sapiens lower leg skin tissue female adult (51 year)

value: Control

value: lower leg skin

value: 51 year

value: ENCBS207AJN at ENCODE; https://www.encodeproject.org/ENCBS207AJN/

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


title: ChIP-seq from spleen (ENCLB318RMY)

description:
https://www.encodeproject.org/experiments/ENCSR289VTP/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human spleen
experiment encode accession: ENCSR289VTP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR236WEQ
encode release date: 2017-04-04
lab: Michael Snyder, Stanford
library encode accession: ENCLB318RMY
size range: 450-650

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

value: spleen

value: tissue

value: Michael Snyder, Stanford

value: ENCBS067IFG at ENCODE; https://www.encodeproject.org/ENCBS067IFG/


title: ChIP-seq from HEK293 (ENCLB692ODO)

description:
https://www.encodeproject.org/experiments/ENCSR211GNP/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZSCAN4 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR211GNP
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: 2017-02-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB692ODO
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZSCAN4 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZSCAN4 under the control of a CMV promoter.

value: ENCBS821BBI at ENCODE; https://www.encodeproject.org/ENCBS821BBI/


title: ChIP-seq from HEK293 (ENCLB285OYS)

description:
https://www.encodeproject.org/experiments/ENCSR138RCE/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF132 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR138RCE
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: ENCLB285OYS
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF132 under the control of a CMV promoter.

value: ENCBS274LVS at ENCODE; https://www.encodeproject.org/ENCBS274LVS/


title: ChIP-seq from epithelial cell of prostate (ENCLB881YCH)

description:
https://www.encodeproject.org/experiments/ENCSR131SEB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human epithelial cell of prostate
experiment encode accession: ENCSR131SEB
assay title: ChIP-seq
encode release date: 2017-01-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB881YCH
size range: 450-650

source_name: Homo sapiens epithelial of prostate primary cell male

value: epithelial cell of prostate

value: primary cell

value: male

value: unknown

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

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


title: ChIP-seq from epithelial cell of prostate (ENCLB056QHH)

description:
https://www.encodeproject.org/experiments/ENCSR131SEB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human epithelial cell of prostate
experiment encode accession: ENCSR131SEB
assay title: ChIP-seq
encode release date: 2017-01-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB056QHH
size range: 450-650

value: Control

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


title: ChIP-seq from transverse colon (ENCLB126PTD)

description:
https://www.encodeproject.org/experiments/ENCSR138QGB/
***************
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: ENCSR138QGB
assay title: ChIP-seq
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB126PTD

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

value: transverse colon

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 HEK293 (ENCLB992LPQ)

description:
https://www.encodeproject.org/experiments/ENCSR211GNP/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZSCAN4 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR211GNP
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: 2017-02-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB992LPQ
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line derived from HEK293 stably expressing N-terminal eGFP-ZSCAN4 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZSCAN4 under the control of a CMV promoter.

value: embryonic

value: female

value: Michael Snyder, Stanford

value: ENCBS401QNO at ENCODE; https://www.encodeproject.org/ENCBS401QNO/

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


title: ChIP-seq from HEK293 (ENCLB254PTV)

description:
https://www.encodeproject.org/experiments/ENCSR274LVQ/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF776 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR274LVQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2017-02-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB254PTV
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF776 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF776 under the control of a CMV promoter.

value: unknown

value: ENCBS077CVO at ENCODE; https://www.encodeproject.org/ENCBS077CVO/

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


title: ChIP-seq from K562 (ENCLB921LQN)

description:
https://www.encodeproject.org/experiments/ENCSR264CZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: THRA ChIP-seq on human K562
experiment encode accession: ENCSR264CZJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-06-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB921LQN
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: THRA

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS734NZL at ENCODE; https://www.encodeproject.org/ENCBS734NZL/

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 gastroesophageal sphincter (ENCLB526NQI)

description:
https://www.encodeproject.org/experiments/ENCSR211EXK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human esophagogastric junction
experiment encode accession: ENCSR211EXK
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB526NQI
size range: 450-650

source_name: Homo sapiens gastroesophageal sphincter tissue female adult (51 year)

value: Control

value: gastroesophageal sphincter

value: tissue

value: 51 year

value: adult

value: ENCBS728DKU at ENCODE; https://www.encodeproject.org/ENCBS728DKU/

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


title: ChIP-seq from MCF-7 (ENCLB781ZNK)

description:
https://www.encodeproject.org/experiments/ENCSR126YEB/
***************
biological replicate number: 1
technical replicate number: 1
description: FOXA1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR126YEB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-07-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB781ZNK
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

value: immortalized cell line

value: 69 year

value: female

value: Michael Snyder, Stanford

value: breast cancer (adenocarcinoma)

value: ENCBS959SHH at ENCODE; https://www.encodeproject.org/ENCBS959SHH/

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 gastroesophageal sphincter (ENCLB515BXD)

description:
https://www.encodeproject.org/experiments/ENCSR262CPH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human esophagogastric junction
experiment encode accession: ENCSR262CPH
assay title: ChIP-seq
encode release date: 2016-11-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB515BXD
size range: 450-650

source_name: Homo sapiens gastroesophageal sphincter tissue male adult (37 years)

value: male

value: 37 year

value: ENCBS543LVV at ENCODE; https://www.encodeproject.org/ENCBS543LVV/

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


title: ChIP-seq from esophagus squamous epithelium (ENCLB510TZE)

description:
https://www.encodeproject.org/experiments/ENCSR253FAH/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human esophagus squamous epithelium
experiment encode accession: ENCSR253FAH
assay title: ChIP-seq
encode release date: 2017-03-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB510TZE
size range: 450-650

source_name: Homo sapiens esophagus squamous epithelium tissue male adult (37 years)

value: Control

value: esophagus squamous epithelium

value: tissue

value: ENCBS312CXQ at ENCODE; https://www.encodeproject.org/ENCBS312CXQ/


title: ChIP-seq from MCF-7 (ENCLB003NXX)

description:
https://www.encodeproject.org/experiments/ENCSR126YEB/
***************
biological replicate number: 2
technical replicate number: 1
description: FOXA1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR126YEB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2016-07-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB003NXX
size range: 450-650

value: adult

value: ENCBS670IYV at ENCODE; https://www.encodeproject.org/ENCBS670IYV/


title: ChIP-seq from lower leg skin (ENCLB120LGG)

description:
https://www.encodeproject.org/experiments/ENCSR252XWG/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human lower leg skin
experiment encode accession: ENCSR252XWG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR515JGE
encode release date: 2016-11-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB120LGG
size range: 450-650

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

value: CTCF

value: lower leg skin

value: 54 year

value: ENCBS443VUU at ENCODE; https://www.encodeproject.org/ENCBS443VUU/

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


title: ChIP-seq from MCF-7 (ENCLB804LOH)

description:
https://www.encodeproject.org/experiments/ENCSR125ZYC/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-KLF9 ChIP-seq on human MCF-7
experiment encode accession: ENCSR125ZYC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR931XKA
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB804LOH
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-KLF9 fusion protein

value: immortalized cell line

value: MCF7 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to KLF9

value: female

value: Kevin White, UChicago

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS418UGY at ENCODE; https://www.encodeproject.org/ENCBS418UGY/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA18; http://web.expasy.org/cellosaurus/CVCL_HA18


title: ChIP-seq from MCF-7 (ENCLB215RJH)

description:
https://www.encodeproject.org/experiments/ENCSR125ZYC/
***************
biological replicate number: 4
technical replicate number: 1
description: eGFP-KLF9 ChIP-seq on human MCF-7
experiment encode accession: ENCSR125ZYC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR931XKA
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB215RJH
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: ENCBS180ROE at ENCODE; https://www.encodeproject.org/ENCBS180ROE/


title: ChIP-seq from HEK293 (ENCLB092NVG)

description:
https://www.encodeproject.org/experiments/ENCSR274LVQ/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF776 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR274LVQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2017-02-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB092NVG
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF776 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: unknown

value: embryonic

value: ENCBS816FCW at ENCODE; https://www.encodeproject.org/ENCBS816FCW/

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


title: ChIP-seq from K562 (ENCLB939TSV)

description:
https://www.encodeproject.org/experiments/ENCSR249BHQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF592 ChIP-seq on human K562
experiment encode accession: ENCSR249BHQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB939TSV
size range: 450-650

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

value: ENCBS596DHR at ENCODE; https://www.encodeproject.org/ENCBS596DHR/

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


title: ChIP-seq from RWPE1 (ENCLB495RTI)

description:
https://www.encodeproject.org/experiments/ENCSR248IFK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human RWPE1
experiment encode accession: ENCSR248IFK
assay title: ChIP-seq
encode release date: 2017-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB495RTI
size range: 450-650

source_name: Homo sapiens RWPE1 immortalized cell line

value: Control

value: immortalized cell line

value: male

value: normal

value: 54 year

value: ENCBS192LWI at ENCODE; https://www.encodeproject.org/ENCBS192LWI/

value: derived from ENCODE donor ENCDO000ADM; https://www.encodeproject.org/ENCDO000ADM/


title: ChIP-seq from K562 (ENCLB291MXB)

description:
https://www.encodeproject.org/experiments/ENCSR249BHQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF592 ChIP-seq on human K562
experiment encode accession: ENCSR249BHQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB291MXB
size range: 450-650

value: female

value: Michael Snyder, Stanford

value: ENCBS626VGF at ENCODE; https://www.encodeproject.org/ENCBS626VGF/


title: ChIP-seq from K562 (ENCLB830XEU)

description:
https://www.encodeproject.org/experiments/ENCSR121MVZ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ZNF639 tagged K562 cell line.
experiment encode accession: ENCSR121MVZ
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB830XEU
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-ZNF639 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF639

value: Kevin White, UChicago

value: ENCBS851CNL at ENCODE; https://www.encodeproject.org/ENCBS851CNL/

value: ENCODE dbxrefs Cellosaurus CVCL_HA06; http://web.expasy.org/cellosaurus/CVCL_HA06


title: ChIP-seq from stomach (ENCLB385RVL)

description:
https://www.encodeproject.org/experiments/ENCSR122EYE/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human stomach
experiment encode accession: ENCSR122EYE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR081KET
encode release date: 2016-07-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB385RVL
size range: 450-650

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

value: stomach

value: tissue

value: adult

value: ENCBS424ANS at ENCODE; https://www.encodeproject.org/ENCBS424ANS/

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


title: ChIP-seq from RWPE1 (ENCLB289ZPO)

description:
https://www.encodeproject.org/experiments/ENCSR248IFK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human RWPE1
experiment encode accession: ENCSR248IFK
assay title: ChIP-seq
encode release date: 2017-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB289ZPO
size range: 450-650

value: Control

value: immortalized cell line

value: male

value: ENCBS124FCL at ENCODE; https://www.encodeproject.org/ENCBS124FCL/


title: ChIP-seq from spleen (ENCLB701YRS)

description:
https://www.encodeproject.org/experiments/ENCSR266XFE/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human spleen
experiment encode accession: ENCSR266XFE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR999EPI
encode release date: 2017-03-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB701YRS
size range: 450-650

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

value: spleen

value: 54 year

value: ENCBS400GCR at ENCODE; https://www.encodeproject.org/ENCBS400GCR/


title: ChIP-seq from MCF-7 (ENCLB132WQV)

description:
https://www.encodeproject.org/experiments/ENCSR248IMH/
***************
biological replicate number: 2
technical replicate number: 1
description: NFRKB ChIP-seq on human MCF-7
experiment encode accession: ENCSR248IMH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB132WQV
size range: 450-650

value: NFRKB

value: female

value: Michael Snyder, Stanford

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS737JTX at ENCODE; https://www.encodeproject.org/ENCBS737JTX/

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


title: DC_2552_4

city: Shinjuku-ku

first: Koji

last: Atarashi

state: TOKYO

address: 35 Shinanomachi

department: Dept of Microbiology and Immunology

country: Japan

institute: Keio University School of Medicine

library_source: transcriptomic

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 mm9 whole genome using bowtie v0.12.7 and Tophat v1.4.0
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v1.3.0
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

extract_protocol:
Total RNA was isolated using TRIzol reagent
RNA library preparation was performed using a NEBNext Ultra RNA Library Prep Kit for Illumina

tag: strain

tag: genotype/variation

value: wild type

tag: inoculated bacterial strain

tag: time after inoculation

value: 1 weeks

tag: cell type

value: Colonic LP CD11c+ cells


title: ChIP-seq from K562 (ENCLB431QCU)

description:
https://www.encodeproject.org/experiments/ENCSR119VCX/
***************
biological replicate number: 1
technical replicate number: 1
description: PHF21A ChIP-seq on human K562
experiment encode accession: ENCSR119VCX
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR658AGP
encode release date: 2017-09-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB431QCU
size range: 450-650

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS538DYC at ENCODE; https://www.encodeproject.org/ENCBS538DYC/

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


title: ChIP-seq from K562 (ENCLB304OIE)

description:
https://www.encodeproject.org/experiments/ENCSR264CZJ/
***************
biological replicate number: 2
technical replicate number: 1
description: THRA ChIP-seq on human K562
experiment encode accession: ENCSR264CZJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-06-29
lab: Michael Snyder, Stanford
library encode accession: ENCLB304OIE
size range: 450-650

value: THRA

value: immortalized cell line

value: ENCBS721MSZ at ENCODE; https://www.encodeproject.org/ENCBS721MSZ/


title: DC_2552_3


title: ChIP-seq from MCF-7 (ENCLB421POK)

description:
https://www.encodeproject.org/experiments/ENCSR248IMH/
***************
biological replicate number: 1
technical replicate number: 1
description: NFRKB ChIP-seq on human MCF-7
experiment encode accession: ENCSR248IMH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB421POK
size range: 450-650

value: NFRKB

value: female

value: ENCBS242FXL at ENCODE; https://www.encodeproject.org/ENCBS242FXL/


title: ChIP-seq from HEK293T (ENCLB444BYJ)

description:
https://www.encodeproject.org/experiments/ENCSR240XWM/
***************
biological replicate number: 2
technical replicate number: 1
description: LEF1 ChIP-seq on human HEK293T
experiment encode accession: ENCSR240XWM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR272LXW
encode release date: 2017-04-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB444BYJ
size range: 450-650

source_name: Homo sapiens HEK293T immortalized cell line

value: embryonic

value: unknown

value: Michael Snyder, Stanford

value: ENCBS582KZL at ENCODE; https://www.encodeproject.org/ENCBS582KZL/

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


title: DC_2552_2

value: wild type

value: 1 weeks

value: Colonic LP CD11c+ cells


title: DC_2552_1


title: ChIP-seq from HEK293T (ENCLB037WNN)

description:
https://www.encodeproject.org/experiments/ENCSR240XWM/
***************
biological replicate number: 1
technical replicate number: 1
description: LEF1 ChIP-seq on human HEK293T
experiment encode accession: ENCSR240XWM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR272LXW
encode release date: 2017-04-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB037WNN
size range: 450-650

value: ENCBS276VDW at ENCODE; https://www.encodeproject.org/ENCBS276VDW/


title: DC_2H7_4


title: ChIP-seq from Panc1 (ENCLB941MSL)

description:
https://www.encodeproject.org/experiments/ENCSR203QEB/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human Panc1
experiment encode accession: ENCSR203QEB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR141ITZ
encode release date: 2017-07-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB941MSL
size range: 450-650

source_name: Homo sapiens Panc1 immortalized cell line

value: CTCF

value: male

value: pancreatic carcinoma

value: 56 year

value: ENCBS830QHD at ENCODE; https://www.encodeproject.org/ENCBS830QHD/

value: derived from ENCODE donor ENCDO000ABB; https://www.encodeproject.org/ENCDO000ABB/


title: ChIP-seq from HepG2 (ENCLB761EDW)

description:
https://www.encodeproject.org/experiments/ENCSR210ZYL/
***************
biological replicate number: 3
technical replicate number: 1
description: NBN ChIP-seq on human HepG2
experiment encode accession: ENCSR210ZYL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV
encode release date: 2017-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB761EDW
size range: 450-650

source_name: Homo sapiens HepG2 immortalized cell line

value: NBN

value: immortalized cell line

value: child

value: 15 year

value: hepatocellular carcinoma

value: ENCBS541YFT at ENCODE; https://www.encodeproject.org/ENCBS541YFT/

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 Panc1 (ENCLB342MOC)

description:
https://www.encodeproject.org/experiments/ENCSR203QEB/
***************
biological replicate number: 2
technical replicate number: 1
description: CTCF ChIP-seq on human Panc1
experiment encode accession: ENCSR203QEB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR141ITZ
encode release date: 2017-07-21
lab: Michael Snyder, Stanford
library encode accession: ENCLB342MOC
size range: 450-650

value: Michael Snyder, Stanford

value: unknown

value: ENCBS314FVF at ENCODE; https://www.encodeproject.org/ENCBS314FVF/


title: ChIP-seq from HepG2 (ENCLB611SYU)

description:
https://www.encodeproject.org/experiments/ENCSR238QRG/
***************
biological replicate number: 1
technical replicate number: 1
description: TBX3 ChIP-seq on human HepG2
experiment encode accession: ENCSR238QRG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR399VVK, ENCSR121CWV
encode release date: 2017-01-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB611SYU
size range: 450-650

value: Hepatocellular carcinoma

value: ENCBS591PPP at ENCODE; https://www.encodeproject.org/ENCBS591PPP/

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


title: ChIP-seq from HepG2 (ENCLB912XPB)

description:
https://www.encodeproject.org/experiments/ENCSR210ZYL/
***************
biological replicate number: 4
technical replicate number: 1
description: NBN ChIP-seq on human HepG2
experiment encode accession: ENCSR210ZYL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV
encode release date: 2017-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB912XPB
size range: 450-650

value: male

value: ENCBS225ERF at ENCODE; https://www.encodeproject.org/ENCBS225ERF/


title: ChIP-seq from esophagus muscularis mucosa (ENCLB642UGQ)

description:
https://www.encodeproject.org/experiments/ENCSR116RGC/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on muscle layer of esophagus
experiment encode accession: ENCSR116RGC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR249UPE
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB642UGQ

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

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 K562 (ENCLB298JJW)

description:
https://www.encodeproject.org/experiments/ENCSR119VCX/
***************
biological replicate number: 2
technical replicate number: 1
description: PHF21A ChIP-seq on human K562
experiment encode accession: ENCSR119VCX
assay title: ChIP-seq
assembly: hg19
possible controls: ENCSR658AGP
encode release date: 2017-09-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB298JJW
size range: 450-650

value: immortalized cell line

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS562NAQ at ENCODE; https://www.encodeproject.org/ENCBS562NAQ/

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


title: DC_2H7_2

value: wild type

value: 1 weeks

value: Colonic LP CD11c+ cells


title: DC_2H7_1


title: ChIP-seq from HepG2 (ENCLB007NDA)

description:
https://www.encodeproject.org/experiments/ENCSR115BLD/
***************
biological replicate number: 1
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: ENCLB007NDA
size range: 300-600

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: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS289AAB at ENCODE; https://www.encodeproject.org/ENCBS289AAB/

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


title: DC_GF_1

value: no

value: control


title: DC_GF_3


title: ChIP-seq from HepG2 (ENCLB802CQC)

description:
https://www.encodeproject.org/experiments/ENCSR238QRG/
***************
biological replicate number: 2
technical replicate number: 1
description: TBX3 ChIP-seq on human HepG2
experiment encode accession: ENCSR238QRG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR399VVK, ENCSR121CWV
encode release date: 2017-01-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB802CQC
size range: 450-650

value: immortalized cell line

value: Michael Snyder, Stanford

value: ENCBS225ERF at ENCODE; https://www.encodeproject.org/ENCBS225ERF/

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 sigmoid colon (ENCLB431MNC)

description:
https://www.encodeproject.org/experiments/ENCSR187FNC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human sigmoid colon
experiment encode accession: ENCSR187FNC
assay title: ChIP-seq
encode release date: 2016-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB431MNC
size range: 450-650

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

value: Control

value: sigmoid colon

value: tissue

value: 54 year

value: adult

value: ENCBS345HRP at ENCODE; https://www.encodeproject.org/ENCBS345HRP/

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


title: B6_2552_4

value: wild type

value: 1 weeks

value: Colonic epithelial cells


title: B6_2552_3


title: DC_2H7_3

value: Colonic LP CD11c+ cells


title: ChIP-seq from spleen (ENCLB158AXD)

description:
https://www.encodeproject.org/experiments/ENCSR236WEQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human spleen
experiment encode accession: ENCSR236WEQ
assay title: ChIP-seq
encode release date: 2017-03-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB158AXD
size range: 450-650

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

value: spleen

value: female

value: 53 year

value: ENCBS067IFG at ENCODE; https://www.encodeproject.org/ENCBS067IFG/

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


title: B6_2H7_2


title: B6_2552_2


title: ChIP-seq from gastroesophageal sphincter (ENCLB799RLX)

description:
https://www.encodeproject.org/experiments/ENCSR186NVR/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human gastroesophageal sphincter
experiment encode accession: ENCSR186NVR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR262CPH
encode release date: 2017-06-23
lab: Michael Snyder, Stanford
library encode accession: ENCLB799RLX
size range: 450-650

value: CTCF

value: gastroesophageal sphincter

value: male

value: Michael Snyder, Stanford

value: 37 year

value: ENCBS543LVV at ENCODE; https://www.encodeproject.org/ENCBS543LVV/

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


title: ChIP-seq from MCF-7 (ENCLB007RMT)

description:
https://www.encodeproject.org/experiments/ENCSR109ODF/
***************
biological replicate number: 2
technical replicate number: 1
description: HES1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR109ODF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2017-04-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB007RMT
size range: 450-650

value: immortalized cell line

value: adult

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS308QKF at ENCODE; https://www.encodeproject.org/ENCBS308QKF/

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 MCF-7 (ENCLB764GBS)

description:
https://www.encodeproject.org/experiments/ENCSR109ODF/
***************
biological replicate number: 1
technical replicate number: 1
description: HES1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR109ODF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2017-04-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB764GBS
size range: 450-650

value: female

value: ENCBS957OEW at ENCODE; https://www.encodeproject.org/ENCBS957OEW/


title: DC_GF_2

value: wild type

value: no

value: control

value: Colonic LP CD11c+ cells


title: B6_2H7_3

value: 1 weeks

value: Colonic epithelial cells


title: ChIP-seq from K562 (ENCLB152UJT)

description:
https://www.encodeproject.org/experiments/ENCSR178DEG/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-NR2C1 ChIP-seq on human K562
experiment encode accession: ENCSR178DEG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR805ITZ, ENCSR176UHI
encode release date: 2017-01-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB152UJT
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-NR2C1 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to NR2C1-L

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS706YBL at ENCODE; https://www.encodeproject.org/ENCBS706YBL/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW36; http://web.expasy.org/cellosaurus/CVCL_AW36


title: ChIP-seq from K562 (ENCLB766EJE)

description:
https://www.encodeproject.org/experiments/ENCSR176UHI/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human K562
experiment encode accession: ENCSR176UHI
assay title: ChIP-seq
encode release date: 2017-01-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB766EJE
size range: 450-650

value: Control

value: immortalized cell line

value: adult

value: ENCBS936SUX at ENCODE; https://www.encodeproject.org/ENCBS936SUX/


title: B6_GF_3

value: wild type


title: B6_2H7_1


title: ChIP-seq from MCF-7 (ENCLB207LKP)

description:
https://www.encodeproject.org/experiments/ENCSR038RXU/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-GABPA ChIP-seq on human MCF-7
experiment encode accession: ENCSR038RXU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR814KDE
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB207LKP
size range: 200-800

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

value: eGFP-GABPA

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

value: female

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS980KNO at ENCODE; https://www.encodeproject.org/ENCBS980KNO/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA14; http://web.expasy.org/cellosaurus/CVCL_HA14


title: B6_GF_2

value: no

value: control

value: Colonic epithelial cells


title: ChIP-seq from HepG2 (ENCLB464DVZ)

description:
https://www.encodeproject.org/experiments/ENCSR115BLD/
***************
biological replicate number: 1
technical replicate number: 2
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: ENCLB464DVZ
size range: 300-600

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: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS289AAB at ENCODE; https://www.encodeproject.org/ENCBS289AAB/

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


title: ChIP-seq from GM12878 (ENCLB853FPR)

description:
https://www.encodeproject.org/experiments/ENCSR173ZVL/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF592 ChIP-seq on human GM12878
experiment encode accession: ENCSR173ZVL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-06-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB853FPR
size range: 450-650

source_name: Homo sapiens GM12878 immortalized cell line

value: immortalized cell line

value: female

value: Michael Snyder, Stanford

value: unknown

value: adult

value: ENCBS501RRP at ENCODE; https://www.encodeproject.org/ENCBS501RRP/

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


title: ChIP-seq from K562 (ENCLB755WMD)

description:
https://www.encodeproject.org/experiments/ENCSR178DEG/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-NR2C1 ChIP-seq on human K562
experiment encode accession: ENCSR178DEG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR805ITZ, ENCSR176UHI
encode release date: 2017-01-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB755WMD
size range: 450-650

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to NR2C1-L

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS707WFI at ENCODE; https://www.encodeproject.org/ENCBS707WFI/

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

value: ENCODE dbxrefs Cellosaurus CVCL_AW36; http://web.expasy.org/cellosaurus/CVCL_AW36


title: B6_2552_1

value: wild type

value: 1 weeks

value: Colonic epithelial cells


title: B6_2H7_4


title: ChIP-seq from K562 (ENCLB774PTZ)

description:
https://www.encodeproject.org/experiments/ENCSR201NQZ/
***************
biological replicate number: 1
technical replicate number: 1
description: CTBP1 ChIP-seq on human K562
experiment encode accession: ENCSR201NQZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-11-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB774PTZ
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: immortalized cell line

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

value: ENCBS543YEP at ENCODE; https://www.encodeproject.org/ENCBS543YEP/

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

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

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


title: WT_SPF_1

value: SPF

value: control


title: WT_SPF_2


title: ChIP-seq from K562 (ENCLB493DRJ)

description:
https://www.encodeproject.org/experiments/ENCSR201NQZ/
***************
biological replicate number: 2
technical replicate number: 1
description: CTBP1 ChIP-seq on human K562
experiment encode accession: ENCSR201NQZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2016-11-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB493DRJ
size range: 450-650

value: adult

value: female

value: Michael Snyder, Stanford

value: ENCBS232KKV at ENCODE; https://www.encodeproject.org/ENCBS232KKV/


title: ChIP-seq from GM12878 (ENCLB285VWF)

description:
https://www.encodeproject.org/experiments/ENCSR173ZVL/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF592 ChIP-seq on human GM12878
experiment encode accession: ENCSR173ZVL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-06-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB285VWF
size range: 450-650

value: unknown

value: ENCBS397JTN at ENCODE; https://www.encodeproject.org/ENCBS397JTN/

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


title: MyDTrif_2H7_4

value: Myd88/Trif double deficient

value: 3 weeks


title: MyDTrif_2H7_3

value: Colonic epithelial cells


title: MyDTrif_2H7_2


title: ChIP-seq from MCF-7 (ENCLB163THL)

description:
https://www.encodeproject.org/experiments/ENCSR038RXU/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-GABPA ChIP-seq on human MCF-7
experiment encode accession: ENCSR038RXU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR814KDE
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB163THL
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: eGFP-GABPA

value: immortalized cell line

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

value: Kevin White, UChicago

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS368ZAX at ENCODE; https://www.encodeproject.org/ENCBS368ZAX/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA14; http://web.expasy.org/cellosaurus/CVCL_HA14


title: ChIP-seq from suprapubic skin (ENCLB297ZYB)

description:
https://www.encodeproject.org/experiments/ENCSR038FOS/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human suprapubic skin
experiment encode accession: ENCSR038FOS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR277LNZ
encode release date: 2016-07-11
lab: Michael Snyder, Stanford
library encode accession: ENCLB297ZYB
size range: 450-650

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

value: CTCF

value: suprapubic skin

value: tissue

value: male

value: Michael Snyder, Stanford

value: 54 year

value: adult

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

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


title: TLR4_2H7_5

value: Tlr4 deficient

value: 3 weeks

value: Colonic epithelial cells


title: ChIP-seq from HEK293 (ENCLB136FFY)

description:
https://www.encodeproject.org/experiments/ENCSR229DYF/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZBTB26 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR229DYF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2016-12-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB136FFY
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZBTB26 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZBTB26 under the control of a CMV promoter.

value: female

value: unknown

value: embryonic

value: ENCBS097KFU at ENCODE; https://www.encodeproject.org/ENCBS097KFU/

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


title: ChIP-seq from stomach (ENCLB428WNL)

description:
https://www.encodeproject.org/experiments/ENCSR033FDW/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on stomach
experiment encode accession: ENCSR033FDW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR890ONE
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB428WNL

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

value: stomach

value: tissue

value: Richard Myers, HAIB

value: 37 year

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

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


title: ChIP-seq from HEK293 (ENCLB815JRZ)

description:
https://www.encodeproject.org/experiments/ENCSR229DYF/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZBTB26 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR229DYF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2016-12-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB815JRZ
size range: 450-650

value: Michael Snyder, Stanford

value: ENCBS587LLP at ENCODE; https://www.encodeproject.org/ENCBS587LLP/


title: TLR4_2H7_2

value: Tlr4 deficient

value: 3 weeks


title: ChIP-seq from transverse colon (ENCLB645CKS)

description:
https://www.encodeproject.org/experiments/ENCSR107EUS/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human transverse colon
experiment encode accession: ENCSR107EUS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR567EKU
encode release date: 2016-07-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB645CKS
size range: 450-650

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

value: transverse colon

value: 53 year

value: adult

value: ENCBS659AMF at ENCODE; https://www.encodeproject.org/ENCBS659AMF/

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


title: Hi-C from SK-N-DZ (ENCLB952BSP)

description:
https://www.encodeproject.org/experiments/ENCSR105KFX/
***************
biological replicate number: 2
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: ENCLB952BSP

source_name: Homo sapiens SK-N-DZ immortalized cell line treated with dimethyl sulfoxide for 72 hours

value: SK-N-DZ

value: immortalized cell line

value: 2 year

value: child

value: female

tag: treatments

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical; duration:72; duration_units:hour;

value: John Stamatoyannopoulos, UW

value: ENCBS520AAA at ENCODE; https://www.encodeproject.org/ENCBS520AAA/

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 MCF-7 (ENCLB851DDN)

description:
https://www.encodeproject.org/experiments/ENCSR173EEH/
***************
biological replicate number: 2
technical replicate number: 1
description: COPS2 ChIP-seq on human MCF-7
experiment encode accession: ENCSR173EEH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2017-06-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB851DDN
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

tag: antibody

value: Michael Snyder, Stanford

value: breast cancer (adenocarcinoma)

value: 69 year

value: ENCBS028FSB at ENCODE; https://www.encodeproject.org/ENCBS028FSB/

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


title: TLR4_2H7_1

value: Tlr4 deficient

value: 3 weeks

value: Colonic epithelial cells


title: ChIP-seq from MCF-7 (ENCLB120XMX)

description:
https://www.encodeproject.org/experiments/ENCSR173EEH/
***************
biological replicate number: 1
technical replicate number: 1
description: COPS2 ChIP-seq on human MCF-7
experiment encode accession: ENCSR173EEH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR882IYK
encode release date: 2017-06-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB120XMX
size range: 450-650

tag: line

value: immortalized cell line

value: adult

value: ENCBS726ASX at ENCODE; https://www.encodeproject.org/ENCBS726ASX/


title: B6_GF_1

value: wild type

value: no

value: control


title: MyD_2H7_5

value: Myd88 deficient


title: MyD_2H7_4


title: ChIP-seq from omental fat pad (ENCLB913IOS)

description:
https://www.encodeproject.org/experiments/ENCSR225OKX/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human omental fat pad
experiment encode accession: ENCSR225OKX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR117KTL
encode release date: 2016-12-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB913IOS
size range: 450-650

source_name: Homo sapiens omental fat pad tissue female adult (51 year)

value: CTCF

value: omental fat pad

value: tissue

tag: biosample encode accession

value: female

value: 51 year

value: ENCBS971HUW at ENCODE; https://www.encodeproject.org/ENCBS971HUW/

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


title: MyD_2H7_2


title: ChIP-seq from HEK293 (ENCLB953AML)

description:
https://www.encodeproject.org/experiments/ENCSR224NFP/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF426 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR224NFP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR429LAP, ENCSR274OGE, ENCSR342AGU, ENCSR688NWK, ENCSR354FNX, ENCSR157LMX, 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: 2017-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB953AML
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF426 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF426 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: unknown

tag: dev stage

value: embryonic

value: ENCBS441ZDG at ENCODE; https://www.encodeproject.org/ENCBS441ZDG/

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


title: TLR4_2H7_4

value: Tlr4 deficient

value: 3 weeks

value: Colonic epithelial cells


title: ChIP-seq from suprapubic skin (ENCLB824HXL)

description:
https://www.encodeproject.org/experiments/ENCSR106JXD/
***************
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: ENCSR106JXD
assay title: ChIP-seq
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB824HXL

source_name: Homo sapiens suprapubic skin tissue female adult (53 years)

value: Control

value: suprapubic skin

tag: Sex

value: Richard Myers, HAIB

value: 53 year

value: adult

value: ENCBS540IQT at ENCODE; https://www.encodeproject.org/ENCBS540IQT/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/8451a384-078f-4ea8-9ada-0d2a1532fc4f/@@download/attachment/83400.svs


title: WT_2H7_4

value: wild type


title: ChIP-seq from HepG2 (ENCLB503ZEK)

description:
https://www.encodeproject.org/experiments/ENCSR029LBT/
***************
biological replicate number: 3
technical replicate number: 1
description: FOXP1 ChIP-seq on human HepG2
experiment encode accession: ENCSR029LBT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV, ENCSR770GTP
encode release date: 2017-01-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB503ZEK
size range: 450-650

source_name: Homo sapiens HepG2 immortalized cell line

value: immortalized cell line

value: child

tag: age

value: 15 year

value: male

value: Michael Snyder, Stanford

value: hepatocellular carcinoma

value: ENCBS541YFT at ENCODE; https://www.encodeproject.org/ENCBS541YFT/

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: MyDTrif_2H7_1

value: Myd88/Trif double deficient

value: 3 weeks

value: Colonic epithelial cells


title: TLR4_2H7_3

value: Tlr4 deficient


title: ChIP-seq from HEK293 (ENCLB710VIJ)

description:
https://www.encodeproject.org/experiments/ENCSR224NFP/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF426 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR224NFP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR429LAP, ENCSR274OGE, ENCSR342AGU, ENCSR688NWK, ENCSR354FNX, ENCSR157LMX, 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: 2017-03-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB710VIJ
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF426 under the control of a CMV promoter.

value: female

tag: health state

value: unknown

value: embryonic

value: ENCBS888UAN at ENCODE; https://www.encodeproject.org/ENCBS888UAN/

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


title: ChIP-seq from K562 (ENCLB082ZYY)

description:
https://www.encodeproject.org/experiments/ENCSR168CEE/
***************
biological replicate number: 2
technical replicate number: 1
description: NCOA6 ChIP-seq on human K562
experiment encode accession: ENCSR168CEE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB082ZYY
size range: 450-650

value: immortalized cell line

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

tag: lab

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

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


title: WT_2H7_1

value: wild type


title: WT_2H7_3


title: WT_2H7_2


title: ChIP-seq from K562 (ENCLB969PLT)

description:
https://www.encodeproject.org/experiments/ENCSR168CEE/
***************
biological replicate number: 1
technical replicate number: 1
description: NCOA6 ChIP-seq on human K562
experiment encode accession: ENCSR168CEE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB969PLT
size range: 450-650

value: Michael Snyder, Stanford

tag: link

value: ENCBS538DYC at ENCODE; https://www.encodeproject.org/ENCBS538DYC/


title: WT_GF_1

value: germ-free

value: control

value: Colonic epithelial cells


title: ChIP-seq from HepG2 (ENCLB167DYD)

description:
https://www.encodeproject.org/experiments/ENCSR032EZQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR032EZQ
assay title: ChIP-seq
encode release date: 2017-02-13
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB167DYD
size range: 200-400

value: Control

tag: description

value: Control ChIP-seq on HepG2 cells

value: male

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS423ZZH at ENCODE; https://www.encodeproject.org/ENCBS423ZZH/

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


title: ChIP-seq from HepG2 (ENCLB572NYO)

description:
https://www.encodeproject.org/experiments/ENCSR029LBT/
***************
biological replicate number: 4
technical replicate number: 1
description: FOXP1 ChIP-seq on human HepG2
experiment encode accession: ENCSR029LBT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV, ENCSR770GTP
encode release date: 2017-01-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB572NYO
size range: 450-650

value: immortalized cell line

value: Hepatocellular carcinoma

value: ENCBS716YFX at ENCODE; https://www.encodeproject.org/ENCBS716YFX/

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

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

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


title: ChIP-seq from HEK293 (ENCLB866DFU)

description:
https://www.encodeproject.org/experiments/ENCSR167XFW/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF544 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR167XFW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR429LAP, ENCSR274OGE, ENCSR342AGU, ENCSR688NWK, ENCSR354FNX, ENCSR157LMX
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB866DFU
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF544 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF544 under the control of a CMV promoter.

value: female

value: Michael Snyder, Stanford

value: unknown

value: embryonic

value: ENCBS738KJB at ENCODE; https://www.encodeproject.org/ENCBS738KJB/

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


title: ChIP-seq from HEK293 (ENCLB622YNQ)

description:
https://www.encodeproject.org/experiments/ENCSR167XFW/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF544 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR167XFW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR429LAP, ENCSR274OGE, ENCSR342AGU, ENCSR688NWK, ENCSR354FNX, ENCSR157LMX
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB622YNQ
size range: 450-650

value: ENCBS123EBR at ENCODE; https://www.encodeproject.org/ENCBS123EBR/


title: ChIP-seq from HepG2 (ENCLB994MJC)

description:
https://www.encodeproject.org/experiments/ENCSR032EZQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on HepG2
experiment encode accession: ENCSR032EZQ
assay title: ChIP-seq
encode release date: 2017-02-13
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB994MJC
size range: 200-400

value: Control

value: Control ChIP-seq on HepG2 cells

value: male

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS604BAZ at ENCODE; https://www.encodeproject.org/ENCBS604BAZ/


title: N-SPEN_HS_38_15'

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

data_processing:
Reads were mapped to the mouse genome (mm10) with Bowtie2.
Aligned files were converted to bam and sorted using Samtools.
Peaks detection was carried with case-control strategy (detected peaks are given in bed files)
SPEN target sites were annotated to genomic regions using HOMER software (annotated binding sites are given in text file)
Genome_build: mm10
Supplementary_files_format_and_content: bed - detected peaks, can be open in text editors/Excel; txt - annotated binding sites, can be opened in text editors/Excel.

source_name: testicular cells

growth_protocol: Testicular cells for ChIP experiments were collected after collagenase type IA digestion of decapsulated testes (1mg/ml in CO2 saturated RPMI medium for 20 min at 32°C in a shaking water bath operated at 120 cycles/min). The dispersed seminiferous tubules were isolated by allowing them to sediment for 2-3 min under 5% CO2 in air and decanting the supernatant. The process was repeated 3 times with 10 ml RPMI to stop the reaction and to ensure removal of the dissociated interstitial cells and blood cells. Cell aggregates were dissociated gently by repeated pipetting for 3-5 min. Cells were suspended in CO2 saturated RPMI medium supplemented with 10% (v/v) fetal bovine serum, 0.004% (v/v) gentamycin (KRKA), and 6mM sodium lactate (Sigma) at 32°C (physiological temperature of testes). Population of cells enriched in spermatocytes (up to 80%) was obtained by unit gravity sedimentation of testicular cells obtained after enzymatic treatment (collagenase type IA, trypsin, and DNase I)  in a Sta-Put chamber (SP-120, ProScience Inc, Ontario, Canada) containing a 1-3% (w/v) linear BSA gradient in PBS. Finally cells were suspended in RPMI medium as the mixture of testicular cells.

extract_protocol:
The ChIP assay was carried out according to the protocol of a ChIP kit from Upstate Biotechnology (Lake Placid, NY) using protein A-sepharose beads (Amersham). Standard crosslinking procedure was used. For each IP reaction 48-50 µg of chromatin sonicated to 100-500 bp fragments and 5 µg of anti-SPEN polyclonal antibodies, or IgG from rabbit serum (Sigma) as a negative control were used. Immunoprecipitated DNA was additionally digested by RNase A (in a final concentration 70 μg/ml, 30 minutes, 37°C) before Proteinase K treatment and organic solvents extraction. Glycogen (70 μg/ml) was added at the precipitation step. DNA was dissolved in H2O. In each experimental point five to six ChIP replicates were collected and combined in one sample before DNA sequencing.
Sequencing libraries were generated using KAPA library preparation kit (for Illumina) KK8201. Template amplification and cluster generation were performed using the TruSeq SBS Kit.

treatment_protocol: For heat shock, equal volumes of CO2 saturated, pre-heated media (to 53°C or 60°C) were added to the cells suspensions, which immediately raised their temperature from 32°C (physiological temperature) to 38°C or 43°C, respectively. Tubes were submerged in a water bath at the appropriate temperature for an additional 15-30 minutes with recovery at 32°C in a cell culture incubator.

value: FVB/N

value: adult (10-16 weeks)

tag: tissue/cells

value: testes

tag: chip antibody

value: N-terminal SPEN ( Abnova, PAB20849)

tag: treatment

value: heat shocked at 38°C for 15 min


title: MyD_2H7_3

tag: strain

tag: genotype/variation

value: Myd88 deficient

tag: inoculated bacterial strain

value: 3 weeks

value: Colonic epithelial cells


title: ChIP-seq from uterus (ENCLB497UBD)

description:
https://www.encodeproject.org/experiments/ENCSR224COZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human uterus
experiment encode accession: ENCSR224COZ
assay title: ChIP-seq
encode release date: 2016-11-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB497UBD
size range: 450-650

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

value: uterus

value: tissue

value: female

value: Michael Snyder, Stanford

value: 51 year

value: adult

value: ENCBS867AWW at ENCODE; https://www.encodeproject.org/ENCBS867AWW/

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


title: MyD_2H7_1

tag: time after inoculation

tag: cell type


title: ChIP-seq from spleen (ENCLB409APT)

description:
https://www.encodeproject.org/experiments/ENCSR028YEV/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human spleen
experiment encode accession: ENCSR028YEV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR485ITK
encode release date: 2016-07-11
lab: Michael Snyder, Stanford
library encode accession: ENCLB409APT
size range: 450-650

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

tag: antibody

value: CTCF

value: spleen

value: male

value: 54 year

value: ENCBS009ALA at ENCODE; https://www.encodeproject.org/ENCBS009ALA/

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


title: N-SPEN_HS_38_30'_rec2h

value: FVB/N

value: adult (10-16 weeks)

value: testes

value: N-terminal SPEN ( Abnova, PAB20849)

value: heat shocked at 38°C for 30 min & 2h of recovery


title: WT_GF_2

value: wild type

value: germ-free

value: control

value: Colonic epithelial cells


title: ChIP-seq from K562 (ENCLB342MDN)

description:
https://www.encodeproject.org/experiments/ENCSR223MLH/
***************
biological replicate number: 2
technical replicate number: 1
description: BRCA1 ChIP-seq on human K562
experiment encode accession: ENCSR223MLH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB342MDN
size range: 450-650

tag: line

value: immortalized cell line

tag: biosample encode accession

value: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

value: ENCBS596DHR at ENCODE; https://www.encodeproject.org/ENCBS596DHR/

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


title: ChIP-seq from HEK293 (ENCLB686TNO)

description:
https://www.encodeproject.org/experiments/ENCSR028EGI/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF26 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR028EGI
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: ENCLB686TNO
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF26 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF26 under the control of a CMV promoter.

tag: Sex

value: unknown

tag: dev stage

value: embryonic

value: ENCBS022NMA at ENCODE; https://www.encodeproject.org/ENCBS022NMA/

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


title: ChIP-seq from K562 (ENCLB966CLO)

description:
https://www.encodeproject.org/experiments/ENCSR162IEM/
***************
biological replicate number: 1
technical replicate number: 1
description: MYBL2 ChIP-seq on human K562
experiment encode accession: ENCSR162IEM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG, ENCSR173USI
encode release date: 2017-08-25
lab: Michael Snyder, Stanford
library encode accession: ENCLB966CLO
size range: 450-650

value: Leukemia, the continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. - ATCC

tag: age

tag: health state

value: ENCBS953HJY at ENCODE; https://www.encodeproject.org/ENCBS953HJY/

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

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

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