title: ChIP-seq from transverse colon (ENCLB140PUZ)

description:
https://www.encodeproject.org/experiments/ENCSR974HQI/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human transverse colon
experiment encode accession: ENCSR974HQI
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR457NQR
encode release date: 2016-07-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB140PUZ
size range: 450-650

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

value: transverse colon

value: tissue

value: 51 year

value: ENCBS360EPF at ENCODE; https://www.encodeproject.org/ENCBS360EPF/

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


title: ChIP-seq from vagina (ENCLB095INY)

status: Public on Oct 24 2017

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR997NXO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human vagina
experiment encode accession: ENCSR997NXO
assay title: ChIP-seq
encode release date: 2017-01-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB095INY
size range: 450-650

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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

extract_protocol: not provided

tag: antibody

value: Control

value: vagina

tag: biosample encode accession

tag: Sex

value: female

tag: lab

value: Michael Snyder, Stanford

tag: age

tag: dev stage

value: adult

tag: link

value: ENCBS688NIO at ENCODE; https://www.encodeproject.org/ENCBS688NIO/


title: ChIP-seq from K562 (ENCLB852VNZ)

description:
https://www.encodeproject.org/experiments/ENCSR972ZBV/
***************
biological replicate number: 1
technical replicate number: 1
description: ATF7 ChIP-seq on human K562
experiment encode accession: ENCSR972ZBV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB852VNZ
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

tag: line

value: immortalized cell line

tag: description

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: 53 year

tag: health state

value: chronic myelogenous leukemia (CML)

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: ChIP-seq from K562 (ENCLB527OEI)

description:
https://www.encodeproject.org/experiments/ENCSR744WOO/
***************
biological replicate number: 2
technical replicate number: 1
description: TCF12 ChIP-seq on human K562
experiment encode accession: ENCSR744WOO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB527OEI
size range: 450-650

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


title: ChIP-seq from K562 (ENCLB030KOP)

description:
https://www.encodeproject.org/experiments/ENCSR997NGQ/
***************
biological replicate number: 2
technical replicate number: 1
description: XRCC3 ChIP-seq on human K562
experiment encode accession: ENCSR997NGQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-09-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB030KOP
size range: 450-650

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

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


title: ChIP-seq from K562 (ENCLB324CQL)

description:
https://www.encodeproject.org/experiments/ENCSR847LBF/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-FOXJ2 ChIP-seq on human K562
experiment encode accession: ENCSR847LBF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR765SXU
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB324CQL
size range: 200-800

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-FOXJ2 fusion protein

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to FOXJ2

value: Kevin White, UChicago

tag: passage number

value: ENCBS032TNV at ENCODE; https://www.encodeproject.org/ENCBS032TNV/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ85; http://web.expasy.org/cellosaurus/CVCL_GZ85


title: ChIP-seq from K562 (ENCLB993OZH)

description:
https://www.encodeproject.org/experiments/ENCSR972ZBV/
***************
biological replicate number: 2
technical replicate number: 1
description: ATF7 ChIP-seq on human K562
experiment encode accession: ENCSR972ZBV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI, ENCSR554FDZ
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB993OZH
size range: 450-650

value: adult

value: female

value: Michael Snyder, Stanford

value: ENCBS293ZDP at ENCODE; https://www.encodeproject.org/ENCBS293ZDP/


title: ChIP-seq from adrenal gland (ENCLB733WTO)

description:
https://www.encodeproject.org/experiments/ENCSR770IWO/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human adrenal gland
experiment encode accession: ENCSR770IWO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR641MGI
encode release date: 2017-01-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB733WTO
size range: 450-650

source_name: Homo sapiens adrenal gland tissue female adult (53 years)

value: CTCF

value: adrenal gland

value: tissue

value: 53 year

value: ENCBS926VJZ at ENCODE; https://www.encodeproject.org/ENCBS926VJZ/

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


title: ChIP-seq from K562 (ENCLB231JZO)

description:
https://www.encodeproject.org/experiments/ENCSR997NGQ/
***************
biological replicate number: 1
technical replicate number: 1
description: XRCC3 ChIP-seq on human K562
experiment encode accession: ENCSR997NGQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-09-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB231JZO
size range: 450-650

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: chronic myelogenous leukemia (CML)

value: ENCBS576ESJ at ENCODE; https://www.encodeproject.org/ENCBS576ESJ/

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

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


title: ChIP-seq from esophagus squamous epithelium (ENCLB972TWN)

description:
https://www.encodeproject.org/experiments/ENCSR773JBP/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human esophagus squamous epithelium
experiment encode accession: ENCSR773JBP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR311TCB
encode release date: 2016-12-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB972TWN
size range: 450-650

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

value: esophagus squamous epithelium

value: ENCBS927UKP at ENCODE; https://www.encodeproject.org/ENCBS927UKP/


title: ChIP-seq from HEK293 (ENCLB150DNH)

description:
https://www.encodeproject.org/experiments/ENCSR767XSF/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF555 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR767XSF
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: ENCLB150DNH
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF555 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF555 under the control of a CMV promoter.

value: female

value: unknown

value: embryonic

value: ENCBS920ICL at ENCODE; https://www.encodeproject.org/ENCBS920ICL/

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


title: ChIP-seq from Peyer's patch (ENCLB742ROQ)

description:
https://www.encodeproject.org/experiments/ENCSR995QNB/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human Peyer's patch
experiment encode accession: ENCSR995QNB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR588APY
encode release date: 2017-03-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB742ROQ
size range: 450-650

source_name: Homo sapiens Peyer's patch tissue female adult (53 years)

value: Peyer's patch

value: tissue

value: Michael Snyder, Stanford

value: 53 year

value: adult

value: ENCBS944UJX at ENCODE; https://www.encodeproject.org/ENCBS944UJX/


title: ChIP-seq from tibial nerve (ENCLB594FEQ)

description:
https://www.encodeproject.org/experiments/ENCSR846VRM/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Tue Nov 08 2016 00:00:00 GMT-0600 (CST)
experiment encode accession: ENCSR846VRM
assay title: ChIP-seq
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB594FEQ

source_name: Homo sapiens tibial nerve tissue male adult (37 years)

extract_protocol: extraction method: see document

value: Control

value: tibial nerve

value: male

value: Richard Myers, HAIB

value: 37 year

value: ENCBS182BFY at ENCODE; https://www.encodeproject.org/ENCBS182BFY/

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


title: ChIP-seq from omental fat pad (ENCLB217YAX)

description:
https://www.encodeproject.org/experiments/ENCSR846TPT/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on adipose tissue of omentum
experiment encode accession: ENCSR846TPT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR875UDE
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB217YAX

source_name: Homo sapiens omental fat pad tissue male adult (37 years)

value: omental fat pad

value: ENCBS822PPS at ENCODE; https://www.encodeproject.org/ENCBS822PPS/


title: ChIP-seq from HepG2 (ENCLB978KWF)

description:
https://www.encodeproject.org/experiments/ENCSR784FYS/
***************
biological replicate number: 1
technical replicate number: 1
description: RBFOX2 ChIP-seq in HepG2
experiment encode accession: ENCSR784FYS
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545RWZ
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB978KWF
size range: 200-400

source_name: Homo sapiens HepG2 immortalized cell line

value: immortalized cell line

value: RBFOX2 ChIP-seq in HepG2

value: Xiang-Dong Fu, UCSD

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS354HQF at ENCODE; https://www.encodeproject.org/ENCBS354HQF/

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


title: ChIP-seq from GM12878 (ENCLB786PXA)

description:
https://www.encodeproject.org/experiments/ENCSR987MTA/
***************
biological replicate number: 4
technical replicate number: 1
description: BHLHE40 ChIP-seq on human GM12878
experiment encode accession: ENCSR987MTA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-01-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB786PXA
size range: 450-650

source_name: Homo sapiens GM12878 immortalized cell line

value: adult

value: female

value: unknown

value: Michael Snyder, Stanford

value: ENCBS339VHO at ENCODE; https://www.encodeproject.org/ENCBS339VHO/

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

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


title: ChIP-seq from GM12878 (ENCLB215HFO)

description:
https://www.encodeproject.org/experiments/ENCSR987MTA/
***************
biological replicate number: 5
technical replicate number: 1
description: BHLHE40 ChIP-seq on human GM12878
experiment encode accession: ENCSR987MTA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-01-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB215HFO
size range: 450-650

value: ENCBS436SAI at ENCODE; https://www.encodeproject.org/ENCBS436SAI/


title: ChIP-seq from K562 (ENCLB652RKL)

description:
https://www.encodeproject.org/experiments/ENCSR836COE/
***************
biological replicate number: 1
technical replicate number: 1
description: RBM17 ChIP-seq in K562
experiment encode accession: ENCSR836COE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR084AIG
encode release date: 2017-08-17
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB652RKL
size range: 200-400

value: RBM17 ChIP-seq in K562

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS246UOA at ENCODE; https://www.encodeproject.org/ENCBS246UOA/

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


title: ChIP-seq from K562 (ENCLB004MQD)

description:
https://www.encodeproject.org/experiments/ENCSR737UST/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF740 ChIP-seq on human K562
experiment encode accession: ENCSR737UST
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR822DUK
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB004MQD
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-ZNF740 fusion protein

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF740

value: Kevin White, UChicago

value: ENCBS450DNI at ENCODE; https://www.encodeproject.org/ENCBS450DNI/

value: ENCODE dbxrefs Cellosaurus CVCL_HA08; http://web.expasy.org/cellosaurus/CVCL_HA08


title: ChIP-seq from HEK293 (ENCLB994FEU)

description:
https://www.encodeproject.org/experiments/ENCSR767XSF/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF555 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR767XSF
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: ENCLB994FEU
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF555 under the control of a CMV promoter.

value: female

value: embryonic

value: ENCBS044VBG at ENCODE; https://www.encodeproject.org/ENCBS044VBG/

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


title: ChIP-seq from breast epithelium (ENCLB269ZTI)

description:
https://www.encodeproject.org/experiments/ENCSR986YXU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human breast epithelium
experiment encode accession: ENCSR986YXU
assay title: ChIP-seq
encode release date: 2017-02-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB269ZTI
size range: 450-650

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

value: Control

value: breast epithelium

value: tissue

value: male

value: Michael Snyder, Stanford

value: 54 year

value: adult

value: ENCBS236MDX at ENCODE; https://www.encodeproject.org/ENCBS236MDX/

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


title: ChIP-seq from GM12878 (ENCLB197KOI)

description:
https://www.encodeproject.org/experiments/ENCSR764CZW/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF217 ChIP-seq on human GM12878
experiment encode accession: ENCSR764CZW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-06-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB197KOI
size range: 450-650

value: immortalized cell line

value: unknown

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

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


title: ChIP-seq from GM12878 (ENCLB144PGC)

description:
https://www.encodeproject.org/experiments/ENCSR764CZW/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF217 ChIP-seq on human GM12878
experiment encode accession: ENCSR764CZW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-06-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB144PGC
size range: 450-650

value: female

value: ENCBS436SAI at ENCODE; https://www.encodeproject.org/ENCBS436SAI/

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


title: ChIP-seq from K562 (ENCLB940YUD)

description:
https://www.encodeproject.org/experiments/ENCSR737UST/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF740 ChIP-seq on human K562
experiment encode accession: ENCSR737UST
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR822DUK
encode release date: 2016-06-13
lab: Kevin White, UChicago
library encode accession: ENCLB940YUD
size range: 200-800
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF740

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS020CGZ at ENCODE; https://www.encodeproject.org/ENCBS020CGZ/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA08; http://web.expasy.org/cellosaurus/CVCL_HA08


title: ChIP-seq from MCF-7 (ENCLB386SRZ)

description:
https://www.encodeproject.org/experiments/ENCSR966YYJ/
***************
biological replicate number: 1
technical replicate number: 1
description: BMI1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR966YYJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB386SRZ
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

value: adult

value: 69 year

value: Michael Snyder, Stanford

value: breast cancer (adenocarcinoma)

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

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

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


title: microRNA-seq from GM23338 (ENCLB781RZI)

description:
https://www.encodeproject.org/experiments/ENCSR958UOC/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on human induced pluripotent stem cell
experiment encode accession: ENCSR958UOC
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB781RZI
size range: <30

library_source: transcriptomic

molecule: total RNA

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

value: induced pluripotent stem cell line

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

value: male

value: Thomas Gingeras, CSHL

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

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

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

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


title: ChIP-seq from GM12878 (ENCLB875SAF)

description:
https://www.encodeproject.org/experiments/ENCSR859FDL/
***************
biological replicate number: 1
technical replicate number: 1
description: ZNF687 ChIP-seq on human GM12878
experiment encode accession: ENCSR859FDL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-06-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB875SAF
size range: 450-650

value: immortalized cell line

value: female

value: unknown

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

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


title: ChIP-seq from K562 (ENCLB700KXU)

description:
https://www.encodeproject.org/experiments/ENCSR836COE/
***************
biological replicate number: 2
technical replicate number: 1
description: RBM17 ChIP-seq in K562
experiment encode accession: ENCSR836COE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR084AIG
encode release date: 2017-08-17
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB700KXU
size range: 200-400

value: RBM17 ChIP-seq in K562

value: Xiang-Dong Fu, UCSD

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

value: ENCBS217XCN at ENCODE; https://www.encodeproject.org/ENCBS217XCN/

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


title: microRNA-seq from GM23338 (ENCLB840TKN)

description:
https://www.encodeproject.org/experiments/ENCSR958UOC/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on human induced pluripotent stem cell
experiment encode accession: ENCSR958UOC
assay title: microRNA-seq
assembly: GRCh38
encode release date: 2017-01-31
lab: Ali Mortazavi, UCI
library encode accession: ENCLB840TKN
size range: <30

value: induced pluripotent stem cell line

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

value: male

value: Thomas Gingeras, CSHL

value: ENCBS368AAA at ENCODE; https://www.encodeproject.org/ENCBS368AAA/


title: ChIP-seq from GM12878 (ENCLB830XBR)

description:
https://www.encodeproject.org/experiments/ENCSR859FDL/
***************
biological replicate number: 2
technical replicate number: 1
description: ZNF687 ChIP-seq on human GM12878
experiment encode accession: ENCSR859FDL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-06-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB830XBR
size range: 450-650

value: immortalized cell line

value: Michael Snyder, Stanford

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


title: ChIP-seq from MCF-7 (ENCLB425WSI)

description:
https://www.encodeproject.org/experiments/ENCSR966YYJ/
***************
biological replicate number: 2
technical replicate number: 1
description: BMI1 ChIP-seq on human MCF-7
experiment encode accession: ENCSR966YYJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR217LRF
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB425WSI
size range: 450-650

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS200IWR at ENCODE; https://www.encodeproject.org/ENCBS200IWR/

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 subcutaneous adipose tissue (ENCLB457QWU)

description:
https://www.encodeproject.org/experiments/ENCSR956TLA/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Tue Aug 30 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR956TLA
assay title: ChIP-seq
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB457QWU

source_name: Homo sapiens subcutaneous adipose tissue female adult (51 year)

value: Control

value: subcutaneous adipose tissue

value: tissue

value: Richard Myers, HAIB

value: 51 year

value: adult

value: ENCBS583NII at ENCODE; https://www.encodeproject.org/ENCBS583NII/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/45ff1f4b-b3ee-4da5-835b-e8b83ec49932/@@download/attachment/84283.svs


title: ChIP-seq from stomach (ENCLB221SCC)

description:
https://www.encodeproject.org/experiments/ENCSR955OCL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human stomach
experiment encode accession: ENCSR955OCL
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB221SCC
size range: 450-650

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

value: stomach

value: Michael Snyder, Stanford

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


title: ChIP-seq from HepG2 (ENCLB221CNQ)

description:
https://www.encodeproject.org/experiments/ENCSR950NAZ/
***************
biological replicate number: 3
technical replicate number: 1
description: LCORL ChIP-seq on human HepG2
experiment encode accession: ENCSR950NAZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV
encode release date: 2017-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB221CNQ
size range: 450-650

value: LCORL

value: immortalized cell line

value: child

value: 15 year

value: male

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 HEK293 (ENCLB090DHG)

description:
https://www.encodeproject.org/experiments/ENCSR985MYI/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF114 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR985MYI
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: ENCLB090DHG
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF114 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF114 under the control of a CMV promoter.

value: female

value: unknown

value: embryonic

value: ENCBS619DUK at ENCODE; https://www.encodeproject.org/ENCBS619DUK/

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


title: ChIP-seq from HEK293 (ENCLB156IKK)

description:
https://www.encodeproject.org/experiments/ENCSR858FAN/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF621 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR858FAN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2017-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB156IKK
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF621 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF621 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: ENCBS249HTE at ENCODE; https://www.encodeproject.org/ENCBS249HTE/


title: ChIP-seq from HEK293 (ENCLB258WFN)

description:
https://www.encodeproject.org/experiments/ENCSR985MYI/
***************
biological replicate number: 3
technical replicate number: 1
description: eGFP-ZNF114 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR985MYI
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: ENCLB258WFN
size range: 450-650

value: immortalized cell line

value: ENCBS963ZTO at ENCODE; https://www.encodeproject.org/ENCBS963ZTO/


title: ChIP-seq from K562 (ENCLB041JMU)

description:
https://www.encodeproject.org/experiments/ENCSR744WOO/
***************
biological replicate number: 1
technical replicate number: 1
description: TCF12 ChIP-seq on human K562
experiment encode accession: ENCSR744WOO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR173USI
encode release date: 2016-10-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB041JMU
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

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

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

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


title: ChIP-seq from HepG2 (ENCLB317KZP)

description:
https://www.encodeproject.org/experiments/ENCSR950NAZ/
***************
biological replicate number: 4
technical replicate number: 1
description: LCORL ChIP-seq on human HepG2
experiment encode accession: ENCSR950NAZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR121CWV
encode release date: 2017-07-28
lab: Michael Snyder, Stanford
library encode accession: ENCLB317KZP
size range: 450-650

value: LCORL

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

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 testis (ENCLB924BTK)

description:
https://www.encodeproject.org/experiments/ENCSR981CID/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human testis
experiment encode accession: ENCSR981CID
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR953MEE
encode release date: 2017-01-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB924BTK
size range: 450-650

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

value: CTCF

value: testis

value: tissue

value: Michael Snyder, Stanford

value: 54 year

value: ENCBS746YNW at ENCODE; https://www.encodeproject.org/ENCBS746YNW/

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


title: ChIP-seq from HEK293 (ENCLB200PPK)

description:
https://www.encodeproject.org/experiments/ENCSR950ACO/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF785 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR950ACO
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: ENCLB200PPK
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF785 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF785 under the control of a CMV promoter.

value: female

value: unknown

value: embryonic

value: ENCBS273GWY at ENCODE; https://www.encodeproject.org/ENCBS273GWY/

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


title: ChIP-seq from HEK293 (ENCLB749OZM)

description:
https://www.encodeproject.org/experiments/ENCSR950ACO/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF785 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR950ACO
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: ENCLB749OZM
size range: 450-650

value: ENCBS764OVL at ENCODE; https://www.encodeproject.org/ENCBS764OVL/


title: ChIP-seq from HEK293T (ENCLB530JDO)

description:
https://www.encodeproject.org/experiments/ENCSR760UKJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ARNT ChIP-seq on human HEK293T
experiment encode accession: ENCSR760UKJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR272LXW
encode release date: 2017-04-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB530JDO
size range: 450-650

source_name: Homo sapiens HEK293T immortalized cell line

value: ARNT

value: ENCBS323RYE at ENCODE; https://www.encodeproject.org/ENCBS323RYE/

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


title: ChIP-seq from K562 (ENCLB736UKF)

description:
https://www.encodeproject.org/experiments/ENCSR832OGB/
***************
biological replicate number: 3
technical replicate number: 1
description: LEF1 ChIP-seq on human K562
experiment encode accession: ENCSR832OGB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR658AGP
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB736UKF
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

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS994WPS at ENCODE; https://www.encodeproject.org/ENCBS994WPS/

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

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

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


title: ChIP-seq from K562 (ENCLB949TNV)

description:
https://www.encodeproject.org/experiments/ENCSR979QYJ/
***************
biological replicate number: 2
technical replicate number: 1
description: MNT ChIP-seq on human K562
experiment encode accession: ENCSR979QYJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-01-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB949TNV
size range: 450-650

value: MNT

value: immortalized cell line

value: female

value: Michael Snyder, Stanford

value: ENCBS948ZNZ at ENCODE; https://www.encodeproject.org/ENCBS948ZNZ/

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


title: ChIP-seq from sigmoid colon (ENCLB965GUX)

description:
https://www.encodeproject.org/experiments/ENCSR983XKG/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human sigmoid colon
experiment encode accession: ENCSR983XKG
assay title: ChIP-seq
encode release date: 2016-09-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB965GUX
size range: 450-650

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

value: Control

value: sigmoid colon

value: tissue

value: male

value: 37 year

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

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


title: ChIP-seq from HEK293T (ENCLB437FPD)

description:
https://www.encodeproject.org/experiments/ENCSR760UKJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ARNT ChIP-seq on human HEK293T
experiment encode accession: ENCSR760UKJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR272LXW
encode release date: 2017-04-14
lab: Michael Snyder, Stanford
library encode accession: ENCLB437FPD
size range: 450-650

value: ARNT

value: embryonic

value: unknown

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

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


title: ChIP-seq from HEK293 (ENCLB846HBQ)

description:
https://www.encodeproject.org/experiments/ENCSR731AGO/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZSCAN5CP ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR731AGO
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: ENCLB846HBQ
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZSCAN5C fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZSCAN5CP under the control of a CMV promoter.

value: ENCBS055WSF at ENCODE; https://www.encodeproject.org/ENCBS055WSF/

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


title: ChIP-seq from K562 (ENCLB862OTV)

description:
https://www.encodeproject.org/experiments/ENCSR832OGB/
***************
biological replicate number: 4
technical replicate number: 1
description: LEF1 ChIP-seq on human K562
experiment encode accession: ENCSR832OGB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR658AGP
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB862OTV
size range: 450-650

value: adult

value: 53 year

value: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: ENCBS520IYS at ENCODE; https://www.encodeproject.org/ENCBS520IYS/

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


title: ChIP-seq from body of pancreas (ENCLB114OOQ)

description:
https://www.encodeproject.org/experiments/ENCSR979DMN/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human body of pancreas
experiment encode accession: ENCSR979DMN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR326AHF
encode release date: 2016-12-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB114OOQ
size range: 450-650

source_name: Homo sapiens body of pancreas tissue female adult (53 years)

value: body of pancreas

value: tissue

value: ENCBS372UUZ at ENCODE; https://www.encodeproject.org/ENCBS372UUZ/

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


title: ChIP-seq from HEK293 (ENCLB067BTI)

description:
https://www.encodeproject.org/experiments/ENCSR731AGO/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZSCAN5CP ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR731AGO
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: ENCLB067BTI
size range: 450-650

value: unknown

value: embryonic

value: ENCBS665DNN at ENCODE; https://www.encodeproject.org/ENCBS665DNN/


title: ChIP-seq from lower leg skin (ENCLB472LUW)

description:
https://www.encodeproject.org/experiments/ENCSR978LBS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human lower leg skin
experiment encode accession: ENCSR978LBS
assay title: ChIP-seq
encode release date: 2016-11-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB472LUW
size range: 450-650

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

value: Control

value: lower leg skin

value: ENCBS439RNG at ENCODE; https://www.encodeproject.org/ENCBS439RNG/


title: Hi-C from SK-N-MC (ENCLB914GYK)

description:
https://www.encodeproject.org/experiments/ENCSR834DXR/
***************
biological replicate number: 2
technical replicate number: 1
description: HiC experiment done on SK-N-MC
experiment encode accession: ENCSR834DXR
assay title: Hi-C
assembly: hg19
encode release date: 2016-05-13
lab: Job Dekker, UMass
library encode accession: ENCLB914GYK

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

value: SK-N-MC

value: immortalized cell line

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

value: John Stamatoyannopoulos, UW

value: Ewing's sarcoma

value: 14 year

value: child

value: ENCBS400ENC at ENCODE; https://www.encodeproject.org/ENCBS400ENC/

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

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

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


title: ChIP-seq from upper lobe of left lung (ENCLB913MEN)

description:
https://www.encodeproject.org/experiments/ENCSR949XFR/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Mon Sep 26 2016 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR949XFR
assay title: ChIP-seq
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB913MEN

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

value: upper lobe of left lung

value: tissue

value: male

value: Richard Myers, HAIB

value: 54 year

value: adult

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

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

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


title: ChIP-seq from K562 (ENCLB226MVW)

description:
https://www.encodeproject.org/experiments/ENCSR979QYJ/
***************
biological replicate number: 1
technical replicate number: 1
description: MNT ChIP-seq on human K562
experiment encode accession: ENCSR979QYJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-01-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB226MVW
size range: 450-650

value: MNT

value: immortalized cell line

value: female

value: Michael Snyder, Stanford

value: chronic myelogenous leukemia (CML)

value: 53 year

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

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


title: ChIP-seq from HEK293 (ENCLB022VOW)

description:
https://www.encodeproject.org/experiments/ENCSR854ORP/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF350 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR854ORP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR274OGE, ENCSR429LAP, ENCSR688NWK, ENCSR342AGU, ENCSR157LMX, ENCSR354FNX
encode release date: 2017-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB022VOW
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF350 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF174 under the control of a CMV promoter.

value: unknown

value: embryonic

value: ENCBS923GRR at ENCODE; https://www.encodeproject.org/ENCBS923GRR/

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


title: ChIP-seq from K562 (ENCLB236IXL)

description:
https://www.encodeproject.org/experiments/ENCSR832DMO/
***************
biological replicate number: 1
technical replicate number: 1
description: SRSF1 ChIP-seq in K562
experiment encode accession: ENCSR832DMO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR966DOU
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB236IXL
size range: 200-400

value: SRSF1 ChIP-seq in K562

value: Xiang-Dong Fu, UCSD

value: adult

value: ENCBS979EXE at ENCODE; https://www.encodeproject.org/ENCBS979EXE/


title: ChIP-seq from K562 (ENCLB933JUT)

description:
https://www.encodeproject.org/experiments/ENCSR832DMO/
***************
biological replicate number: 2
technical replicate number: 1
description: SRSF1 ChIP-seq in K562
experiment encode accession: ENCSR832DMO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR966DOU
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB933JUT
size range: 200-400

value: ENCBS312CFO at ENCODE; https://www.encodeproject.org/ENCBS312CFO/


title: ChIP-seq from K562 (ENCLB930BTK)

description:
https://www.encodeproject.org/experiments/ENCSR943AOR/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-USF2 tagged K562 cell line.
experiment encode accession: ENCSR943AOR
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB930BTK
size range: 200-800

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal eGFP-USF2 fusion protein

value: Control

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to USF2

value: Kevin White, UChicago

value: ENCBS889FGM at ENCODE; https://www.encodeproject.org/ENCBS889FGM/

value: ENCODE dbxrefs Cellosaurus CVCL_GZ95; http://web.expasy.org/cellosaurus/CVCL_GZ95


title: ChIP-seq from ovary (ENCLB646FIH)

description:
https://www.encodeproject.org/experiments/ENCSR754DWU/
***************
biological replicate number: 1
technical replicate number: 1
description: POLR2A ChIP-seq on human ovary
experiment encode accession: ENCSR754DWU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR628RAE
encode release date: 2017-01-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB646FIH
size range: 450-650

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

value: ovary

value: tissue

value: female

value: Michael Snyder, Stanford

value: 53 year

value: ENCBS165BJP at ENCODE; https://www.encodeproject.org/ENCBS165BJP/

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


title: ChIP-seq from HEK293 (ENCLB254VDF)

description:
https://www.encodeproject.org/experiments/ENCSR858FAN/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF621 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR858FAN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2017-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB254VDF
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF621 under the control of a CMV promoter.

value: unknown

value: embryonic

value: ENCBS865AIG at ENCODE; https://www.encodeproject.org/ENCBS865AIG/

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


title: ChIP-seq from 22Rv1 (ENCLB509KOU)

description:
https://www.encodeproject.org/experiments/ENCSR933UGQ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human 22Rv1
experiment encode accession: ENCSR933UGQ
assay title: ChIP-seq
encode release date: 2016-11-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB509KOU
size range: 450-650

source_name: Homo sapiens 22Rv1 immortalized cell line

value: Control

value: immortalized cell line

value: not collected

value: carcinoma (prostate)

value: ENCBS737IZN at ENCODE; https://www.encodeproject.org/ENCBS737IZN/

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


title: ChIP-seq from 22Rv1 (ENCLB527PRR)

description:
https://www.encodeproject.org/experiments/ENCSR933UGQ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human 22Rv1
experiment encode accession: ENCSR933UGQ
assay title: ChIP-seq
encode release date: 2016-11-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB527PRR
size range: 450-650

value: ENCBS822DIG at ENCODE; https://www.encodeproject.org/ENCBS822DIG/


title: ChIP-seq from sigmoid colon (ENCLB802CDJ)

description:
https://www.encodeproject.org/experiments/ENCSR747VNS/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human sigmoid colon
experiment encode accession: ENCSR747VNS
assay title: ChIP-seq
encode release date: 2016-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB802CDJ
size range: 450-650

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

value: sigmoid colon

value: tissue

value: female

value: adult

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


title: ChIP-seq from upper lobe of left lung (ENCLB275HIS)

description:
https://www.encodeproject.org/experiments/ENCSR828PZH/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on upper lobe of left lung
experiment encode accession: ENCSR828PZH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR976HZM
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB275HIS

source_name: Homo sapiens upper lobe of left lung tissue male adult (37 years)

value: upper lobe of left lung

value: male

value: Richard Myers, HAIB

value: 37 year

value: ENCBS623YOK at ENCODE; https://www.encodeproject.org/ENCBS623YOK/

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


title: ChIP-seq from HEK293 (ENCLB095YAC)

description:
https://www.encodeproject.org/experiments/ENCSR751PNN/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF112 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR751PNN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2017-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB095YAC
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF112 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF112 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: unknown

value: embryonic

value: ENCBS294ZAB at ENCODE; https://www.encodeproject.org/ENCBS294ZAB/

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


title: ChIP-seq from K562 (ENCLB306ZJE)

description:
https://www.encodeproject.org/experiments/ENCSR932KYH/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq in K562
experiment encode accession: ENCSR932KYH
assay title: ChIP-seq
encode release date: 2017-02-13
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB306ZJE
size range: 200-400

source_name: Homo sapiens K562 immortalized cell line

value: Control

value: Control ChIP-seq on K562 cells

value: Xiang-Dong Fu, UCSD

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS158SWP at ENCODE; https://www.encodeproject.org/ENCBS158SWP/

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


title: ChIP-seq from body of pancreas (ENCLB246XUY)

description:
https://www.encodeproject.org/experiments/ENCSR853XCA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human body of pancreas
experiment encode accession: ENCSR853XCA
assay title: ChIP-seq
encode release date: 2016-11-01
lab: Michael Snyder, Stanford
library encode accession: ENCLB246XUY
size range: 450-650

source_name: Homo sapiens body of pancreas tissue female adult (51 year)

value: body of pancreas

value: tissue

value: female

value: 51 year

value: adult

value: ENCBS425WFZ at ENCODE; https://www.encodeproject.org/ENCBS425WFZ/

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


title: BRD4 ChIP-Seq

city: Sacramento

first: Clifford

middle: G.

last: Tepper

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

data_processing:
Image processing, base calling, quality scoring (Phred), and sample demultiplexing were executed by HiSeq Control Software with Real Time Analysis (HCS 1.5/RTA 1.13) and CASAVA 1.8 software (Illumina; San Diego, CA).
FASTQ-formatted ChIP-Seq reads were aligned to the human hg19 reference genome and reference KSHV genome sequence (Human herpesvirus 8, strain JSC-1, clone BAC16, GenBank: GQ994935.1) with Bowtie 2.
Peak finding was performed using MACS2 (Model-based Analysis for ChIP-Seq) utilizing the default parameters and commands described in the developer's manual, including a minimum FDR (q-value) cutoff of 0.05.
Genome_build: Human hg19 + HHV8/KSHV strain JSC-1 (GenBank: GQ994935.1)
Supplementary_files_format_and_content: Tab-delimited text files that include information pertaining to the peaks identified, including location (chromosome,  start site, end site), length, summit, tags, -10*log10(pvalue), fold_enrichment, and FDR(%) and were prepared from the MACS2 output files.

source_name: TREx-(F3H3)-K-Rta BCBL-1 cells

growth_protocol: TREx-(F3H3)-K-Rta BCBL-1 ( TREx-K-Rta BCBL-1) cells, which have tetracycline/doxycycline (Dox)-inducible expression of N-terminal Flagx3- and HAx3-tagged K-Rta, were cultured in complete RPMI 1640 (supplemented with 15% FBS and L-Glutamine) containing blasticidin (50 ug/ml) and hygromycin B (100 mg/ml). The cultures were maintained at 37°C in a humidified atmosphere containing 5% CO2 (v/v).

extract_protocol:
Following treatment with doxycycline, cells (1 x 10^8) were fixed with 1% formaldehyde, lysed, and chromatin DNA was sonicated to an average size of ~300 bp using a Diagenode Bioruptor. Chromatin immunoprecipitation (ChIP) of BRD4-associated chromatin was performed with anti-BRD4 monoclonal antibody (10 ug).  Subsequently, DNA was isolated with the QIAquick PCR Purification Kit (Qiagen) from the BRD4 immunoprecipitates (ChIP DNA) and from input DNA controls.
ChIP-enriched and input DNA samples (1 ng) were used to generate indexed, Illumina-compatible libraries with the KAPA LTP Library Preparation Kit (Kapa Biosystems, KK8230) according to manufacturer’s recommendations for end repair and A-tailing, adapter ligation, size selection, and library amplification.

treatment_protocol: Reactivation of endogenous KSHV in TREx-(F3H3)-K-Rta BCBL-1 cells was performed by inducing expression of Flag- and HA-tagged K-Rta by treatment of TREx-(F3H3)-K-Rta BCBL-1 cells with Dox (1 µg/ml) for 24 hours.

tag: cell line

value: TREx-(F3H3)-K-Rta BCBL-1 cells

tag: cell type

value: human primary effusion lymphoma cells

value: KSHV-positive human B cell lymphoma cells

tag: passages

tag: chip antibody

value: anti-BRD4 antibody (Bethyl Laboratories)


title: ChIP-seq from breast epithelium (ENCLB285BDM)

description:
https://www.encodeproject.org/experiments/ENCSR728WVG/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on -human (fragmentation date:Fri Nov 11 2016 00:00:00 GMT-0600 (CST)
experiment encode accession: ENCSR728WVG
assay title: ChIP-seq
encode release date: 2017-02-02
lab: Richard Myers, HAIB
library encode accession: ENCLB285BDM

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

value: Control

value: breast epithelium

value: Richard Myers, HAIB

value: ENCBS377TON at ENCODE; https://www.encodeproject.org/ENCBS377TON/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/0d43876e-94ba-4c85-a056-01dbc5065e3d/@@download/attachment/83392.svs


title: ChIP-seq from HEK293 (ENCLB168CDM)

description:
https://www.encodeproject.org/experiments/ENCSR854ORP/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF350 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR854ORP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR274OGE, ENCSR429LAP, ENCSR688NWK, ENCSR342AGU, ENCSR157LMX, ENCSR354FNX
encode release date: 2017-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB168CDM
size range: 450-650

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF350 under the control of a CMV promoter.

value: Michael Snyder, Stanford

value: unknown

value: embryonic

value: ENCBS413FJW at ENCODE; https://www.encodeproject.org/ENCBS413FJW/

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


title: ChIP-seq from GM12878 (ENCLB303WOX)

description:
https://www.encodeproject.org/experiments/ENCSR746XEG/
***************
biological replicate number: 1
technical replicate number: 1
description: NFXL1 ChIP-seq on human GM12878
experiment encode accession: ENCSR746XEG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB303WOX
size range: 450-650

source_name: Homo sapiens GM12878 immortalized cell line

value: adult

value: female

value: ENCBS436SAI at ENCODE; https://www.encodeproject.org/ENCBS436SAI/

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


title: ChIP-seq from GM12878 (ENCLB085BBJ)

description:
https://www.encodeproject.org/experiments/ENCSR746XEG/
***************
biological replicate number: 2
technical replicate number: 1
description: NFXL1 ChIP-seq on human GM12878
experiment encode accession: ENCSR746XEG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-05-17
lab: Michael Snyder, Stanford
library encode accession: ENCLB085BBJ
size range: 450-650

value: ENCBS607NAA at ENCODE; https://www.encodeproject.org/ENCBS607NAA/


title: ChIP-seq from HEK293 (ENCLB140IWJ)

description:
https://www.encodeproject.org/experiments/ENCSR751PNN/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF112 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR751PNN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR157LMX, ENCSR274OGE, ENCSR342AGU, ENCSR354FNX, ENCSR429LAP, ENCSR688NWK
encode release date: 2017-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB140IWJ
size range: 450-650

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF112 under the control of a CMV promoter.

value: ENCBS934EWU at ENCODE; https://www.encodeproject.org/ENCBS934EWU/


title: GDC555d41

description: BL0269 PDX tumor grown in NSG mice and developed resistance to treatment with pictilisib (GDC-0941)

data_processing:
Image processing, base calling, quality scoring (Phred), and sample demultiplexing were executed by HiSeq Control Software with Real Time Analysis (HCS 1.5/RTA 1.13) and CASAVA 1.8 software (Illumina).
FASTQ-formatted sequence data was analyzed using a standard Xenome-TopHat-Cufflinks workflow. RNA-Seq sequence reads (FASTQ format) were classified as human (graft) or mouse (host) using Xenome and subsequently aligned to the reference human genome assembly (Feb. 2009, GRCh37/hg19) using TopHat software. Gene- and transcript-level expression were comprehensively quantified with Cufflinks software, which performed 1) transcript assembly, 2) identification of splice variants, 3) quantification of expression as FPKM (fragments per kilobase of transcript per million mapped reads) values, and 4) normalization. Normalized FPKM values were utilized for downstream analysis steps.
Processed data are Cufflinks-Cufffnorm output files and contain Gene_Symbol (Ensembl ID), FPKM values, and FPKM status.
Genome_build: Feb. 2009, GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text files include Gene Symbol (Ensembl ID), FPKM values, and normalized FPKM status for each transcript and were prepared from the Cufflinks-Cuffnorm gene-level output files.

source_name: BL0269 human bladder cancer patient-derived xenograft (PDX)

growth_protocol: A freshly harvested BL0269 PDX tumor was sectioned and specimens (3-5mm3) were implanted subcutaneously into the flanks of 4–5-week-old NOD scid gamma (NSG) mice. When tumor volumes reached 100-300 mm3, the mice were randomized into 5 treatment groups (8 mice per group): control (untreated), cisplatin, pictilisib (GDC-0941), combination (cisplatin+pictilisib), and sequential (cisplatin -> pictilisib) treatments. The mice were treated with the corresponding agents and tumors were regarded as resistant to treatment when tumors reached logarithmic growth phases. Subsequently, two tumors were randomly selected from the control, pictilisib, cisplatin, combination, and sequential treatment groups for RNA-seq analysis.

extract_protocol:
Total cellular RNA was isolated from snap-frozen xenograft tumor pieces using the TRIzol Plus RNA Purification Kit (Life Technologies).  RNA quantity and quality were assessed on a NanoDrop spectrophotometer (Thermo Scientific) and the Agilent 2100 Bioanalyzer (Agilent Technologies), respectively.
RNA-Sequencing (RNA-Seq) libraries were prepared using a “total” RNA-Seq approach. Briefly, RNA preparations (1 ug) were depleted of rRNA using Ribo-Zero rRNA removal beads and indexed RNA-Seq libraries were prepared using the TruSeq Stranded Total RNA Sample Prep Kit (Illumina Inc., San Diego, CA) according to the manufacturer’s standard protocol.

tag: phenotype

value: Pictilisib (GDC-0941)-resistant

tag: drug treatment

value: Pictilisib (GDC-0941) (100 mg/kg P.O.)

tag: duration of drug treatment

value: 41 days


title: SEQ562d43

description: BL0269 PDX tumor grown in NSG mice and developed resistance to sequential treatment with cisplatin plus pictilisib (GDC-0941)

value: 43 days


title: CIS363D35

description: BL0269 PDX tumor grown in NSG mice and developed resistance to treatment with cisplatin

value: Cisplatin-resistant

value: Cisplatin (2 mg/kg I.V.)

value: 35 days


title: GDC563d49

value: 49 days


title: CIS554d29

value: 29 days


title: COM362d43

description: BL0269 PDX tumor grown in NSG mice and developed resistance to combination treatment with cisplatin plus pictilisib (GDC-0941)


title: ChIP-seq from thyroid gland (ENCLB140TEI)

description:
https://www.encodeproject.org/experiments/ENCSR744YJR/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human thyroid gland
experiment encode accession: ENCSR744YJR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR611RVL
encode release date: 2017-01-30
lab: Michael Snyder, Stanford
library encode accession: ENCLB140TEI
size range: 450-650

source_name: Homo sapiens thyroid gland tissue female adult (53 years)

tag: antibody

value: CTCF

value: thyroid gland

value: tissue

tag: biosample encode accession

value: Michael Snyder, Stanford

value: 53 year

value: ENCBS131UEI at ENCODE; https://www.encodeproject.org/ENCBS131UEI/

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


title: Ctrl560

description: BL0269 PDX tumor grown in NSG mice

value: Control

value: Untreated

value: Not applicable


title: ChIP-seq from HEK293 (ENCLB121GOT)

description:
https://www.encodeproject.org/experiments/ENCSR728MWW/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZIC2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR728MWW
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: ENCLB121GOT
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZIC2 fusion protein

value: immortalized cell line

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZIC2 under the control of a CMV promoter.

tag: Sex

value: female

tag: lab

value: unknown

value: embryonic

value: ENCBS763QCP at ENCODE; https://www.encodeproject.org/ENCBS763QCP/

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


title: ChIP-seq from HEK293 (ENCLB638TRX)

description:
https://www.encodeproject.org/experiments/ENCSR728MWW/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZIC2 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR728MWW
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: ENCLB638TRX
size range: 450-650

tag: age

tag: dev stage

value: ENCBS629IXE at ENCODE; https://www.encodeproject.org/ENCBS629IXE/


title: ChIP-seq from upper lobe of left lung (ENCLB618CIA)

description:
https://www.encodeproject.org/experiments/ENCSR972LYL/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human upper lobe of left lung
experiment encode accession: ENCSR972LYL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR061CNP
encode release date: 2016-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB618CIA
size range: 450-650

source_name: Homo sapiens upper lobe of left lung tissue female adult (51 year)

value: CTCF

value: upper lobe of left lung

value: 51 year

value: adult

tag: link

value: ENCBS011GFV at ENCODE; https://www.encodeproject.org/ENCBS011GFV/

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


title: ChIP-seq from suprapubic skin (ENCLB468LCQ)

description:
https://www.encodeproject.org/experiments/ENCSR928LDG/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on suprapubic skin
experiment encode accession: ENCSR928LDG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR106JXD
encode release date: 2017-06-15
lab: Richard Myers, HAIB
library encode accession: ENCLB468LCQ

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

value: suprapubic skin

value: tissue

value: Richard Myers, HAIB

value: 53 year

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: Ctrl378

description: BL0269 PDX tumor grown in NSG mice

value: Control

value: Untreated

value: Not applicable


title: ChIP-seq from suprapubic skin (ENCLB258EQD)

description:
https://www.encodeproject.org/experiments/ENCSR827FNU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human suprapubic skin
experiment encode accession: ENCSR827FNU
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB258EQD
size range: 450-650

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

value: female

value: Michael Snyder, Stanford

value: ENCBS351RRY at ENCODE; https://www.encodeproject.org/ENCBS351RRY/


title: Input DNA

value: TREx-(F3H3)-K-Rta BCBL-1 cells

value: human primary effusion lymphoma cells

value: KSHV-positive human B cell lymphoma cells


title: ChIP-seq from K562 (ENCLB463BWS)

description:
https://www.encodeproject.org/experiments/ENCSR742IDN/
***************
biological replicate number: 1
technical replicate number: 1
description: NR2C1 ChIP-seq on human K562
experiment encode accession: ENCSR742IDN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-01-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB463BWS
size range: 450-650

tag: line

value: immortalized cell line

value: adult

value: chronic myelogenous leukemia (CML)

value: ENCBS465MWC at ENCODE; https://www.encodeproject.org/ENCBS465MWC/

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 spleen (ENCLB868TAQ)

description:
https://www.encodeproject.org/experiments/ENCSR728EBP/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human spleen
experiment encode accession: ENCSR728EBP
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Michael Snyder, Stanford
library encode accession: ENCLB868TAQ
size range: 450-650

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

value: spleen

value: tissue

value: 51 year

value: ENCBS214FBD at ENCODE; https://www.encodeproject.org/ENCBS214FBD/

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


title: COM330

value: 40 days


title: ChIP-seq from esophagus squamous epithelium (ENCLB560HMJ)

description:
https://www.encodeproject.org/experiments/ENCSR746FMO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human esophagus squamous epithelium
experiment encode accession: ENCSR746FMO
assay title: ChIP-seq
encode release date: 2017-03-24
lab: Michael Snyder, Stanford
library encode accession: ENCLB560HMJ
size range: 450-650

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

value: Control

value: esophagus squamous epithelium

value: female

value: Michael Snyder, Stanford

value: 53 year

value: ENCBS927UKP at ENCODE; https://www.encodeproject.org/ENCBS927UKP/

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


title: ChIP-seq from MCF-7 (ENCLB488YKU)

description:
https://www.encodeproject.org/experiments/ENCSR924TVL/
***************
biological replicate number: 2
technical replicate number: 1
description: RFX5 ChIP-seq on human MCF-7
experiment encode accession: ENCSR924TVL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB488YKU
size range: 450-650

source_name: Homo sapiens MCF-7 immortalized cell line

value: immortalized cell line

tag: description

value: Mammary gland, adenocarcinoma. (PMID:4357757)

value: adult

value: 69 year

tag: health state

value: breast cancer (adenocarcinoma)

value: ENCBS536NWC at ENCODE; https://www.encodeproject.org/ENCBS536NWC/

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

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

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


title: ChIP-seq from transverse colon (ENCLB108KPB)

description:
https://www.encodeproject.org/experiments/ENCSR930CPA/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on transverse colon
experiment encode accession: ENCSR930CPA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR138QGB
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB108KPB

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

value: transverse colon

value: tissue

value: male

value: Richard Myers, HAIB

value: 37 year

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

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


title: ChIP-seq from HepG2 (ENCLB794TBO)

description:
https://www.encodeproject.org/experiments/ENCSR968QDP/
***************
biological replicate number: 2
technical replicate number: 1
description: SMARCE1 ChIP-seq on human HepG2
experiment encode accession: ENCSR968QDP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR399VVK
encode release date: 2017-06-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB794TBO
size range: 450-650

source_name: Homo sapiens HepG2 immortalized cell line

value: child

value: 15 year

value: Michael Snyder, Stanford

value: hepatocellular carcinoma

value: ENCBS667BFL at ENCODE; https://www.encodeproject.org/ENCBS667BFL/

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


title: ChIP-seq from K562 (ENCLB340WHX)

description:
https://www.encodeproject.org/experiments/ENCSR825KUF/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-CEBPG tagged K562 cell line.
experiment encode accession: ENCSR825KUF
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB340WHX
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-CEBPG fusion protein

value: Control

value: immortalized cell line

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

value: female

value: Kevin White, UChicago

tag: passage number

value: chronic myelogenous leukemia (CML)

value: 53 year

value: adult

value: ENCBS008URG at ENCODE; https://www.encodeproject.org/ENCBS008URG/

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

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


title: ChIP-seq from MCF-7 (ENCLB797PRV)

description:
https://www.encodeproject.org/experiments/ENCSR924TVL/
***************
biological replicate number: 1
technical replicate number: 1
description: RFX5 ChIP-seq on human MCF-7
experiment encode accession: ENCSR924TVL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR594UCI, ENCSR217LRF
encode release date: 2014-07-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB797PRV
size range: 450-650

value: Mammary gland, adenocarcinoma. (PMID:4357757)

value: 69 year

value: breast cancer (adenocarcinoma)

value: ENCBS216AOQ at ENCODE; https://www.encodeproject.org/ENCBS216AOQ/

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

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

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


title: ChIP-seq from HepG2 (ENCLB470QDO)

description:
https://www.encodeproject.org/experiments/ENCSR968QDP/
***************
biological replicate number: 1
technical replicate number: 1
description: SMARCE1 ChIP-seq on human HepG2
experiment encode accession: ENCSR968QDP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR399VVK
encode release date: 2017-06-07
lab: Michael Snyder, Stanford
library encode accession: ENCLB470QDO
size range: 450-650

value: immortalized cell line

value: male

value: Michael Snyder, Stanford

value: hepatocellular carcinoma

value: 15 year

value: child

value: ENCBS425BJH at ENCODE; https://www.encodeproject.org/ENCBS425BJH/

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


title: zmddm1a/zmddm1b 18 DAP embryo small RNA seq,rep1

city: Beijing

first: Jincheng

last: Long

state: Beijing

address: Hai Dian district ,Yuanmingyuan Road.Beijing

department: National Maize improvement center

country: China

institute: China Agricultural University

description: mCHH_island_zmddm1a_zmddm1b_24nt_siRNA_aboundance_.bed

data_processing:
Base calling  was performed following the standard Illumina protocol.
small RNA sequenced reads were trimmed to remove adaptor sequence and low-quality sequence. Then,reads that mapped to mapped to MicroRNA, transfer RNA and ribosomal RNA sequence were filter out. Quality passed reads were aligned to the B73 reference genome version 2 using Bowtie with -m 1,-v 1.
genome build: B73 reference genome version 2
processed data files format and content: bed file with 24 nt siRNA abundance on mCHH island in WT or zmddm1a/zmddm1b genotype. For small RNA -seq, the reads length range from 18 to 26 nt length, and 24 nt-length small RNA is the predominant type of all reads (about 70 %), which is the main interest of our study thus the processed data files include data only for 24 nt siRNA in mCHH islands. The definition of a mCHH island is that a 100 bp regions that contains extremely high level of mCHH. Columns are: 1. chromosome, 2. mCHH island start position, 3. mCHH island end position, 4. 24 nt siRNA reads abundance.

organism: Zea mays

source_name: Embryo

growth_protocol: Plants were grown in field from 2014-2016

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invotrogen).
Small RNA-seq libraries were constructed from total RNAs isolated from the same tissues as for the mRNA libraries, using the TruSeq Small RNA Sample Preparation Kit (Illumina) following manufacturer’s instructions.

treatment_protocol: Embryos were isolated and collected from 18 DAP developing kernel by manual dissection.

tag: cultivar

value: W22 inbred line

tag: developmental stage

value: 18 days after pollination (DAP)

tag: tissue

value: embryo

tag: genotype


title: zmddm1a/zmddm1b 18 DAP embryo small RNA seq,rep2


title: ChIP-seq from stomach (ENCLB067EKV)

description:
https://www.encodeproject.org/experiments/ENCSR823FFR/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on stomach
experiment encode accession: ENCSR823FFR
assay title: ChIP-seq
assembly: GRCh38
possible controls: ENCSR493PYN
encode release date: 2016-11-09
lab: Richard Myers, HAIB
library encode accession: ENCLB067EKV

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

value: stomach

value: tissue

value: female

value: Richard Myers, HAIB

value: 53 year

value: adult

value: ENCBS829SAQ at ENCODE; https://www.encodeproject.org/ENCBS829SAQ/

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

value: high resolution pathology slide image; https://www.encodeproject.org/documents/a307e129-388c-445e-b260-f655a14237dc/@@download/attachment/83401.svs


title: Wild type 18 DAP embryo small RNA seq,rep1

description: mCHH_island_WT_24nt_siRNA_aboundance.bed

value: WT


title: ChIP-seq from GM12878 (ENCLB597RSH)

description:
https://www.encodeproject.org/experiments/ENCSR841NDX/
***************
biological replicate number: 1
technical replicate number: 1
description: ELF1 ChIP-seq on human GM12878
experiment encode accession: ENCSR841NDX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-06-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB597RSH
size range: 450-650

value: immortalized cell line

value: Michael Snyder, Stanford

value: unknown

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

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


title: Wild type 18 DAP embryo small RNA seq,rep2

value: W22 inbred line

value: 18 days after pollination (DAP)


title: zmddm1a/zmddm1b 18 DAP embryo BS-seq,rep2

data_processing:
Base calling  was performed following the standard Illumina protocol.
Bisulfite sequencing reads were trimmed to remove adaptor sequence and low-quality sequence using Trim_galore,then aligned to the B73 reference genome version 2 using BS-seeke2 with default parameter.Then information of the methylation level of each cytosine was extracted using specific software contained by BS-seeker2
genome build: B73 reference genome version 2
processed data files format and content: CGmap file was generated by BS-seeker2.  Columns are: 1. chromosome, 2. nucleotide on Watson (+) strand, 3. position, 4. context (CG/CHG/CHH), 5. dinucleotide context (CA/CC/CG/CT), 6. methylation-level = #_of_C/ (#_of_C + #_of_T), 7. #_of_C (methylated C, the count of reads showing C here), 8. #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here).

extract_protocol:
Genomic DNA was extracted using CTAB method.
10 ug of genomic DNA was sheared to fragments between 300 and 500 bp. The fragments were subject to end repair, dA tailing, and ligating to methylated adapters, followed by bisulfate conversion.The bisulfate converted library were then PCR amplified (13 cycle) and purified, and sequenced on Illumina Hiseq 2500 platform.

value: embryo


title: ChIP-seq from HEK293 (ENCLB928VFX)

description:
https://www.encodeproject.org/experiments/ENCSR736ZKL/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF148 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR736ZKL
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: ENCLB928VFX
size range: 450-650

source_name: Homo sapiens HEK293 immortalized cell line originated from HEK293 stably expressing N-terminal eGFP-ZNF148 fusion protein

value: HEK293 cell line stably expressing N-terminal tagged eGFP-ZNF148 under the control of a CMV promoter.

value: embryonic

value: ENCBS978LXB at ENCODE; https://www.encodeproject.org/ENCBS978LXB/

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


title: ChIP-seq from HEK293 (ENCLB515IJS)

description:
https://www.encodeproject.org/experiments/ENCSR736ZKL/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF148 ChIP-seq on human HEK293 cells.
experiment encode accession: ENCSR736ZKL
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: ENCLB515IJS
size range: 450-650

value: female

value: ENCBS282JFQ at ENCODE; https://www.encodeproject.org/ENCBS282JFQ/


title: zmddm1a/zmddm1b 18 DAP embryo BS-seq,rep1


title: ChIP-seq from GM12878 (ENCLB081NDC)

description:
https://www.encodeproject.org/experiments/ENCSR841NDX/
***************
biological replicate number: 2
technical replicate number: 1
description: ELF1 ChIP-seq on human GM12878
experiment encode accession: ENCSR841NDX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR956WYO
encode release date: 2017-06-26
lab: Michael Snyder, Stanford
library encode accession: ENCLB081NDC
size range: 450-650

value: adult

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


title: Wild type 18 DAP embryo BS-seq,rep2

value: WT


title: ChIP-seq from K562 (ENCLB596NLN)

description:
https://www.encodeproject.org/experiments/ENCSR822DUK/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on human eGFP-ZNF740 tagged K562 cell line.
experiment encode accession: ENCSR822DUK
assay title: ChIP-seq
encode release date: 2016-05-18
lab: Kevin White, UChicago
library encode accession: ENCLB596NLN
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-ZNF740 fusion protein

value: Control

value: immortalized cell line

value: K562 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to ZNF740

value: Kevin White, UChicago

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS523ORN at ENCODE; https://www.encodeproject.org/ENCBS523ORN/

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

value: ENCODE dbxrefs Cellosaurus CVCL_HA08; http://web.expasy.org/cellosaurus/CVCL_HA08


title: Wild type 18 DAP embryo BS-seq,rep1

value: W22 inbred line

value: 18 days after pollination (DAP)

value: embryo


title: ChIP-seq from K562 (ENCLB408KAB)

description:
https://www.encodeproject.org/experiments/ENCSR742IDN/
***************
biological replicate number: 2
technical replicate number: 1
description: NR2C1 ChIP-seq on human K562
experiment encode accession: ENCSR742IDN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR632PAG
encode release date: 2017-01-27
lab: Michael Snyder, Stanford
library encode accession: ENCLB408KAB
size range: 450-650

source_name: Homo sapiens K562 immortalized cell line

value: female

value: Michael Snyder, Stanford

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 K562 (ENCLB516WEE)

description:
https://www.encodeproject.org/experiments/ENCSR822LBD/
***************
biological replicate number: 1
technical replicate number: 1
description: RBFOX2 ChIP-seq in K562
experiment encode accession: ENCSR822LBD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR932KYH
encode release date: 2017-02-27
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB516WEE
size range: 200-400

value: RBFOX2 ChIP-seq in K562

value: Xiang-Dong Fu, UCSD

value: adult

value: ENCBS074NGX at ENCODE; https://www.encodeproject.org/ENCBS074NGX/


title: ChIP-seq from esophagus squamous epithelium (ENCLB372GNE)

description:
https://www.encodeproject.org/experiments/ENCSR838RUX/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human esophagus squamous epithelium
experiment encode accession: ENCSR838RUX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR783XDX
encode release date: 2016-12-13
lab: Michael Snyder, Stanford
library encode accession: ENCLB372GNE
size range: 450-650

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

value: CTCF

value: esophagus squamous epithelium

value: tissue

value: male

value: 37 year

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

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


title: Pre-immune repeat 3, Input DNA [13764X13]

city: Salt Lake City

first: Tim

last: Formosa

state: UT

address: 15 N Medical Dr East RM 4100

department: Biochemistry

institute: University of Utah School of Medicine

data_processing:
Illumina sequencing reads for each biological replicate were sequentially aligned to both the S. cerevisiae genome (SGD release R64, UCSC SacCer3) and the Candida glabrata genome (Ensembl Fungi release 30, GCA_000002545.2) using Novoalign, allowing for one random assignment of multi-mapping reads. Alignments were assigned to the genome based on the best alignment metrics. Reads aligning to both genomes equally were considered orthologous and discarded.
Fragment coverage for S. cerevisiae was generated with BioToolBox bam2wig with an extension of 130 bp, a consensus fragment length as determined by peak cross-strand correlation, and depth-normalized by scaling to reads per million mapped (RPM).
The coverage tracks were further normalized for ChIP efficiency by dividing by the number of unique C. glabrata alignments (scaled to millions) in each sample (Orlando et al, 2014).
After normalization, a mean consensus track was generated by merging the replicates using bedtools and dividing by the number of replicates.
To generate fold enrichment tracks, genomic intervals with zero coverage in the Input samples were artificially set to a non-zero value of 1 (a value well below the genomic mean) and a fold enrichment calculated with macs2 bdgcmp. Coverage track manipulation was performed using the script manipulate_wig.
Genome_build: Saccharomyces cerevisiae: SGD release R64, UCSC SacCer3
Genome_build: Candida glabrata: Ensembl Fungi release 30, GCA_000002545.2
Supplementary_files_format_and_content: Calibrated BigWig files (ending in .cal.bw) represent individual replicate ChIP fragment coverage normalized for depth (RPM, Reads Per Million mapped) and calibrated for ChIP efficiency based on the number of Candida glabrata alignments.
Supplementary_files_format_and_content: Log2 fold enrichment BigWig files (ending in _log2FE.bw) represent ChIP fragment coverage normalized for depth, calibrated to Candida glabrata, averaged between all three biological replicates, divided by the Input coverage, and converted to a log2 scale. The Log2 fold enrichmnet BigWig files are available on the series record.

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

source_name: Whole yeast cells

growth_protocol: Cultures were grown to logarithmic phase and harvested by centrigugation.

extract_protocol:
Cells were subjected to cross-linking with formaldehyde (1%) for 20 min at room temperature. Glycine (0.125 mM) was added to quench crosslinking and cells were washed with 1X phosphate-buffered saline. For the reference genome, Candida glabrata (ATCC® 36909) was grown at 25°C and cross-linked with formaldehyde as described above. Cross-linked S. cerevisiae (40 × 10^7) and C. glabrata (20 × 10^7) cells were mixed in FA140+SDS buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 140 mM NaCl, 0.1% SDS) and lysed by bead beating. Lysates from two sets of S. cerevisiae and C. glabrata mixture (120 × 10^7 cells) were pooled for sonication using a Diagenode Bioruptor™ (6 cycles of 5 min each, 30 sec ON and 30 sec OFF at high setting). Soluble chromatin was obtained by two sequential high-speed centrifugations. To remove SDS, soluble chromatin obtained from four batches of yeast cells were pooled and transferred to a 5 mL Float-A-Lyzer G2 dialysis device (3.5 - 5 kD MWCO) (Spectra/Por), dialyzed initially for 2 h in 1 L FA buffer (50 mM HEPES-KOH, pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate) with 140 mM NaCl followed by an overnight dialysis against 4 L of the same buffer.
The dialysate was centrifuged at 13,000 rpm for 15 min at 4°C. A 100 ml aliquot was set aside for isolating input DNA. The remaining dialysate was split equally into three tubes and pre-cleared using 50 ml of blocked Dynabeads® Protein A for 1h at 4°C with end-over-end rotation. Blocking of Dynabeads® Protein A beads was performed at 4°C with end-over-end rotation for 4h using FA buffer containing 140 mM NaCl, bovine serum albumin (BSA) (0.2 mg/mL, New England Biolabs) and fish skin gelatin (0.5%, Sigma). Pre-cleared dialysate was combined with the custom-made rabbit polyclonal a-Spt6 antibody (30 ml; McCullough 2015). Cross-reactivity of the antibody, which was raised against S. cerevisiae Spt6, for C. glabrata Spt6 was verified by western blot (Figure S6). For a background control, the additional set of pre-cleared dialysate prepared from the wild type control strain was combined with pre-immune serum (30 ml). 100 ml blocked Dynabeads® Protein A was then added and incubated overnight at 4°C with end-over-end rotation. Beads were sequentially washed 5 min each with end-over-end rotation at 4°C with FA buffer + 140 mM NaCl (three washes), FA buffer + 1000 mM NaCl (two washes), FA buffer + 500 mM NaCl (two washes), and one wash each with LiCl/NP40 buffer (10 mM Tris.Cl, pH 8.0, 250 mM LiCl, 0.5% NP40, 0.5% sodium deoxycholate) and TE (10 mM Tris.Cl, pH 8.0, 1 mM EDTA). Elution and reverse crosslinking of ChIP and input DNA followed by RNase A and Proteinase K digestion steps were performed as described previously (Chandrasekharan et al., 2011). ChIP and input DNA were purified using the Qiagen MinElute PCR Purification kit according to the manufacturer's instructions, except two washes each with buffer QG and PE were performed.
Sequencing libraries were constructed using NEBNext® Multiplex Oligos (Index Primers Set 1 and Set 2) and NEBNext® ChIP-seq Library Prep Reagent Set for Illumina, and subjected to 50 bp single-end sequencing in an Illumina Hiseq2000 sequencer.
HiSeq 50 Cycle Single-Read Sequencing version 4: Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot.  Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001).  Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002)

tag: reference control

value: Candida glabrata

tag: strain

tag: relevant genotype

value: WT


title: ChIP-seq from upper lobe of left lung (ENCLB967YHB)

description:
https://www.encodeproject.org/experiments/ENCSR961NYO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human upper lobe of left lung
experiment encode accession: ENCSR961NYO
assay title: ChIP-seq
encode release date: 2016-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB967YHB
size range: 450-650

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

tag: antibody

value: Control

value: upper lobe of left lung

tag: biosample encode accession

value: Michael Snyder, Stanford

value: 54 year

value: ENCBS423TVO at ENCODE; https://www.encodeproject.org/ENCBS423TVO/

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


title: Pre-immune repeat 2, Input DNA [13764X7]


title: ChIP-seq from upper lobe of left lung (ENCLB602MUW)

description:
https://www.encodeproject.org/experiments/ENCSR964BKO/
***************
biological replicate number: 1
technical replicate number: 1
description: CTCF ChIP-seq on human upper lobe of left lung
experiment encode accession: ENCSR964BKO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR961NYO
encode release date: 2016-12-08
lab: Michael Snyder, Stanford
library encode accession: ENCLB602MUW
size range: 450-650

tag: Sex

tag: lab

value: adult