title: ChIP-seq from HepG2 (ENCLB915ZSE)

description:
https://www.encodeproject.org/experiments/ENCSR184SVO/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR184SVO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB915ZSE

value: ENCBS492KIP at ENCODE; https://www.encodeproject.org/ENCBS492KIP/


title: ChIP-seq from Loucy (ENCLB112WPX)

status: Public on Mar 09 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/ENCSR183CQK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR183CQK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR648HLP
encode release date: 2014-09-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB112WPX
size range: 200-600

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Homo sapiens Loucy immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/cc43df05-7513-412b-8abd-3b987569b91c/@@download/attachment/ChIP_New_General_ChIP_Protocol_03232012_v09.pdf

tag: antibody

tag: line

value: Loucy

value: immortalized cell line

tag: description

value: Established in 1987 from the peripheral blood of a patient with T-cell acute lymphoblastic leukemia (T-ALL) obtained two months prior to her death. May be of value in evaluating the role of t(16;20) in the etiology of T-ALL.

tag: biosample encode accession

tag: dev stage

value: adult

tag: Sex

value: female

tag: age

value: 38 year

tag: health state

value: T-cell acute lymphoblastic leukemia cell line ATCC CRL-2629

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS080PZG at ENCODE; https://www.encodeproject.org/ENCBS080PZG/

value: Derived from ENCODE donor ENCDO732PDS; https://www.encodeproject.org/ENCDO732PDS/

value: ENCODE dbxrefs Cellosaurus CVCL_1380; http://web.expasy.org/cellosaurus/CVCL_1380

value: ATCC sample source; http://www.atcc.org/Products/All/CRL-2629.aspx


title: ChIP-seq from bipolar spindle neuron (ENCLB313GBV)

description:
https://www.encodeproject.org/experiments/ENCSR170WVI/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on biopolar spindle neuron-human (fragmentation date:Tue Sep 29 2015 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR170WVI
assay title: ChIP-seq
encode release date: 2016-10-11
lab: Richard Myers, HAIB
library encode accession: ENCLB313GBV

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

value: Control

value: bipolar spindle neuron

value: in vitro differentiated cells

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

value: 53 year

value: male

value: Thomas Gingeras, CSHL

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

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


title: ChIP-seq from PC-9 (ENCLB351FTG)

description:
https://www.encodeproject.org/experiments/ENCSR180AAB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR180AAB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2017-01-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB351FTG
size range: 200-600

source_name: Homo sapiens PC-9 immortalized cell line

value: immortalized cell line

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

value: unknown

value: not collected

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

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

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


title: ChIP-seq from PC-9 (ENCLB448BXO)

description:
https://www.encodeproject.org/experiments/ENCSR180AAB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR180AAB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2017-01-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB448BXO
size range: 200-600

value: Bradley Bernstein, Broad

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


title: ChIP-seq from HCT116 (ENCLB113ZNN)

description:
https://www.encodeproject.org/experiments/ENCSR179BUC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR179BUC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2017-01-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB113ZNN
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens HCT116 immortalized cell line

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

value: cells obtained from ATCC

value: colorectal carcinoma

value: ENCBS494OPB at ENCODE; https://www.encodeproject.org/ENCBS494OPB/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ATCC sample source; http://www.atcc.org/products/all/CCL-247.aspx#357C3571006A4259B64650D34DF19048


title: ChIP-seq from HepG2 (ENCLB777BWC)

description:
https://www.encodeproject.org/experiments/ENCSR173CTF/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR173CTF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB777BWC

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-ZNF580 fusion protein, N-terminal FLAG-ZNF580 fusion protein

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS791AMU at ENCODE; https://www.encodeproject.org/ENCBS791AMU/

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


title: ChIP-seq from HepG2 (ENCLB311VYC)

description:
https://www.encodeproject.org/experiments/ENCSR173CTF/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR173CTF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB311VYC

value: immortalized cell line

value: ENCBS912QJN at ENCODE; https://www.encodeproject.org/ENCBS912QJN/


title: ChIP-seq from liver (ENCLB255FWI)

description:
https://www.encodeproject.org/experiments/ENCSR168SMX/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on NR2F2-human
experiment encode accession: ENCSR168SMX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR849OTN, ENCSR769JUI
encode release date: 2016-08-18
lab: Richard Myers, HAIB
library encode accession: ENCLB255FWI

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

value: liver

value: tissue

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

value: 4 year

value: female

value: healthy

value: Michael Snyder, Stanford

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

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


title: ChIP-seq from liver (ENCLB956CFN)

description:
https://www.encodeproject.org/experiments/ENCSR168SMX/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on NR2F2-human
experiment encode accession: ENCSR168SMX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR849OTN, ENCSR769JUI
encode release date: 2016-08-18
lab: Richard Myers, HAIB
library encode accession: ENCLB956CFN

value: child


title: ChIP-seq from Loucy (ENCLB499JYK)

description:
https://www.encodeproject.org/experiments/ENCSR165LOF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR165LOF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR648HLP
encode release date: 2014-09-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB499JYK
size range: 200-600

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/61c0d277-54c3-4e17-afcd-4059b22d89f6/@@download/attachment/ChIP_Protocol_For_Fresh_or_Frozen_Cells_v09.1.pdf

value: Loucy

value: Established in 1987 from the peripheral blood of a patient with T-cell acute lymphoblastic leukemia (T-ALL) obtained two months prior to her death. May be of value in evaluating the role of t(16;20) in the etiology of T-ALL.

value: adult

value: 38 year

value: T-cell acute lymphoblastic leukemia cell line ATCC CRL-2629

value: Bradley Bernstein, Broad

value: ENCBS708EFA at ENCODE; https://www.encodeproject.org/ENCBS708EFA/

value: Derived from ENCODE donor ENCDO732PDS; https://www.encodeproject.org/ENCDO732PDS/

value: ENCODE dbxrefs Cellosaurus CVCL_1380; http://web.expasy.org/cellosaurus/CVCL_1380

value: ATCC sample source; http://www.atcc.org/Products/All/CRL-2629.aspx


title: ChIP-seq from HCT116 (ENCLB010GQD)

description:
https://www.encodeproject.org/experiments/ENCSR161MXP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR161MXP
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR198WIH
encode release date: 2017-01-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB010GQD
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: immortalized cell line

value: cells obtained from ATCC

value: unknown

value: male

value: colorectal carcinoma

value: ENCBS494OPB at ENCODE; https://www.encodeproject.org/ENCBS494OPB/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ATCC sample source; http://www.atcc.org/products/all/CCL-247.aspx#357C3571006A4259B64650D34DF19048


title: ChIP-seq from B cell (ENCLB452TRM)

description:
https://www.encodeproject.org/experiments/ENCSR162DGX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR162DGX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AUW
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB452TRM
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens B primary cell female adult (27 years)

value: B cell

value: primary cell

value: adult

value: female

value: 27 year

value: normal

value: ENCBS836CYW at ENCODE; https://www.encodeproject.org/ENCBS836CYW/

value: Derived from ENCODE donor ENCDO115AAA; https://www.encodeproject.org/ENCDO115AAA/


title: ChIP-seq from Loucy (ENCLB215OIX)

description:
https://www.encodeproject.org/experiments/ENCSR165LOF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR165LOF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR648HLP
encode release date: 2014-09-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB215OIX
size range: 200-600

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/eaafee87-23f3-4bb4-adb1-585af01db120/@@download/attachment/ChIP%20New%20General%20ChIP%20Protocol%20041510%20v05.pdf

value: Loucy

value: immortalized cell line

value: Established in 1987 from the peripheral blood of a patient with T-cell acute lymphoblastic leukemia (T-ALL) obtained two months prior to her death. May be of value in evaluating the role of t(16;20) in the etiology of T-ALL.

value: 38 year

value: T-cell acute lymphoblastic leukemia cell line ATCC CRL-2629

value: Bradley Bernstein, Broad

value: ENCBS080PZG at ENCODE; https://www.encodeproject.org/ENCBS080PZG/

value: Derived from ENCODE donor ENCDO732PDS; https://www.encodeproject.org/ENCDO732PDS/

value: ENCODE dbxrefs Cellosaurus CVCL_1380; http://web.expasy.org/cellosaurus/CVCL_1380

value: ATCC sample source; http://www.atcc.org/Products/All/CRL-2629.aspx


title: ChIP-seq from B cell (ENCLB366WQS)

description:
https://www.encodeproject.org/experiments/ENCSR162DGX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR162DGX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AUW
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB366WQS
size range: 200-600

value: B cell

value: primary cell

value: ENCBS400ARI at ENCODE; https://www.encodeproject.org/ENCBS400ARI/


title: ChIP-seq from PC-9 (ENCLB676BDU)

description:
https://www.encodeproject.org/experiments/ENCSR152YYY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR152YYY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2017-01-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB676BDU
size range: 200-600

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

value: unknown

value: not collected

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

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

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


title: ChIP-seq from MCF-7 (ENCLB370SIT)

description:
https://www.encodeproject.org/experiments/ENCSR155VDK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on MCF7-human
experiment encode accession: ENCSR155VDK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR610GTD, ENCSR511PAE
encode release date: 2016-04-25
lab: Richard Myers, HAIB
library encode accession: ENCLB370SIT

source_name: Homo sapiens MCF-7 immortalized cell line

value: immortalized cell line

value: MCF-7, mammary gland adenocarcinoma

value: adult

value: female

value: 69 year

value: breast cancer (adenocarcinoma)

tag: passage number

value: Richard Myers, HAIB

value: ENCBS530DHL at ENCODE; https://www.encodeproject.org/ENCBS530DHL/

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 Karpas-422 (ENCLB892ZTC)

description:
https://www.encodeproject.org/experiments/ENCSR159CDJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR159CDJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB892ZTC
size range: 200-600

source_name: Homo sapiens Karpas-422 immortalized cell line

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: human B cell non-Hodgkin's lymphoma

value: Bradley Bernstein, Broad

value: ENCBS850UIV at ENCODE; https://www.encodeproject.org/ENCBS850UIV/

value: Derived from ENCODE donor ENCDO354AAA; https://www.encodeproject.org/ENCDO354AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1325; http://web.expasy.org/cellosaurus/CVCL_1325


title: ChIP-seq from HepG2 (ENCLB893TFK)

description:
https://www.encodeproject.org/experiments/ENCSR156CWW/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR156CWW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR346XJA
encode release date: 2016-09-26
lab: Richard Myers, HAIB
library encode accession: ENCLB893TFK

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-DNMT3B fusion protein

value: immortalized cell line

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS774QLP at ENCODE; https://www.encodeproject.org/ENCBS774QLP/

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 PC-9 (ENCLB886VEE)

description:
https://www.encodeproject.org/experiments/ENCSR152YYY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR152YYY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR011GWK
encode release date: 2017-01-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB886VEE
size range: 200-600

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

value: unknown

value: not collected

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

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

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


title: ChIP-seq from HepG2 (ENCLB525CXR)

description:
https://www.encodeproject.org/experiments/ENCSR156CWW/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR156CWW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR346XJA
encode release date: 2016-09-26
lab: Richard Myers, HAIB
library encode accession: ENCLB525CXR

value: Richard Myers, HAIB

value: ENCBS864XFG at ENCODE; https://www.encodeproject.org/ENCBS864XFG/


title: ChIP-seq from K562 (ENCLB076XWH)

description:
https://www.encodeproject.org/experiments/ENCSR159OCC/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on K562
experiment encode accession: ENCSR159OCC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000FCA
encode release date: 2016-06-14
lab: Richard Myers, HAIB
library encode accession: ENCLB076XWH

source_name: Homo sapiens K562 immortalized cell line stably expressing C-terminal FLAG-ATF1 fusion protein

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS947EGW at ENCODE; https://www.encodeproject.org/ENCBS947EGW/

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 SK-N-MC (ENCLB657QHS)

description:
https://www.encodeproject.org/experiments/ENCSR143HBU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against H3K27me3 using SK-N-MC cell line which was previously described as a neuroepithelioma (ATCC HTB-10). However recent evidence reveals it is Ewing's Sarcoma (www.ncbi.nlm.nih.gov/pubmed/15548687, www.ncbi.nlm.nih.gov/biosample/3151999, www.ncbi.nlm.nih.gov/pubmed/25453903).
experiment encode accession: ENCSR143HBU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR899XXQ
encode release date: 2017-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB657QHS
size range: 200-600

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

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/b4b48e6e-d14b-4359-96de-5e8c782c7bcf/@@download/attachment/TF_ChIP_Protocol_from_Shawn.pdf

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: child

value: 14 year

value: Ewing's sarcoma

value: Bradley Bernstein, Broad

value: ENCBS556HGY at ENCODE; https://www.encodeproject.org/ENCBS556HGY/

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

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


title: ChIP-seq from K562 (ENCLB263WLY)

description:
https://www.encodeproject.org/experiments/ENCSR129NAJ/
***************
biological replicate number: 1
technical replicate number: 1
description: Reverse crosslink control Chip-Seq on K562 human (fragmentation date 06-20-14)
experiment encode accession: ENCSR129NAJ
assay title: ChIP-seq
encode release date: 2016-01-08
lab: Richard Myers, HAIB
library encode accession: ENCLB263WLY

source_name: Homo sapiens K562 immortalized cell line

value: Control

value: K562, myelogenous leukemia

value: adult

value: Richard Myers, HAIB

value: ENCBS577JGM at ENCODE; https://www.encodeproject.org/ENCBS577JGM/

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


title: ChIP-seq from GM12878 (ENCLB013AHG)

description:
https://www.encodeproject.org/experiments/ENCSR142REC/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR142REC
assay title: ChIP-seq
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB013AHG
size range: 200-600

source_name: Homo sapiens GM12878 immortalized cell line

value: female

value: unknown

value: ENCBS830FPU at ENCODE; https://www.encodeproject.org/ENCBS830FPU/

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


title: ChIP-seq from SK-N-SH (ENCLB937LHB)

description:
https://www.encodeproject.org/experiments/ENCSR125IJY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR125IJY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2016-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB937LHB
size range: 200-600

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

value: SK-N-SH

value: immortalized cell line

value: 4 year

value: child

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

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

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


title: ChIP-seq from HepG2 (ENCLB659AMP)

description:
https://www.encodeproject.org/experiments/ENCSR130VQL/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR130VQL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB659AMP

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-PPARG_isoform1 fusion protein, N-terminal FLAG-PPARG_isoform1 fusion protein

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS643FYF at ENCODE; https://www.encodeproject.org/ENCBS643FYF/

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


title: ChIP-seq from K562 (ENCLB933PVT)

description:
https://www.encodeproject.org/experiments/ENCSR159OCC/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on K562
experiment encode accession: ENCSR159OCC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000FCA
encode release date: 2016-06-14
lab: Richard Myers, HAIB
library encode accession: ENCLB933PVT

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: ENCBS852VOH at ENCODE; https://www.encodeproject.org/ENCBS852VOH/

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 (ENCLB221ETD)

description:
https://www.encodeproject.org/experiments/ENCSR142IGM/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR142IGM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB221ETD

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

value: FLAG-CEBPA

value: immortalized cell line

value: ENCBS763IAS at ENCODE; https://www.encodeproject.org/ENCBS763IAS/


title: ChIP-seq from HepG2 (ENCLB639JEY)

description:
https://www.encodeproject.org/experiments/ENCSR125DAD/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR125DAD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB639JEY

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

value: FLAG-MLX

value: child

value: ENCBS165CEX at ENCODE; https://www.encodeproject.org/ENCBS165CEX/


title: ChIP-seq from radial glial cell (ENCLB601QJE)

description:
https://www.encodeproject.org/experiments/ENCSR136NUH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR136NUH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR689ICI
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB601QJE
size range: 300-1000

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

value: radial glial cell

value: in vitro differentiated cells

value: Early Radial Glia were collected at day 14 of differentiation (see protocol)

value: embryonic

value: female

value: 5 day

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS772AEX at ENCODE; https://www.encodeproject.org/ENCBS772AEX/

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


title: ChIP-seq from HepG2 (ENCLB534QJG)

description:
https://www.encodeproject.org/experiments/ENCSR125DAD/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR125DAD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB534QJG

value: male

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS434CAR at ENCODE; https://www.encodeproject.org/ENCBS434CAR/

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


title: ChIP-seq from neural cell (ENCLB269HZI)

description:
https://www.encodeproject.org/experiments/ENCSR124VOE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR124VOE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR308JFE
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB269HZI
size range: 300-800

source_name: Homo sapiens neural in vitro differentiated cells male embryo

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/97a73f1c-6372-4dd2-b275-0b8e855cbd5a/@@download/attachment/Cell_Paper_ChIP_protocol.pdf

value: neural cell

value: unknown

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

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


title: ChIP-seq from SK-N-MC (ENCLB619AEK)

description:
https://www.encodeproject.org/experiments/ENCSR143HBU/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against H3K27me3 using SK-N-MC cell line which was previously described as a neuroepithelioma (ATCC HTB-10). However recent evidence reveals it is Ewing's Sarcoma (www.ncbi.nlm.nih.gov/pubmed/15548687, www.ncbi.nlm.nih.gov/biosample/3151999, www.ncbi.nlm.nih.gov/pubmed/25453903).
experiment encode accession: ENCSR143HBU
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR899XXQ
encode release date: 2017-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB619AEK
size range: 200-600

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: child

value: 14 year

value: Ewing's sarcoma

value: ENCBS387QLW at ENCODE; https://www.encodeproject.org/ENCBS387QLW/

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


title: ChIP-seq from HepG2 (ENCLB099HKO)

description:
https://www.encodeproject.org/experiments/ENCSR117CHD/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR117CHD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB099HKO

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

value: FLAG-HOMEZ

value: male

value: 15 year

value: ENCBS015AWQ at ENCODE; https://www.encodeproject.org/ENCBS015AWQ/


title: ChIP-seq from SUDHL6 (ENCLB347WVC)

description:
https://www.encodeproject.org/experiments/ENCSR114GLZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR114GLZ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR179YLS
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB347WVC
size range: 200-600

source_name: Homo sapiens SUDHL6 immortalized cell line

value: also called SU-DHL-6 (diffuse histiocytic lymphoma) - disease:large cell lymphoma; diffuse mixed histiocytic and lymphocytic lymphoma; follicular B cell lymphoma; ATCC CRL-2959

value: 43 year

value: adult

value: Bradley Bernstein, Broad

value: ENCBS107PVI at ENCODE; https://www.encodeproject.org/ENCBS107PVI/

value: Derived from ENCODE donor ENCDO353AAA; https://www.encodeproject.org/ENCDO353AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2206; http://web.expasy.org/cellosaurus/CVCL_2206


title: ChIP-seq from HepG2 (ENCLB336ZDC)

description:
https://www.encodeproject.org/experiments/ENCSR115PIK/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR115PIK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB336ZDC

source_name: Homo sapiens HepG2 immortalized cell line stably expressing N-terminal FLAG-MIER2 fusion protein, C-terminal FLAG-MIER2 fusion protein

value: immortalized cell line

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS856VUC at ENCODE; https://www.encodeproject.org/ENCBS856VUC/

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


title: ChIP-seq from HepG2 (ENCLB744NPM)

description:
https://www.encodeproject.org/experiments/ENCSR115PIK/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR115PIK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB744NPM

value: child

value: ENCBS696ZBR at ENCODE; https://www.encodeproject.org/ENCBS696ZBR/


title: ChIP-seq from bipolar spindle neuron (ENCLB077ELA)

description:
https://www.encodeproject.org/experiments/ENCSR138PGW/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on biopolar spindle neuron-human (fragmentation date:Tue Sep 29 2015 00:00:00 GMT-0500 (CDT)
experiment encode accession: ENCSR138PGW
assay title: ChIP-seq
encode release date: 2016-10-05
lab: Richard Myers, HAIB
library encode accession: ENCLB077ELA

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

value: Control

value: bipolar spindle neuron

value: in vitro differentiated cells

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

value: 53 year

value: male

value: Thomas Gingeras, CSHL

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

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


title: ChIP-seq from HepG2 (ENCLB260LVJ)

description:
https://www.encodeproject.org/experiments/ENCSR130VQL/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR130VQL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB260LVJ

value: 15 year

value: ENCBS838SUU at ENCODE; https://www.encodeproject.org/ENCBS838SUU/


title: ChIP-seq from HepG2 (ENCLB764KLS)

description:
https://www.encodeproject.org/experiments/ENCSR142IGM/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR142IGM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB764KLS

value: FLAG-CEBPA

value: immortalized cell line

value: hepatocellular carcinoma

value: ENCBS448PNJ at ENCODE; https://www.encodeproject.org/ENCBS448PNJ/


title: ChIP-seq from mid-neurogenesis radial glial cells (ENCLB409ZZR)

description:
https://www.encodeproject.org/experiments/ENCSR113LFZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR113LFZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR287XMW
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB409ZZR
size range: 300-1000

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

value: mid-neurogenesis radial glial cells

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

value: embryonic

value: female

value: 5 day

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS741FXQ at ENCODE; https://www.encodeproject.org/ENCBS741FXQ/

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


title: ChIP-seq from HepG2 (ENCLB170KEE)

description:
https://www.encodeproject.org/experiments/ENCSR108TYQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR108TYQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB170KEE

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-GATAD1 fusion protein

value: child

value: male

value: Richard Myers, HAIB

value: ENCBS997GPU at ENCODE; https://www.encodeproject.org/ENCBS997GPU/

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


title: ChIP-seq from HepG2 (ENCLB935TDD)

description:
https://www.encodeproject.org/experiments/ENCSR108TYQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR108TYQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB935TDD

value: immortalized cell line

value: 15 year

value: ENCBS629EXZ at ENCODE; https://www.encodeproject.org/ENCBS629EXZ/


title: ChIP-seq from MM.1S (ENCLB790RMK)

description:
https://www.encodeproject.org/experiments/ENCSR120LGC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR120LGC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR264HOB
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB790RMK
size range: 300-600
nucleic acid starting quantity: 256.36
nucleic acid starting quantity units: ng

source_name: Homo sapiens MM.1S immortalized cell line

value: The parent cell line, MM.1, was established from peripheral blood of a multiple myeloma patient who had become resistant to steroid-based therapy. this line is sensitive to dexamethasone

value: adult

value: 42 year

value: immunoglobulin A lambda myeloma

value: ENCBS205VYW at ENCODE; https://www.encodeproject.org/ENCBS205VYW/

value: Derived from ENCODE donor ENCDO697GBW; https://www.encodeproject.org/ENCDO697GBW/

value: ENCODE dbxrefs Cellosaurus CVCL_8792; http://web.expasy.org/cellosaurus/CVCL_8792


title: ChIP-seq from HepG2 (ENCLB749JVK)

description:
https://www.encodeproject.org/experiments/ENCSR117CHD/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR117CHD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB749JVK

value: FLAG-HOMEZ

value: hepatocellular carcinoma

value: ENCBS884OKX at ENCODE; https://www.encodeproject.org/ENCBS884OKX/


title: ChIP-seq from radial glial cell (ENCLB422OPG)

description:
https://www.encodeproject.org/experiments/ENCSR104BSN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR104BSN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR689ICI
encode release date: 2017-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB422OPG
size range: 300-1000

value: radial glial cell

value: in vitro differentiated cells

value: Early Radial Glia were collected at day 14 of differentiation (see protocol)

value: embryonic

value: female

value: 5 day

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS772AEX at ENCODE; https://www.encodeproject.org/ENCBS772AEX/

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


title: ChIP-seq from K562 (ENCLB951ZFP)

description:
https://www.encodeproject.org/experiments/ENCSR102KIN/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on K562
experiment encode accession: ENCSR102KIN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR129NAJ, ENCSR264VDP
encode release date: 2016-10-12
lab: Richard Myers, HAIB
library encode accession: ENCLB951ZFP

value: immortalized cell line

value: K562, myelogenous leukemia

value: 53 year

value: adult

value: chronic myelogenous leukemia (CML)

value: Richard Myers, HAIB

value: ENCBS577JGM at ENCODE; https://www.encodeproject.org/ENCBS577JGM/

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 HepG2 (ENCLB145YQX)

description:
https://www.encodeproject.org/experiments/ENCSR103SZL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2-human
experiment encode accession: ENCSR103SZL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR649FPL, ENCSR716SYG
encode release date: 2016-03-11
lab: Richard Myers, HAIB
library encode accession: ENCLB145YQX

source_name: Homo sapiens HepG2 immortalized cell line

value: HepG2, hepatocellular carcinoma

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS485OKN at ENCODE; https://www.encodeproject.org/ENCBS485OKN/

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

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

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


title: ChIP-seq from HepG2 (ENCLB752UWA)

description:
https://www.encodeproject.org/experiments/ENCSR103SZL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2-human
experiment encode accession: ENCSR103SZL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR649FPL, ENCSR716SYG
encode release date: 2016-03-11
lab: Richard Myers, HAIB
library encode accession: ENCLB752UWA

value: immortalized cell line

value: ENCBS250DDC at ENCODE; https://www.encodeproject.org/ENCBS250DDC/


title: ChIP-seq from K562 (ENCLB515XQN)

description:
https://www.encodeproject.org/experiments/ENCSR102KIN/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on K562
experiment encode accession: ENCSR102KIN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR129NAJ, ENCSR264VDP
encode release date: 2016-10-12
lab: Richard Myers, HAIB
library encode accession: ENCLB515XQN

value: K562, myelogenous leukemia

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

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


title: ChIP-seq from HepG2 (ENCLB125ZMG)

description:
https://www.encodeproject.org/experiments/ENCSR087NSR/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR087NSR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB125ZMG

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-KDM1A fusion protein

value: Richard Myers, HAIB

value: ENCBS916LIB at ENCODE; https://www.encodeproject.org/ENCBS916LIB/


title: ChIP-seq from K562 (ENCLB704OVG)

description:
https://www.encodeproject.org/experiments/ENCSR077DKV/
***************
biological replicate number: 1
technical replicate number: 1
description: CREM ChIP-seq on human K562
experiment encode accession: ENCSR077DKV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR599SPN, ENCSR000FCA
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB704OVG

source_name: Homo sapiens K562 immortalized cell line

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

value: CREM

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

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

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

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


title: ChIP-seq from HepG2 (ENCLB252RJX)

description:
https://www.encodeproject.org/experiments/ENCSR092OVN/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR092OVN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB252RJX

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-FOXA3 fusion protein, N-terminal FLAG-FOXA3 fusion protein

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: ENCBS528TYU at ENCODE; https://www.encodeproject.org/ENCBS528TYU/

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


title: ChIP-seq from HepG2 (ENCLB913TIQ)

description:
https://www.encodeproject.org/experiments/ENCSR071YVR/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR071YVR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB913TIQ

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-KMT2B fusion protein

value: immortalized cell line

value: ENCBS714KKA at ENCODE; https://www.encodeproject.org/ENCBS714KKA/


title: ChIP-seq from Karpas-422 (ENCLB685ASQ)

description:
https://www.encodeproject.org/experiments/ENCSR058SHN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR058SHN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB685ASQ
size range: 200-600

source_name: Homo sapiens Karpas-422 immortalized cell line

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: adult

value: female

value: human B cell non-Hodgkin's lymphoma

value: Bradley Bernstein, Broad

value: ENCBS850UIV at ENCODE; https://www.encodeproject.org/ENCBS850UIV/

value: Derived from ENCODE donor ENCDO354AAA; https://www.encodeproject.org/ENCDO354AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1325; http://web.expasy.org/cellosaurus/CVCL_1325


title: ChIP-seq from HCT116 (ENCLB901TMI)

description:
https://www.encodeproject.org/experiments/ENCSR091QXP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR091QXP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2016-12-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB901TMI
size range: 200-600

source_name: Homo sapiens HCT116 immortalized cell line

value: cells obtained from ATCC

value: unknown

value: colorectal carcinoma

value: ENCBS494OPB at ENCODE; https://www.encodeproject.org/ENCBS494OPB/

value: Derived from ENCODE donor ENCDO000ABE; https://www.encodeproject.org/ENCDO000ABE/

value: ENCODE dbxrefs Cellosaurus CVCL_0291; http://web.expasy.org/cellosaurus/CVCL_0291

value: ATCC sample source; http://www.atcc.org/products/all/CCL-247.aspx#357C3571006A4259B64650D34DF19048


title: ChIP-seq from HepG2 (ENCLB179PZW)

description:
https://www.encodeproject.org/experiments/ENCSR071YVR/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR071YVR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB179PZW

value: immortalized cell line

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS973AQL at ENCODE; https://www.encodeproject.org/ENCBS973AQL/

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


title: ChIP-seq from HCT116 (ENCLB740TOC)

description:
https://www.encodeproject.org/experiments/ENCSR093SHE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR093SHE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2016-12-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB740TOC
size range: 200-600

value: Bradley Bernstein, Broad


title: ChIP-seq from K562 (ENCLB542MZH)

description:
https://www.encodeproject.org/experiments/ENCSR077DKV/
***************
biological replicate number: 2
technical replicate number: 1
description: CREM ChIP-seq on human K562
experiment encode accession: ENCSR077DKV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR599SPN, ENCSR000FCA
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB542MZH

value: CREM

value: K562, myelogenous leukemia

value: 53 year

value: adult

value: female

value: chronic myelogenous leukemia (CML)

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

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

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

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


title: ChIP-seq from K562 (ENCLB272JTK)

description:
https://www.encodeproject.org/experiments/ENCSR076YPO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562-human
experiment encode accession: ENCSR076YPO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR700IEB, ENCSR571CEX
encode release date: 2016-03-30
lab: Richard Myers, HAIB
library encode accession: ENCLB272JTK

value: immortalized cell line

value: ENCBS577JGM at ENCODE; https://www.encodeproject.org/ENCBS577JGM/


title: ChIP-seq from MCF-7 (ENCLB802TFV)

description:
https://www.encodeproject.org/experiments/ENCSR057MWG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR057MWG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2016-11-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB802TFV
size range: 200-600

source_name: Homo sapiens MCF-7 immortalized cell line

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

value: 69 year

value: breast cancer (adenocarcinoma)

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

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

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

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


title: ChIP-seq from HepG2 (ENCLB323UJR)

description:
https://www.encodeproject.org/experiments/ENCSR055XHN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR055XHN
assay title: ChIP-seq
encode release date: 2017-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB323UJR
size range: 200-600

extract_protocol: not provided

value: Control

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

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Bradley Bernstein, Broad

value: ENCBS295NFS at ENCODE; https://www.encodeproject.org/ENCBS295NFS/

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 neural cell (ENCLB981YPW)

description:
https://www.encodeproject.org/experiments/ENCSR045HLL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR045HLL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR308JFE
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB981YPW
size range: 200-600

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

value: neural cell

value: in vitro differentiated cells

value: embryonic

value: unknown

value: healthy

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

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


title: ChIP-seq from OCI-LY1 (ENCLB468UEO)

description:
https://www.encodeproject.org/experiments/ENCSR076JBA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR076JBA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB468UEO
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens OCI-LY1 immortalized cell line

value: immortalized cell line

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

value: 44 year

value: adult

value: B cell lymphoma

value: ENCBS397COL at ENCODE; https://www.encodeproject.org/ENCBS397COL/

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

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


title: ChIP-seq from MCF-7 (ENCLB286MNG)

description:
https://www.encodeproject.org/experiments/ENCSR056UBA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR056UBA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2017-01-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB286MNG
size range: 200-600
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

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

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

value: Bradley Bernstein, Broad

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

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

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

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


title: ChIP-seq from HepG2 (ENCLB429UUM)

description:
https://www.encodeproject.org/experiments/ENCSR054FKH/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR054FKH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR226ULX
encode release date: 2016-06-14
lab: Richard Myers, HAIB
library encode accession: ENCLB429UUM

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-RAD21 fusion protein

value: immortalized cell line

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS070YKP at ENCODE; https://www.encodeproject.org/ENCBS070YKP/

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 liver (ENCLB548MJV)

description:
https://www.encodeproject.org/experiments/ENCSR038GMB/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on GABPA-human
experiment encode accession: ENCSR038GMB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR931XLP, ENCSR019XRC
encode release date: 2016-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB548MJV

source_name: Homo sapiens liver tissue male adult (32 years)

value: GABPA

value: liver

value: tissue

value: Human liver Tissue obtained from a healthy, 32 year old Caucasian male donor

value: 32 year

value: adult

value: healthy with non-obstructive CAD (coronary artery disease)

value: Thomas Gingeras, CSHL

value: ENCBS046RNA at ENCODE; https://www.encodeproject.org/ENCBS046RNA/

value: Derived from ENCODE donor ENCDO060AAA; https://www.encodeproject.org/ENCDO060AAA/

value: ENCODE dbxrefs Liver_STL011; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Liver_STL011


title: ChIP-seq from HepG2 (ENCLB188SDQ)

description:
https://www.encodeproject.org/experiments/ENCSR072GJV/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR072GJV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB188SDQ

source_name: Homo sapiens HepG2 immortalized cell line stably expressing N-terminal FLAG-HMG20A fusion protein, C-terminal FLAG-HMG20A fusion protein

value: immortalized cell line

value: child

value: male

value: 15 year

value: ENCBS187GKM at ENCODE; https://www.encodeproject.org/ENCBS187GKM/


title: ChIP-seq from neural cell (ENCLB712HHN)

description:
https://www.encodeproject.org/experiments/ENCSR045HLL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR045HLL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR308JFE
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB712HHN
size range: 300-800

source_name: Homo sapiens neural in vitro differentiated cells male embryo

value: neural cell

value: in vitro differentiated cells

value: embryonic

value: unknown

value: healthy

value: Bradley Bernstein, Broad

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

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


title: ChIP-seq from HepG2 (ENCLB844QNI)

description:
https://www.encodeproject.org/experiments/ENCSR072GJV/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR072GJV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB844QNI

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS803OSI at ENCODE; https://www.encodeproject.org/ENCBS803OSI/

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


title: ChIP-seq from K562 (ENCLB252OEO)

description:
https://www.encodeproject.org/experiments/ENCSR076YPO/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562-human
experiment encode accession: ENCSR076YPO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR700IEB, ENCSR571CEX
encode release date: 2016-03-30
lab: Richard Myers, HAIB
library encode accession: ENCLB252OEO

value: immortalized cell line

value: K562, myelogenous leukemia

value: adult

value: female

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS149SJX at ENCODE; https://www.encodeproject.org/ENCBS149SJX/

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 HepG2 (ENCLB783ZPL)

description:
https://www.encodeproject.org/experiments/ENCSR087NSR/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR087NSR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB783ZPL

value: child

value: male

value: 15 year

value: ENCBS198VSH at ENCODE; https://www.encodeproject.org/ENCBS198VSH/


title: ChIP-seq from liver (ENCLB128AHN)

description:
https://www.encodeproject.org/experiments/ENCSR038GMB/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on GABPA-human
experiment encode accession: ENCSR038GMB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR931XLP, ENCSR019XRC
encode release date: 2016-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB128AHN

value: GABPA

value: liver

value: tissue

value: Human liver Tissue obtained from a healthy, 32 year old Caucasian male donor

value: 32 year

value: healthy with non-obstructive CAD (coronary artery disease)

value: Thomas Gingeras, CSHL

value: ENCBS046RNA at ENCODE; https://www.encodeproject.org/ENCBS046RNA/

value: Derived from ENCODE donor ENCDO060AAA; https://www.encodeproject.org/ENCDO060AAA/

value: ENCODE dbxrefs Liver_STL011; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Liver_STL011


title: ChIP-seq from liver (ENCLB759WCB)

description:
https://www.encodeproject.org/experiments/ENCSR019XRC/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on STL011-human (fragmentation date: 2015-12-09)
experiment encode accession: ENCSR019XRC
assay title: ChIP-seq
encode release date: 2016-01-29
lab: Richard Myers, HAIB
library encode accession: ENCLB759WCB

value: Control

value: adult


title: ChIP-seq from HepG2 (ENCLB129GYX)

description:
https://www.encodeproject.org/experiments/ENCSR092OVN/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR092OVN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB129GYX

value: immortalized cell line

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS501TPE at ENCODE; https://www.encodeproject.org/ENCBS501TPE/

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


title: ChIP-seq from HepG2 (ENCLB842IXB)

description:
https://www.encodeproject.org/experiments/ENCSR019NPF/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR019NPF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB842IXB

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-SP5 fusion protein, N-terminal FLAG-SP5 fusion protein

value: child

value: male

value: 15 year

value: ENCBS851GOG at ENCODE; https://www.encodeproject.org/ENCBS851GOG/


title: ChIP-seq from HepG2 (ENCLB721MOB)

description:
https://www.encodeproject.org/experiments/ENCSR054FKH/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR054FKH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR226ULX
encode release date: 2016-06-14
lab: Richard Myers, HAIB
library encode accession: ENCLB721MOB

value: ENCBS811PND at ENCODE; https://www.encodeproject.org/ENCBS811PND/

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


title: ChIP-seq from neural cell (ENCLB366QUP)

description:
https://www.encodeproject.org/experiments/ENCSR045HLL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR045HLL
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR308JFE
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB366QUP
size range: 200-600

value: neural cell

value: in vitro differentiated cells

value: embryonic

value: unknown

value: healthy

value: Bradley Bernstein, Broad

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

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


title: ChIP-seq from Loucy (ENCLB135KTM)

description:
https://www.encodeproject.org/experiments/ENCSR036KFJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR036KFJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR648HLP
encode release date: 2014-09-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB135KTM
size range: 200-600

source_name: Homo sapiens Loucy immortalized cell line

value: Loucy

value: immortalized cell line

value: Established in 1987 from the peripheral blood of a patient with T-cell acute lymphoblastic leukemia (T-ALL) obtained two months prior to her death. May be of value in evaluating the role of t(16;20) in the etiology of T-ALL.

value: adult

value: female

value: 38 year

value: T-cell acute lymphoblastic leukemia cell line ATCC CRL-2629

value: ENCBS080PZG at ENCODE; https://www.encodeproject.org/ENCBS080PZG/

value: Derived from ENCODE donor ENCDO732PDS; https://www.encodeproject.org/ENCDO732PDS/

value: ENCODE dbxrefs Cellosaurus CVCL_1380; http://web.expasy.org/cellosaurus/CVCL_1380

value: ATCC sample source; http://www.atcc.org/Products/All/CRL-2629.aspx


title: ChIP-seq from HepG2 (ENCLB139REO)

description:
https://www.encodeproject.org/experiments/ENCSR019NPF/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR019NPF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB139REO

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

value: Richard Myers, HAIB

value: ENCBS294MNY at ENCODE; https://www.encodeproject.org/ENCBS294MNY/

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


title: ChIP-seq from GM12878 (ENCLB357LFF)

description:
https://www.encodeproject.org/experiments/ENCSR016UEH/
***************
biological replicate number: 1
technical replicate number: 1
description: TARDBP ChIP-seq on human GM12878
experiment encode accession: ENCSR016UEH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR596QDC, ENCSR237VSG
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB357LFF

source_name: Homo sapiens GM12878 immortalized cell line

value: TARDBP

value: immortalized cell line

value: GM12878, B-lymphocyte, lymphoblastoid

value: unknown

value: ENCBS845TXY at ENCODE; https://www.encodeproject.org/ENCBS845TXY/

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

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

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878


title: ChIP-seq from Loucy (ENCLB696SVC)

description:
https://www.encodeproject.org/experiments/ENCSR036KFJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR036KFJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR648HLP
encode release date: 2014-09-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB696SVC
size range: 200-600

value: Loucy

value: Established in 1987 from the peripheral blood of a patient with T-cell acute lymphoblastic leukemia (T-ALL) obtained two months prior to her death. May be of value in evaluating the role of t(16;20) in the etiology of T-ALL.

value: adult

value: female

value: 38 year

value: T-cell acute lymphoblastic leukemia cell line ATCC CRL-2629

value: Bradley Bernstein, Broad

value: ENCBS708EFA at ENCODE; https://www.encodeproject.org/ENCBS708EFA/

value: Derived from ENCODE donor ENCDO732PDS; https://www.encodeproject.org/ENCDO732PDS/

value: ENCODE dbxrefs Cellosaurus CVCL_1380; http://web.expasy.org/cellosaurus/CVCL_1380


title: ChIP-seq from liver (ENCLB231OHF)

description:
https://www.encodeproject.org/experiments/ENCSR016BMM/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on TAF1-human
experiment encode accession: ENCSR016BMM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR904IXG, ENCSR849OTN
encode release date: 2016-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB231OHF

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

value: liver

value: tissue

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

value: 4 year

value: child

value: healthy

value: Michael Snyder, Stanford

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

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


title: ChIP-seq from SUDHL6 (ENCLB865EZS)

description:
https://www.encodeproject.org/experiments/ENCSR018LUP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR018LUP
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR179YLS
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB865EZS
size range: 200-600

source_name: Homo sapiens SUDHL6 immortalized cell line

value: immortalized cell line

value: also called SU-DHL-6 (diffuse histiocytic lymphoma) - disease:large cell lymphoma; diffuse mixed histiocytic and lymphocytic lymphoma; follicular B cell lymphoma; ATCC CRL-2959

value: 43 year

value: adult

value: male

value: ENCBS107PVI at ENCODE; https://www.encodeproject.org/ENCBS107PVI/

value: Derived from ENCODE donor ENCDO353AAA; https://www.encodeproject.org/ENCDO353AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2206; http://web.expasy.org/cellosaurus/CVCL_2206


title: ChIP-seq from liver (ENCLB866RYJ)

description:
https://www.encodeproject.org/experiments/ENCSR016BMM/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on TAF1-human
experiment encode accession: ENCSR016BMM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR904IXG, ENCSR849OTN
encode release date: 2016-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB866RYJ

value: liver

value: female


title: ChIP-seq from GM12878 (ENCLB293MKQ)

description:
https://www.encodeproject.org/experiments/ENCSR016UEH/
***************
biological replicate number: 2
technical replicate number: 1
description: TARDBP ChIP-seq on human GM12878
experiment encode accession: ENCSR016UEH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR596QDC, ENCSR237VSG
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB293MKQ

value: TARDBP

value: GM12878, B-lymphocyte, lymphoblastoid

value: unknown

value: Richard Myers, HAIB

value: ENCBS460NBS at ENCODE; https://www.encodeproject.org/ENCBS460NBS/

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

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

value: Coriell sample source; https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=CC


title: ChIP-seq from HepG2 (ENCLB332RET)

description:
https://www.encodeproject.org/experiments/ENCSR031ING/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR031ING
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB332RET

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-KDM6A fusion protein

value: immortalized cell line

value: child

value: 15 year

value: hepatocellular carcinoma

value: ENCBS378FNW at ENCODE; https://www.encodeproject.org/ENCBS378FNW/

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


title: ChIP-seq from K562 (ENCLB556AAG)

description:
https://www.encodeproject.org/experiments/ENCSR000FCE/
***************
biological replicate number: 1
technical replicate number: 1
description: ETV6 ChIP-seq on human K562
experiment encode accession: ENCSR000FCE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR830KKO, ENCSR000FCA
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB556AAG

source_name: Homo sapiens K562 immortalized cell line

value: K562, myelogenous leukemia

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS601AAA at ENCODE; https://www.encodeproject.org/ENCBS601AAA/

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 (ENCLB556AAH)

description:
https://www.encodeproject.org/experiments/ENCSR000FCE/
***************
biological replicate number: 2
technical replicate number: 1
description: ETV6 ChIP-seq on human K562
experiment encode accession: ENCSR000FCE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR830KKO, ENCSR000FCA
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB556AAH

value: female

value: Richard Myers, HAIB

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


title: ChIP-seq from K562 (ENCLB556AAF)

description:
https://www.encodeproject.org/experiments/ENCSR000FCD/
***************
biological replicate number: 1
technical replicate number: 1
description: SMAD5 ChIP-seq on human K562
experiment encode accession: ENCSR000FCD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR896JFO, ENCSR000FCA
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB556AAF

value: immortalized cell line

value: ENCBS600AAA at ENCODE; https://www.encodeproject.org/ENCBS600AAA/


title: ChIP-seq from HepG2 (ENCLB995YMN)

description:
https://www.encodeproject.org/experiments/ENCSR031ING/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR031ING
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB995YMN

value: child

value: male

value: 15 year

value: ENCBS299QPB at ENCODE; https://www.encodeproject.org/ENCBS299QPB/


title: ChIP-seq from HepG2 (ENCLB044QPM)

description:
https://www.encodeproject.org/experiments/ENCSR009KLQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR009KLQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB044QPM

source_name: Homo sapiens HepG2 immortalized cell line stably expressing C-terminal FLAG-KLF16 fusion protein, N-terminal FLAG-KLF16 fusion protein

value: hepatocellular carcinoma

value: ENCBS481HLR at ENCODE; https://www.encodeproject.org/ENCBS481HLR/

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


title: ChIP-seq from HepG2 (ENCLB928EMT)

description:
https://www.encodeproject.org/experiments/ENCSR009KLQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Chip-Seq on HepG2
experiment encode accession: ENCSR009KLQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR239QGH
encode release date: 2016-11-08
lab: Richard Myers, HAIB
library encode accession: ENCLB928EMT

value: ENCBS528WAN at ENCODE; https://www.encodeproject.org/ENCBS528WAN/


title: ChIP-seq from K562 (ENCLB556AAE)

description:
https://www.encodeproject.org/experiments/ENCSR000FCD/
***************
biological replicate number: 2
technical replicate number: 1
description: SMAD5 ChIP-seq on human K562
experiment encode accession: ENCSR000FCD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR896JFO, ENCSR000FCA
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB556AAE

value: K562, myelogenous leukemia

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)


title: ChIP-seq from K562 (ENCLB556AAD)

description:
https://www.encodeproject.org/experiments/ENCSR000FCC/
***************
biological replicate number: 1
technical replicate number: 1
description: NFE2 ChIP-seq on human K562
experiment encode accession: ENCSR000FCC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR824WND, ENCSR000FCA
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB556AAD

value: female

value: ENCBS601AAA at ENCODE; https://www.encodeproject.org/ENCBS601AAA/

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 (ENCLB556AAC)

description:
https://www.encodeproject.org/experiments/ENCSR000FCC/
***************
biological replicate number: 2
technical replicate number: 1
description: NFE2 ChIP-seq on human K562
experiment encode accession: ENCSR000FCC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR824WND, ENCSR000FCA
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB556AAC

value: immortalized cell line

value: Richard Myers, HAIB

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


title: ChIP-seq from K562 (ENCLB556AAN)

description:
https://www.encodeproject.org/experiments/ENCSR000FCA/
***************
biological replicate number: 13
technical replicate number: 1
description: Reverse Crosslink Control ChIP-seq on human K562 (fragmentation date 07-22-13)
experiment encode accession: ENCSR000FCA
assay title: ChIP-seq
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB556AAN

value: Control


title: ChIP-seq from GM12878 (ENCLB559JPM)

description:
https://www.encodeproject.org/experiments/ENCSR000BVP/
***************
biological replicate number: 3
technical replicate number: 1
description: Control ChIP-seq protocol v042211.1 on human GM12878
experiment encode accession: ENCSR000BVP
assay title: ChIP-seq
encode release date: 2012-09-10
lab: Richard Myers, HAIB
library encode accession: ENCLB559JPM

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/2f645c4a-dea3-49fb-817d-db81c7906ebe/@@download/attachment/wgEncodeHaibTfbs.release3.html.pdf

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: unknown

value: ENCBS110ENC at ENCODE; https://www.encodeproject.org/ENCBS110ENC/

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

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

value: ENCODE dbxrefs GM12878; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=GM12878

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: ChIP-seq from K562 (ENCLB556AAA)

description:
https://www.encodeproject.org/experiments/ENCSR000FCB/
***************
biological replicate number: 2
technical replicate number: 1
description: MITF ChIP-seq on human K562
experiment encode accession: ENCSR000FCB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR824WND, ENCSR000FCA
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB556AAA

value: MITF

value: K562, myelogenous leukemia

value: adult

value: 53 year

value: chronic myelogenous leukemia (CML)


title: ChIP-seq from DND-41 (ENCLB695ATS)

description:
https://www.encodeproject.org/experiments/ENCSR000ASA/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human Dnd41 Control
experiment encode accession: ENCSR000ASA
assay title: ChIP-seq
encode release date: 2012-03-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695ATS

source_name: Homo sapiens DND-41 immortalized cell line

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/f10bdd36-e370-4777-a7f3-83091c115749/@@download/attachment/wgEncodeBroadHistone.html.pdf

value: T cell leukemia with Notch mutation

value: child

value: male

value: 13 year

value: Bradley Bernstein, Broad

value: ENCBS282AAA at ENCODE; https://www.encodeproject.org/ENCBS282AAA/

value: Derived from ENCODE donor ENCDO183AAA; https://www.encodeproject.org/ENCDO183AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_2022; http://web.expasy.org/cellosaurus/CVCL_2022

value: ENCODE dbxrefs Dnd41; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=Dnd41

value: DSMZ  sample source; http://www.dsmz.de/index.htm


title: ChIP-seq from B cell (ENCLB695AIU)

description:
https://www.encodeproject.org/experiments/ENCSR000AUW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq on human CD20+ Control
experiment encode accession: ENCSR000AUW
assay title: ChIP-seq
encode release date: 2012-08-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AIU

source_name: Homo sapiens B primary cell female adult (27 years)

value: Control

value: B cell

value: primary cell

value: female

value: 27 year

value: normal

value: ENCBS400ARI at ENCODE; https://www.encodeproject.org/ENCBS400ARI/

value: Derived from ENCODE donor ENCDO115AAA; https://www.encodeproject.org/ENCDO115AAA/


title: ChIP-seq from DND-41 (ENCLB695ATT)

description:
https://www.encodeproject.org/experiments/ENCSR000ASA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq on human Dnd41 Control
experiment encode accession: ENCSR000ASA
assay title: ChIP-seq
encode release date: 2012-03-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695ATT

value: immortalized cell line

value: child

value: unknown

value: ENCBS688JZQ at ENCODE; https://www.encodeproject.org/ENCBS688JZQ/


title: Chinese origin rep 2 STR

city: Boston

first: Emily

middle: S

last: Mohn

state: MA

address: 711 Washington Street

department: Jean Mayer USDA Human Nutrition Research Center on Aging

institute: Tufts University

description:
processed data file:
STR_Indian_vs_Chinese_origin_Cuffdiff_differential_gene_expression.xlsx

library_source: transcriptomic

data_processing:
Quality of sequenced reads was determined using FastQC. Reads for all samples were of acceptable quality (PHRED score ≥ 30)
High-quality reads were mapped to mmul_1 whole genome using Tophat for illumina v1.5.0 (default settings)
Fragments Per Kilobase Of Exon Per Million Mapped Reads (FPKM) were calculated using Cuffdiff v0.0.5. Cuffdiff automatically calculates log2 transformed fold change
Fold change for each gene was manually calculated by dividing FPKM Chinese origin by FPKM Indian origin in Excel
Genome_build: mmul_1
Supplementary_files_format_and_content: excel files include average FPKM expression values for Indian-origin group and Chinese-origin group, log2 fold change, fold change, as well as statistics for differential gene expression (test statistic, unadjusted p-value, Benjamini Hochberg flase discovery rate q-value)

molecule: total RNA

organism: Macaca mulatta

source_name: Chinese origin_striatum

growth_protocol: Rhesus monkeys were fed a standard stock diet plus a variety of supplemental seasonal fruits and vegetables 2 times/week throughout the course of their lifespan at the Oregon National Primate Research Center

extract_protocol:
Brain regions were removed, frozen on dry ice and stored at -80⁰C. RNA was extracted using the Qiagen Rneasy Lipid Tissue Mini kit (Cat. no. 74804) Illumina TruSeq RNA Sample Prep Kit (Cat. no. RS-122-2001) was used with 1-2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: rhesus monkey origin

value: Chinese origin

tag: age (years)

tag: tissue

value: Brain

tag: tissue region

value: striatum


title: ChIP-seq from H1-hESC (ENCLB182YPD)

description:
https://www.encodeproject.org/experiments/ENCSR000AMI/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR000AMI
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB182YPD
size range: 300-800

source_name: Homo sapiens H1-hESC stem cell male embryo

value: stem cell

value: embryonic

value: male

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS284CPV at ENCODE; https://www.encodeproject.org/ENCBS284CPV/

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


title: Chinese origin rep 3 STR


title: ChIP-seq from GM12878 (ENCLB559JPN)

description:
https://www.encodeproject.org/experiments/ENCSR000BVP/
***************
biological replicate number: 4
technical replicate number: 1
description: Control ChIP-seq protocol v042211.1 on human GM12878
experiment encode accession: ENCSR000BVP
assay title: ChIP-seq
encode release date: 2012-09-10
lab: Richard Myers, HAIB
library encode accession: ENCLB559JPN

value: Control

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: adult

value: female

value: Richard Myers, HAIB

value: ENCBS110ENC at ENCODE; https://www.encodeproject.org/ENCBS110ENC/

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

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

value: ENCODE dbxrefs GM12878; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=GM12878

value: Coriell sample source; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12878&PgId=166


title: Indian origin rep 3 STR

source_name: Indian origin_striatum

value: Indian origin

value: Brain

value: striatum


title: Chinese origin rep 1 STR

value: Chinese origin


title: Indian origin rep 1 STR


title: Indian origin rep 2 STR


title: Chinese origin rep 3 CER

description:
processed data file:
CER_Indian_vs_Chinese_origin_Cuffdiff_differential_gene_expression.xlsx

source_name: Chinese origin_cerebellum

value: cerebellum


title: MCF7_E2_ShMEN1_1

first: Koen

last: Dreijerink

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Basecalls were performed with FastQC version 0.10.0.
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
Genome_build: hg19

source_name: MCF-7 breast cancer cells

growth_protocol: Cells were maintained at 37oC and 5% CO2 in DMEM + 10% FBS and Pen-Strep.

extract_protocol:
RNA was extracted using RNeasy
Libraries were made from total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Samples 1-8. MCF-7 cells that had been lentivirally infected with constructs for inducible expression of small hairpin RNA's directed against the MEN1 mRNA (ShMEN1#1) or a control sequence (ShCtrl) were synchronized for 72 hrs in phenol red-free medium (DMEM) containing 10% charcoal dextran-treated fetal bovine serum (CDT medium). Expression of small hairpin RNA's was induced by adding 100 ng/ml doxycycline for 72 hrs. 10nM estradiol or vehicle was added to the cells for 45 mins. Samples 9-12. MCF-7 cells were treated with 1mM of the menin inhibitor MI-2 or DMSO for 4 days.

tag: cell line

tag: infection

value: lentivirally infected with constructs against shMEN1

tag: treatment

value: 10nM estradiol


title: MCF7_E2_ShMEN1_2


title: Chinese origin rep 1 CER


title: MCF7_Veh_ShMEN1_2

value: vehicle


title: MCF7_Veh_ShMEN1_1


title: ChIP-seq from K562 (ENCLB556AAB)

description:
https://www.encodeproject.org/experiments/ENCSR000FCB/
***************
biological replicate number: 1
technical replicate number: 1
description: MITF ChIP-seq on human K562
experiment encode accession: ENCSR000FCB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR824WND, ENCSR000FCA
encode release date: 2014-07-07
lab: Richard Myers, HAIB
library encode accession: ENCLB556AAB

tag: antibody

value: MITF

tag: line

value: immortalized cell line

value: K562, myelogenous leukemia

value: 53 year

value: chronic myelogenous leukemia (CML)

value: ENCBS601AAA at ENCODE; https://www.encodeproject.org/ENCBS601AAA/

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: Indian origin rep 2 CER

source_name: Indian origin_cerebellum

value: Indian origin


title: MCF7_Veh_ShCtrl_2

value: lentivirally infected with constructs against shCtrl


title: MCF7_E2_ShCtrl_2


title: MCF7_E2_ShCtrl_1


title: Indian origin rep 3 CER

value: Brain


title: Chinese origin rep 3 PFC

description:
processed data file:
PFC_Indian_vs_Chinese_origin_Cuffdiff_differential_gene_expression.xlsx

source_name: Chinese origin_prefrontal cortex

value: Chinese origin

value: prefrontal cortex


title: MCF7_Veh_ShCtrl_1


title: Chinese origin rep 2 PFC


title: Indian origin rep 1 CER

value: cerebellum


title: Chinese origin rep 1 PFC


title: Chinese origin rep 2 CER


title: Indian origin rep 3 PFC

source_name: Indian origin_prefrontal cortex


title: Indian origin rep 2 PFC


title: mRNAseq-Mettl-METTL14KD-repl2

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description:
Sample 22
DEXSeq_exons in HC-m6A-containing genes

data_processing:
The control and IP samples from PAR-CLIP-MeRIP experiments were sequenced together in one flowcell on two lanes, and the reads from two lanes of each sample were combined for remaining analysis. The raw seq data was trimmed using the Trimmomatic computer program version 0.30 to remove adaptor sequences, and mapped to the Human genome version hg19 by Bowtie 1.0.0 without any gaps and allowed for at most two mismatches. HNRNPG binding sites were identified by PARalyzer v1.1 with default settings. Read counts were mapped to the AGRAC motifs within HNRNPG binding peaks, and m6A sites were identified as AGRAC motifs with log2(IP/control) larger than 0.5.
The PAR-CLIP samples from control and METTL3/L14 knockdown HEK293T cells were sequenced together in one flowcell on three lanes, and the reads from two lanes of each sample were combined for remaining analysis. The raw seq data was trimmed using the Trimmomatic computer program version 0.30 to remove adaptor sequences, and mapped to the Human genome version hg19 by Bowtie 1.0.0 without any gaps and allowed for at most two mismatches. HNRNPG binding sites were identified by PARalyzer v1.1 with default settings. Read counts were mapped to the AGRAC motifs within HNRNPG binding peaks, and m6A sites were identified as AGRAC motifs with log2(control/METTL3 KD) larger than 0.5 or log2(control/METTL14 KD) larger than 0.5.
RNA-seq experiments were performed on two replicate RNA samples from HNRNPG, METTL3, METTL14 KD as well as control HEK293T cells (48 hours after transfection). Total RNA samples were extracted according to RNeasy plus kit (Catalog # 74104, Qiagen). Libraries were prepared according to the TruSeq Stranded mRNA LT Sample Prep Kit (Catalog # RS-122-9005DOC). KD and control samples were sequenced together in one flowcell on four lanes, respectively. All samples were sequenced by illumina Hiseq 2000 with pair end 100-bp read length. The reads from the four lanes of each samples were combined for all analysis. The RNA-seq data was mapped using the splice-aware alignment algorithm TopHat version 1.1.4 based on the following parameters: tophat –num-threads 8 –mate-inner-dist 200 –solexa-quals –min-isoform-fraction 0 –coverage-search-segment-mismatches 1. Cufflinks was used to predict exons and cuffdiff was used to detect isoform expression level changes. Differential splicing was determined using DEXSeq based on Cufflinks-predicted, nonoverlapping exons.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with the DEXSeq-called exons in HC-m6A-containing genes

growth_protocol: Embryonic kidney cell line HEK293T (CRL-11268) were obtained from American Type Culture Collection (ATCC) and were cultured under standard conditions

extract_protocol:
All PAR-CLIP RNA samples (samples 1-10) were extracted following normal PAR-CLIP procedures; the total RNA samples (samples 11-22) were extracted according to RNeasy plus kit (Catalog # 74104, Qiagen).
PAR-CLIP-MeRIP samples are the m6A-immunoprecipitated (202003, SYSY) PAR-CLIP samples, so the library construction of PAR-CLIP-MeRIP samples is the same as PAR-CLIP samples. Therefore, PAR-CLIP-MeRIP libraries (Samples 1-4) were prepared using TruSeq Small RNA Sample Preparation Kit (RS-200-0012, Illumina) according to the manufacturer’s instructions, and then sequenced by Illumina Hiseq 2000 with single end 50-bp read length. PAR-CLIP libraries (Samples 5-10) were prepared using TruSeq Small RNA Sample Preparation Kit (RS-200-0012, Illumina) according to the manufacturer’s instructions, and then sequenced by Illumina Hiseq 2000 with single end 50-bp read length. RNA-seq libraries (Samples 11-22) were prepared according to the TruSeq Stranded mRNA LT Sample Prep Kit (Catalog # RS-122-9005DOC). KD and control samples were sequenced together in one flowcell on four lanes, respectively. The reads from the four lanes of each samples were combined for all analysis.

value: embryonic kidney cell line HEK293T

tag: genotype

value: METTL14 Knockdown


title: Indian origin rep 1 PFC


title: mRNAseq-Mettl-Control-repl2

description:
Sample 18
DEXSeq_exons in HC-m6A-containing genes

source_name: mRNAseq-Mettl-Control

value: wild type


title: mRNAseq-Mettl-METTL3KD-repl1

description:
Sample 19
DEXSeq_exons in HC-m6A-containing genes

value: METTL3 Knockdown


title: mRNAseq-Mettl-METTL3KD-repl2

description:
Sample 20
DEXSeq_exons in HC-m6A-containing genes


title: mRNAseq-hnRNPG-KD2-repl2

description:
Sample 16
DEXSeq_exons in HC-m6A-containing genes

value: HNRNPG Knockdown


title: mRNAseq-hnRNPG-KD2-repl1

description:
Sample 15
DEXSeq_exons in HC-m6A-containing genes


title: mRNAseq-Mettl-METTL14KD-repl1

description:
Sample 21
DEXSeq_exons in HC-m6A-containing genes


title: mRNAseq-hnRNPG-KD1-repl1

description:
Sample 13
DEXSeq_exons in HC-m6A-containing genes


title: mRNAseq-Mettl-Control-repl1

description:
Sample 17
DEXSeq_exons in HC-m6A-containing genes