title: TF ChIP-seq from HepG2 (ENCLB756RBT)

description:
https://www.encodeproject.org/experiments/ENCSR313VZG/
***************
biological replicate number: 1
technical replicate number: 1
description: FIP1L1 ChIP-seq on HepG2
experiment encode accession: ENCSR313VZG
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR141EZP
encode release date: 2018-01-19
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB756RBT
size range: 200-400

value: male

value: child

value: 15 year

value: hepatocellular carcinoma

value: ENCBS260UFW at ENCODE; https://www.encodeproject.org/ENCBS260UFW/


title: Histone ChIP-seq from OCI-LY7 (ENCLB247DHE)

status: Public on May 23 2021

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/ENCSR347DAG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR347DAG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR063AUO
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB247DHE
fragmentation methods: sonication (generic)
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 OCI-LY7 immortalized cell line

tag: antibody

tag: line

value: cell line

tag: description

value: established from the peripheral blood sample of a 48-year-old man with B-cell Non-Hodgkin lymphoma (B-NHL, diffuse large cell lymphoma, DLCL, stage 2A, at relapse) in 1984

tag: biosample encode accession

tag: age

value: 48 year

tag: dev stage

value: adult

tag: Sex

tag: health state

value: B cell lymphoma

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS886BJZ at ENCODE; https://www.encodeproject.org/ENCBS886BJZ/

value: Derived from ENCODE donor ENCDO351AAA; https://www.encodeproject.org/ENCDO351AAA/

value: ENCODE dbxrefs Cellosaurus CVCL_1881; http://web.expasy.org/cellosaurus/CVCL_1881


title: Histone ChIP-seq from HEK293 (ENCLB555ACD)

description:
https://www.encodeproject.org/experiments/ENCSR000FCG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 HEK293 ChIP-Seq
experiment encode accession: ENCSR000FCG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000EVA
encode release date: 2014-07-07
lab: Peggy Farnham, USC
library encode accession: ENCLB555ACD
fragmentation methods: sonication (Bioruptor generic)
size range: 200-500

source_name: Homo sapiens HEK293 cell line

value: embryonic kidney, cells contain Adenovirus 5 DNA

value: female

value: embryonic

value: unknown

value: Peggy Farnham, USC

tag: source

value: ATCC

value: ENCBS482AAA at ENCODE; https://www.encodeproject.org/ENCBS482AAA/

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


title: TF ChIP-seq from K562 (ENCLB558GEF)

description:
https://www.encodeproject.org/experiments/ENCSR423FCW/
***************
biological replicate number: 1
technical replicate number: 1
description: RBM14 ChIP-seq in K562
experiment encode accession: ENCSR423FCW
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR457PLC
encode release date: 2018-01-22
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB558GEF
size range: 200-400

source_name: Homo sapiens K562 cell line

value: cell line

value: RBM14 ChIP-seq in K562

value: 53 year

value: Xiang-Dong Fu, UCSD

value: chronic myelogenous leukemia (CML)

value: ENCBS111WEH at ENCODE; https://www.encodeproject.org/ENCBS111WEH/

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


title: TF ChIP-seq from K562 (ENCLB600KEL)

description:
https://www.encodeproject.org/experiments/ENCSR791OZM/
***************
biological replicate number: 2
technical replicate number: 1
description: RBM25 ChIP-seq in K562
experiment encode accession: ENCSR791OZM
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR084AIG
encode release date: 2018-01-18
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB600KEL
size range: 200-400
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: RBM25 ChIP-seq in K562

value: adult

value: ENCBS742ILR at ENCODE; https://www.encodeproject.org/ENCBS742ILR/


title: TF ChIP-seq from K562 (ENCLB789YNG)

description:
https://www.encodeproject.org/experiments/ENCSR268QIQ/
***************
biological replicate number: 1
technical replicate number: 1
description: SRSF3 ChIP-seq in K562
experiment encode accession: ENCSR268QIQ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR457PLC
encode release date: 2016-10-31
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB789YNG
size range: 200-400

value: SRSF3 ChIP-seq in K562

value: female

value: ENCBS735VTB at ENCODE; https://www.encodeproject.org/ENCBS735VTB/


title: TF ChIP-seq from HepG2 (ENCLB901BDW)

description:
https://www.encodeproject.org/experiments/ENCSR932ZRD/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR932ZRD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR776XHE
encode release date: 2020-08-28
lab: Richard Myers, HAIB
library encode accession: ENCLB901BDW
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting ZBTB38

value: male

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS483KLN at ENCODE; https://www.encodeproject.org/ENCBS483KLN/

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


title: TF ChIP-seq from K562 (ENCLB857ZPP)

description:
https://www.encodeproject.org/experiments/ENCSR268QIQ/
***************
biological replicate number: 2
technical replicate number: 1
description: SRSF3 ChIP-seq in K562
experiment encode accession: ENCSR268QIQ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR457PLC
encode release date: 2016-10-31
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB857ZPP
size range: 200-400

value: cell line

value: 53 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS757EXI at ENCODE; https://www.encodeproject.org/ENCBS757EXI/


title: TF ChIP-seq from H1 (ENCLB770HAP)

description:
https://www.encodeproject.org/experiments/ENCSR784VUY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR784VUY
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB770HAP
fragmentation methods: sonication (generic)
size range: 300-1000

source_name: Homo sapiens H1-hESC stem cell male embryo

value: embryonic

value: unknown

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS364BFI at ENCODE; https://www.encodeproject.org/ENCBS364BFI/

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


title: TF ChIP-seq from H1 (ENCLB619PPT)

description:
https://www.encodeproject.org/experiments/ENCSR784VUY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR784VUY
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR000AMI
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB619PPT
fragmentation methods: sonication (generic)
size range: 200-900

source_name: Homo sapiens H1 cell line

value: male

value: CDI

value: ENCBS540UTP at ENCODE; https://www.encodeproject.org/ENCBS540UTP/


title: TF ChIP-seq from HEK293 (ENCLB653BCM)

description:
https://www.encodeproject.org/experiments/ENCSR618HNF/
***************
biological replicate number: 2
technical replicate number: 1
description: TRIM28 ChIP-seq on human HEK293
experiment encode accession: ENCSR618HNF
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR938LXW
encode release date: 2017-06-01
lab: Peggy Farnham, USC
library encode accession: ENCLB653BCM
fragmentation methods: see document

value: Embryonic kidney, cells contain Adenovirus 5 DNA

value: female

value: Peggy Farnham, USC

value: ENCBS037XHS at ENCODE; https://www.encodeproject.org/ENCBS037XHS/

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


title: TF ChIP-seq from HepG2 (ENCLB623QSQ)

description:
https://www.encodeproject.org/experiments/ENCSR243LNQ/
***************
biological replicate number: 1
technical replicate number: 1
description: PRPF4 ChIP-seq on HepG2
experiment encode accession: ENCSR243LNQ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR975KJI
encode release date: 2016-10-31
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB623QSQ
size range: 200-400
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens HepG2 cell line

value: cell line

value: PRPF4 ChIP-seq on HepG2 cells

value: child

value: 15 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: hepatocellular carcinoma

value: ENCBS041GAW at ENCODE; https://www.encodeproject.org/ENCBS041GAW/

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


title: total RNA-seq from activated T-cell (ENCLB919LCG)

description:
https://www.encodeproject.org/experiments/ENCSR900DUO/
***************
biological replicate number: 1
technical replicate number: 1
description: Allcells13168 activated T-cells
experiment encode accession: ENCSR900DUO
assay title: total RNA-seq
assembly: GRCh38
possible controls: ENCSR336VTK
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB919LCG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

library_source: transcriptomic

molecule: total RNA

source_name: Homo sapiens female adult (33 years) activated T-cell primary cell

value: activated T-cell

value: primary cell

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS004WJX at ENCODE; https://www.encodeproject.org/ENCBS004WJX/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: TF ChIP-seq from HepG2 (ENCLB077QSR)

description:
https://www.encodeproject.org/experiments/ENCSR904JEY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR904JEY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR042HRU
encode release date: 2020-07-08
lab: Richard Myers, HAIB
library encode accession: ENCLB077QSR
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting ZNF34

value: cell line

value: male

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS115WVR at ENCODE; https://www.encodeproject.org/ENCBS115WVR/


title: TF ChIP-seq from HepG2 (ENCLB186DQE)

description:
https://www.encodeproject.org/experiments/ENCSR243LNQ/
***************
biological replicate number: 2
technical replicate number: 1
description: PRPF4 ChIP-seq on HepG2
experiment encode accession: ENCSR243LNQ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR975KJI
encode release date: 2016-10-31
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB186DQE
size range: 200-400
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: PRPF4 ChIP-seq on HepG2 cells

value: child

value: 15 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: ENCBS005KKO at ENCODE; https://www.encodeproject.org/ENCBS005KKO/


title: total RNA-seq from upper lobe of left lung (ENCLB542TRU)

description:
https://www.encodeproject.org/experiments/ENCSR500JSJ/
***************
biological replicate number: 1
technical replicate number: 1
description: W78_upper_lobe_of_left_lung
experiment encode accession: ENCSR500JSJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB542TRU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (60 years) upper lobe of left lung tissue, preserved by flash-freezing

value: upper lobe of left lung

value: tissue

value: DM:no; HTN:yes; CAD:no; lungs with severe emphysema

value: adult

value: 60 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS956JIK at ENCODE; https://www.encodeproject.org/ENCBS956JIK/

value: Derived from ENCODE donor ENCDO520EJG; https://www.encodeproject.org/ENCDO520EJG/


title: TF ChIP-seq from HepG2 (ENCLB123TST)

description:
https://www.encodeproject.org/experiments/ENCSR882YYL/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR882YYL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR019ZGX
encode release date: 2020-08-28
lab: Richard Myers, HAIB
library encode accession: ENCLB123TST
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting ZNF883

value: cell line

value: male

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS771GYG at ENCODE; https://www.encodeproject.org/ENCBS771GYG/

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


title: TF ChIP-seq from HepG2 (ENCLB991EAZ)

description:
https://www.encodeproject.org/experiments/ENCSR882YYL/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR882YYL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR019ZGX
encode release date: 2020-08-28
lab: Richard Myers, HAIB
library encode accession: ENCLB991EAZ
fragmentation methods: sonication (generic)

value: child

value: 15 year

value: ENCBS545PCH at ENCODE; https://www.encodeproject.org/ENCBS545PCH/


title: total RNA-seq from GM12878 (ENCLB883QSZ)

description:
https://www.encodeproject.org/experiments/ENCSR820PHH/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12878
experiment encode accession: ENCSR820PHH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB883QSZ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens GM12878 immortalized cell line

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

value: unknown

value: female

value: Ali Mortazavi, UCI

value: ENCBS089RNA at ENCODE; https://www.encodeproject.org/ENCBS089RNA/

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&PgId=166


title: total RNA-seq from activated T-cell (ENCLB605UWS)

description:
https://www.encodeproject.org/experiments/ENCSR844SCP/
***************
biological replicate number: 1
technical replicate number: 1
description: Allcells15824 activated T-cells
experiment encode accession: ENCSR844SCP
assay title: total RNA-seq
assembly: GRCh38
possible controls: ENCSR631FXT
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB605UWS
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (38 years) activated T-cell primary cell

value: activated T-cell

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS529SAJ at ENCODE; https://www.encodeproject.org/ENCBS529SAJ/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: TF ChIP-seq from K562 (ENCLB316FFY)

description:
https://www.encodeproject.org/experiments/ENCSR220YXI/
***************
biological replicate number: 2
technical replicate number: 1
description: PRPF4 ChIP-seq in K562
experiment encode accession: ENCSR220YXI
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR440JAU
encode release date: 2017-03-07
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB316FFY
size range: 200-400

value: cell line

value: PRPF4 ChIP-seq in K562

value: 53 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS952HNJ at ENCODE; https://www.encodeproject.org/ENCBS952HNJ/

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


title: TF ChIP-seq from K562 (ENCLB564HSO)

description:
https://www.encodeproject.org/experiments/ENCSR724GSW/
***************
biological replicate number: 1
technical replicate number: 1
description: SAFB2 ChIP-seq in K562
experiment encode accession: ENCSR724GSW
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR084AIG
encode release date: 2018-01-26
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB564HSO
size range: 200-400

value: SAFB2 ChIP-seq in K562

value: female

value: ENCBS478PEF at ENCODE; https://www.encodeproject.org/ENCBS478PEF/


title: total RNA-seq from left lobe of liver (ENCLB341GAW)

description:
https://www.encodeproject.org/experiments/ENCSR357BYU/
***************
biological replicate number: 1
technical replicate number: 1
description: W82_left_lobe_of_liver
experiment encode accession: ENCSR357BYU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB341GAW
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (45 years) left lobe of liver tissue, preserved by flash-freezing

value: left lobe of liver

value: tissue

value: male

value: DM:no; HTN:yes; CAD:no

value: adult

value: 45 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS534CBI at ENCODE; https://www.encodeproject.org/ENCBS534CBI/

value: Derived from ENCODE donor ENCDO757VPQ; https://www.encodeproject.org/ENCDO757VPQ/


title: TF ChIP-seq from HepG2 (ENCLB408YPP)

description:
https://www.encodeproject.org/experiments/ENCSR799DUB/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR799DUB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR019ZGX
encode release date: 2020-08-28
lab: Richard Myers, HAIB
library encode accession: ENCLB408YPP
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting IKZF4

value: cell line

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS524PBZ at ENCODE; https://www.encodeproject.org/ENCBS524PBZ/

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


title: TF ChIP-seq from HepG2 (ENCLB031ULB)

description:
https://www.encodeproject.org/experiments/ENCSR932ZRD/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR932ZRD
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR776XHE
encode release date: 2020-08-28
lab: Richard Myers, HAIB
library encode accession: ENCLB031ULB
fragmentation methods: sonication (generic)

value: ENCBS425XTD at ENCODE; https://www.encodeproject.org/ENCBS425XTD/


title: TF ChIP-seq from K562 (ENCLB800ELT)

description:
https://www.encodeproject.org/experiments/ENCSR220YXI/
***************
biological replicate number: 1
technical replicate number: 1
description: PRPF4 ChIP-seq in K562
experiment encode accession: ENCSR220YXI
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR440JAU
encode release date: 2017-03-07
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB800ELT
size range: 200-400

value: PRPF4 ChIP-seq in K562

value: female

value: 53 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS075XHE at ENCODE; https://www.encodeproject.org/ENCBS075XHE/

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


title: TF ChIP-seq from K562 (ENCLB597KFL)

description:
https://www.encodeproject.org/experiments/ENCSR724GSW/
***************
biological replicate number: 2
technical replicate number: 1
description: SAFB2 ChIP-seq in K562
experiment encode accession: ENCSR724GSW
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR084AIG
encode release date: 2018-01-26
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB597KFL
size range: 200-400

value: cell line

value: SAFB2 ChIP-seq in K562

value: adult

value: ENCBS644RCS at ENCODE; https://www.encodeproject.org/ENCBS644RCS/


title: TF ChIP-seq from A673 (ENCLB529VEZ)

description:
https://www.encodeproject.org/experiments/ENCSR179SAO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR179SAO
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR196CXJ
encode release date: 2017-11-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB529VEZ
fragmentation methods: sonication (generic)
size range: 200-600
nucleic acid starting quantity: 0
nucleic acid starting quantity units: ng

source_name: Homo sapiens A673 immortalized cell line

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

value: unknown

value: 15 year

value: Bradley Bernstein, Broad

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

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

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


title: TF ChIP-seq from HepG2 (ENCLB253NHW)

description:
https://www.encodeproject.org/experiments/ENCSR904JEY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR904JEY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR042HRU
encode release date: 2020-07-08
lab: Richard Myers, HAIB
library encode accession: ENCLB253NHW
fragmentation methods: sonication (generic)

value: male

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS705ZYX at ENCODE; https://www.encodeproject.org/ENCBS705ZYX/

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


title: total RNA-seq from MCF-7 (ENCLB928KKR)

description:
https://www.encodeproject.org/experiments/ENCSR355JZC/
***************
biological replicate number: 1
technical replicate number: 1
description: MCF-7_rep2
experiment encode accession: ENCSR355JZC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB928KKR
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens MCF-7 cell line

value: cell line

value: female

value: 69 year

value: Mats Ljungman, UMichigan

value: ATCC

value: breast cancer (adenocarcinoma)

value: ENCBS734JMT at ENCODE; https://www.encodeproject.org/ENCBS734JMT/

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


title: TF ChIP-seq from HepG2 (ENCLB807WEO)

description:
https://www.encodeproject.org/experiments/ENCSR799DUB/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR799DUB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR019ZGX
encode release date: 2020-08-28
lab: Richard Myers, HAIB
library encode accession: ENCLB807WEO
fragmentation methods: sonication (generic)

value: 15 year

value: ENCBS636TYH at ENCODE; https://www.encodeproject.org/ENCBS636TYH/


title: total RNA-seq from T-cell (ENCLB047PGP)

description:
https://www.encodeproject.org/experiments/ENCSR336VTK/
***************
biological replicate number: 1
technical replicate number: 1
description: Allcells13168 inactive T-cells
experiment encode accession: ENCSR336VTK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-03-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB047PGP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (33 years) T-cell primary cell

value: T-cell

value: primary cell

value: adult

value: 33 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS873TGL at ENCODE; https://www.encodeproject.org/ENCBS873TGL/

value: Derived from ENCODE donor ENCDO299FMV; https://www.encodeproject.org/ENCDO299FMV/


title: total RNA-seq from IMR-90 (ENCLB351QES)

description:
https://www.encodeproject.org/experiments/ENCSR797RXV/
***************
biological replicate number: 1
technical replicate number: 1
description: IMR90_rep2
experiment encode accession: ENCSR797RXV
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB351QES
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens IMR-90 cell line

value: cell line

value: female

value: embryonic

value: 16 week

value: unknown

value: ENCBS648NSQ at ENCODE; https://www.encodeproject.org/ENCBS648NSQ/

value: Derived from ENCODE donor ENCDO000AAX; https://www.encodeproject.org/ENCDO000AAX/


title: total RNA-seq from T-cell (ENCLB317WCE)

description:
https://www.encodeproject.org/experiments/ENCSR336VTK/
***************
biological replicate number: 1
technical replicate number: 2
description: Allcells13168 inactive T-cells
experiment encode accession: ENCSR336VTK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-03-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB317WCE
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng


title: TF ChIP-seq from HepG2 (ENCLB327EKG)

description:
https://www.encodeproject.org/experiments/ENCSR315VYZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR315VYZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313HFF
encode release date: 2020-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB327EKG
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting PHF21A

value: male

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS004EDA at ENCODE; https://www.encodeproject.org/ENCBS004EDA/

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


title: TF ChIP-seq from K562 (ENCLB828COA)

description:
https://www.encodeproject.org/experiments/ENCSR177DNR/
***************
biological replicate number: 1
technical replicate number: 1
description: FIP1L1 ChIP-seq in K562
experiment encode accession: ENCSR177DNR
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR397ZZR
encode release date: 2018-01-16
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB828COA
size range: 200-400

source_name: Homo sapiens K562 cell line

value: FIP1L1 ChIP-seq in K562

value: adult

value: 53 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS190DUB at ENCODE; https://www.encodeproject.org/ENCBS190DUB/

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


title: TF ChIP-seq from HepG2 (ENCLB468MCU)

description:
https://www.encodeproject.org/experiments/ENCSR315VYZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR315VYZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR313HFF
encode release date: 2020-06-30
lab: Richard Myers, HAIB
library encode accession: ENCLB468MCU
fragmentation methods: sonication (generic)

value: cell line

value: ENCBS289WMF at ENCODE; https://www.encodeproject.org/ENCBS289WMF/


title: TF ChIP-seq from HepG2 (ENCLB265NGL)

description:
https://www.encodeproject.org/experiments/ENCSR696MBC/
***************
biological replicate number: 2
technical replicate number: 1
description: SRSF4 ChIP-seq on HepG2
experiment encode accession: ENCSR696MBC
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR079WWH
encode release date: 2018-01-19
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB265NGL
size range: 200-400

value: SRSF4 ChIP-seq on HepG2 cells

value: male

value: child

value: ENCBS150SBN at ENCODE; https://www.encodeproject.org/ENCBS150SBN/


title: TF ChIP-seq from K562 (ENCLB819GBR)

description:
https://www.encodeproject.org/experiments/ENCSR177DNR/
***************
biological replicate number: 2
technical replicate number: 1
description: FIP1L1 ChIP-seq in K562
experiment encode accession: ENCSR177DNR
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR397ZZR
encode release date: 2018-01-16
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB819GBR
size range: 200-400
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: female

value: ENCBS716JYS at ENCODE; https://www.encodeproject.org/ENCBS716JYS/


title: total RNA-seq from K562 (ENCLB113NQK)

description:
https://www.encodeproject.org/experiments/ENCSR792OIJ/
***************
biological replicate number: 1
technical replicate number: 1
description: K562_rep_A
experiment encode accession: ENCSR792OIJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB113NQK
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens K562 immortalized cell line

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. ENCODE3 RNA-seq evaluation replicate 1.

tag: passage number

value: Brenton Graveley, UConn

value: ENCBS087RNA at ENCODE; https://www.encodeproject.org/ENCBS087RNA/

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: total RNA-seq from K562 (ENCLB900ASP)

description:
https://www.encodeproject.org/experiments/ENCSR792OIJ/
***************
biological replicate number: 2
technical replicate number: 1
description: K562_rep_A
experiment encode accession: ENCSR792OIJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB900ASP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises. ENCODE3 RNA-seq evaluation replicate 2.

value: 53 year

value: adult

value: ENCBS088RNA at ENCODE; https://www.encodeproject.org/ENCBS088RNA/


title: total RNA-seq from T-cell (ENCLB783JVE)

description:
https://www.encodeproject.org/experiments/ENCSR306IAW/
***************
biological replicate number: 1
technical replicate number: 2
description: Allcells6054 inactive T-cells
experiment encode accession: ENCSR306IAW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-03-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB783JVE
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (42 years) T-cell primary cell

value: T-cell

value: primary cell

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS441JUB at ENCODE; https://www.encodeproject.org/ENCBS441JUB/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: total RNA-seq from GM12878 (ENCLB750VUP)

description:
https://www.encodeproject.org/experiments/ENCSR820PHH/
***************
biological replicate number: 2
technical replicate number: 1
description: GM12878
experiment encode accession: ENCSR820PHH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB750VUP
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: cell line

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

value: unknown

value: female

value: Ali Mortazavi, UCI

value: ENCBS090RNA at ENCODE; https://www.encodeproject.org/ENCBS090RNA/

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&PgId=166


title: TF ChIP-seq from HepG2 (ENCLB699RXZ)

description:
https://www.encodeproject.org/experiments/ENCSR696MBC/
***************
biological replicate number: 1
technical replicate number: 1
description: SRSF4 ChIP-seq on HepG2
experiment encode accession: ENCSR696MBC
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR079WWH
encode release date: 2018-01-19
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB699RXZ
size range: 200-400

source_name: Homo sapiens HepG2 cell line

value: SRSF4 ChIP-seq on HepG2 cells

value: male

value: child

value: 15 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: hepatocellular carcinoma

value: ENCBS309MNT at ENCODE; https://www.encodeproject.org/ENCBS309MNT/

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


title: total RNA-seq from T-cell (ENCLB110ZKC)

description:
https://www.encodeproject.org/experiments/ENCSR306IAW/
***************
biological replicate number: 1
technical replicate number: 1
description: Allcells6054 inactive T-cells
experiment encode accession: ENCSR306IAW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-03-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB110ZKC
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: T-cell

value: primary cell

value: adult

value: 42 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS441JUB at ENCODE; https://www.encodeproject.org/ENCBS441JUB/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: TF ChIP-seq from HepG2 (ENCLB285ZFN)

description:
https://www.encodeproject.org/experiments/ENCSR156APP/
***************
biological replicate number: 1
technical replicate number: 1
description: PTBP1 ChIP-seq on HepG2
experiment encode accession: ENCSR156APP
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR792MRQ
encode release date: 2018-01-19
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB285ZFN
size range: 200-400
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: cell line

value: PTBP1 ChIP-seq on HepG2 cells

value: ENCBS495SHD at ENCODE; https://www.encodeproject.org/ENCBS495SHD/


title: total RNA-seq from mucosa of gallbladder (ENCLB169YWY)

description:
https://www.encodeproject.org/experiments/ENCSR343XXH/
***************
biological replicate number: 1
technical replicate number: 1
description: W62_mucosa_of_gallbladder
experiment encode accession: ENCSR343XXH
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB169YWY
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female child (16 years) mucosa of gallbladder tissue, preserved by flash-freezing

value: mucosa of gallbladder

value: tissue

value: female

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS969MVO at ENCODE; https://www.encodeproject.org/ENCBS969MVO/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: TF ChIP-seq from K562 (ENCLB173HES)

description:
https://www.encodeproject.org/experiments/ENCSR214EKV/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-ZNF281 ChIP-seq on human K562
experiment encode accession: ENCSR214EKV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR387OYT, ENCSR328FYU
encode release date: 2021-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB173HES
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting ZNF281

value: adult

value: 53 year

value: Kevin White

value: chronic myelogenous leukemia (CML)

value: ENCBS112ZBB at ENCODE; https://www.encodeproject.org/ENCBS112ZBB/

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


title: TF ChIP-seq from K562 (ENCLB801WIJ)

description:
https://www.encodeproject.org/experiments/ENCSR214EKV/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-ZNF281 ChIP-seq on human K562
experiment encode accession: ENCSR214EKV
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR387OYT, ENCSR328FYU
encode release date: 2021-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB801WIJ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: ENCBS721RIP at ENCODE; https://www.encodeproject.org/ENCBS721RIP/


title: TF ChIP-seq from HepG2 (ENCLB310SOO)

description:
https://www.encodeproject.org/experiments/ENCSR156APP/
***************
biological replicate number: 2
technical replicate number: 1
description: PTBP1 ChIP-seq on HepG2
experiment encode accession: ENCSR156APP
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR792MRQ
encode release date: 2018-01-19
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB310SOO
size range: 200-400
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: PTBP1 ChIP-seq on HepG2 cells

value: male

value: 15 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: hepatocellular carcinoma

value: ENCBS654ERN at ENCODE; https://www.encodeproject.org/ENCBS654ERN/

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


title: TF ChIP-seq from SU-DHL-6 (ENCLB881BYS)

description:
https://www.encodeproject.org/experiments/ENCSR125DKL/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR125DKL
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR179YLS
encode release date: 2017-11-29
lab: Bradley Bernstein, Broad
library encode accession: ENCLB881BYS
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens SUDHL6 immortalized cell line

value: CTCF

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: 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: Histone ChIP-seq from KOPT-K1 (ENCLB388PXI)

description:
https://www.encodeproject.org/experiments/ENCSR630IBN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR630IBN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR255BOF
encode release date: 2018-03-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB388PXI
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens KOPT-K1 immortalized cell line

value: cell line

value: cells from Birgit; a human T-ALL cell line with a chromosome translocation breakpoint at t(11;14)(p13;q11) affecting the putative oncoprotein

value: unknown

value: not collected

value: ENCBS869LIS at ENCODE; https://www.encodeproject.org/ENCBS869LIS/

value: Derived from ENCODE donor ENCDO568LPD; https://www.encodeproject.org/ENCDO568LPD/

value: ENCODE dbxrefs Cellosaurus CVCL_4965; http://web.expasy.org/cellosaurus/CVCL_4965


title: TF ChIP-seq from K562 (ENCLB358ZNJ)

description:
https://www.encodeproject.org/experiments/ENCSR663NFC/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-STAT5B ChIP-seq on human K562
experiment encode accession: ENCSR663NFC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR766WPH
encode release date: 2021-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB358ZNJ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting STAT5B

value: female

value: adult

value: 53 year

value: Michael Snyder, Stanford

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS323ROQ at ENCODE; https://www.encodeproject.org/ENCBS323ROQ/

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


title: TF ChIP-seq from K562 (ENCLB655KHI)

description:
https://www.encodeproject.org/experiments/ENCSR663NFC/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-STAT5B ChIP-seq on human K562
experiment encode accession: ENCSR663NFC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR766WPH
encode release date: 2021-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB655KHI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: ENCBS013XMW at ENCODE; https://www.encodeproject.org/ENCBS013XMW/


title: total RNA-seq from HCT116 (ENCLB041DJG)

description:
https://www.encodeproject.org/experiments/ENCSR698RPL/
***************
biological replicate number: 1
technical replicate number: 1
description: HCT116_rep2
experiment encode accession: ENCSR698RPL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB041DJG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 cell line

value: male

value: 48 year

value: Mats Ljungman, UMichigan

value: colorectal carcinoma

value: ENCBS375FZQ at ENCODE; https://www.encodeproject.org/ENCBS375FZQ/

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


title: total RNA-seq from adrenal gland (ENCLB988TCO)

description:
https://www.encodeproject.org/experiments/ENCSR201XOZ/
***************
biological replicate number: 1
technical replicate number: 1
description: W62_adrenal_gland
experiment encode accession: ENCSR201XOZ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB988TCO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female child (16 years) adrenal gland tissue, preserved by flash-freezing

value: adrenal gland

value: tissue

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: Yiing Lin, MD, PhD

value: ENCBS928RWN at ENCODE; https://www.encodeproject.org/ENCBS928RWN/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: TF ChIP-seq from HepG2 (ENCLB975XRX)

description:
https://www.encodeproject.org/experiments/ENCSR625ORP/
***************
biological replicate number: 1
technical replicate number: 1
description: SYNCRIP ChIP-seq on HepG2
experiment encode accession: ENCSR625ORP
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR792MRQ
encode release date: 2018-05-16
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB975XRX
size range: 200-400

value: SYNCRIP

value: cell line

value: HNRNPQ ChIP-seq on HepG2 cells

value: 15 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: hepatocellular carcinoma

value: ENCBS019QTJ at ENCODE; https://www.encodeproject.org/ENCBS019QTJ/

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


title: total RNA-seq from HepG2 (ENCLB732LUH)

description:
https://www.encodeproject.org/experiments/ENCSR245ATJ/
***************
biological replicate number: 1
technical replicate number: 1
description: HepG2_rep2
experiment encode accession: ENCSR245ATJ
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB732LUH
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: male

value: Mats Ljungman, UMichigan

value: ENCBS365LJQ at ENCODE; https://www.encodeproject.org/ENCBS365LJQ/


title: TF ChIP-seq from HepG2 (ENCLB611KWI)

description:
https://www.encodeproject.org/experiments/ENCSR660ENW/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR660ENW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR693GOR
encode release date: 2020-07-08
lab: Richard Myers, HAIB
library encode accession: ENCLB611KWI
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting CAMTA2

value: child

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS803GED at ENCODE; https://www.encodeproject.org/ENCBS803GED/


title: TF ChIP-seq from HepG2 (ENCLB127BNO)

description:
https://www.encodeproject.org/experiments/ENCSR624GNZ/
***************
biological replicate number: 1
technical replicate number: 1,2
description: SRSF9 ChIP-seq on HepG2
experiment encode accession: ENCSR624GNZ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR079WWH
encode release date: 2018-01-26
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB127BNO
size range: 200-400

value: SRSF9 ChIP-seq on HepG2 cells

value: ENCBS673ABW at ENCODE; https://www.encodeproject.org/ENCBS673ABW/


title: total RNA-seq from PC-3 (ENCLB468VTI)

description:
https://www.encodeproject.org/experiments/ENCSR648KDM/
***************
biological replicate number: 1
technical replicate number: 1
description: PC-3_rep2
experiment encode accession: ENCSR648KDM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB468VTI
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens PC-3 cell line

value: cell line

value: adult

value: 62 year

value: grade IV, adenocarcinoma

value: ENCBS555BGE at ENCODE; https://www.encodeproject.org/ENCBS555BGE/

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


title: total RNA-seq from GM12878 (ENCLB994RBL)

description:
https://www.encodeproject.org/experiments/ENCSR151NGC/
***************
biological replicate number: 1
technical replicate number: 1
description: GM12878_rep2
experiment encode accession: ENCSR151NGC
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB994RBL
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens GM12878 cell line

value: female

value: unknown

value: Coriell

value: ENCBS975OUN at ENCODE; https://www.encodeproject.org/ENCBS975OUN/

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


title: TF ChIP-seq from HepG2 (ENCLB255AHQ)

description:
https://www.encodeproject.org/experiments/ENCSR253HUM/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR253HUM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR693GOR
encode release date: 2020-07-08
lab: Richard Myers, HAIB
library encode accession: ENCLB255AHQ
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting ZNF576

value: male

value: child

value: 15 year

value: hepatocellular carcinoma

value: ENCBS096UGW at ENCODE; https://www.encodeproject.org/ENCBS096UGW/

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


title: TF ChIP-seq from HepG2 (ENCLB068UKO)

description:
https://www.encodeproject.org/experiments/ENCSR625ORP/
***************
biological replicate number: 2
technical replicate number: 1
description: SYNCRIP ChIP-seq on HepG2
experiment encode accession: ENCSR625ORP
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR792MRQ
encode release date: 2018-05-16
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB068UKO
size range: 200-400

value: SYNCRIP

value: cell line

value: HNRNPQ ChIP-seq on HepG2 cells

value: Xiang-Dong Fu, UCSD

value: ATCC

value: ENCBS781AWJ at ENCODE; https://www.encodeproject.org/ENCBS781AWJ/


title: TF ChIP-seq from HepG2 (ENCLB670WZE)

description:
https://www.encodeproject.org/experiments/ENCSR253HUM/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR253HUM
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR693GOR
encode release date: 2020-07-08
lab: Richard Myers, HAIB
library encode accession: ENCLB670WZE
fragmentation methods: sonication (generic)

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS365MJM at ENCODE; https://www.encodeproject.org/ENCBS365MJM/


title: total RNA-seq from ovary (ENCLB827GYM)

description:
https://www.encodeproject.org/experiments/ENCSR140DCD/
***************
biological replicate number: 1
technical replicate number: 1
description: W72_ovary
experiment encode accession: ENCSR140DCD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB827GYM
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (46 years) ovary tissue, preserved by flash-freezing

value: ovary

value: tissue

value: female

value: DM:no; HTN:no; CAD:no

value: adult

value: 46 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS598ITE at ENCODE; https://www.encodeproject.org/ENCBS598ITE/

value: Derived from ENCODE donor ENCDO411EVD; https://www.encodeproject.org/ENCDO411EVD/


title: TF ChIP-seq from HepG2 (ENCLB147RYX)

description:
https://www.encodeproject.org/experiments/ENCSR624GNZ/
***************
biological replicate number: 2
technical replicate number: 1,2
description: SRSF9 ChIP-seq on HepG2
experiment encode accession: ENCSR624GNZ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR079WWH
encode release date: 2018-01-26
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB147RYX
size range: 200-400

value: cell line

value: SRSF9 ChIP-seq on HepG2 cells

value: male

value: child

value: 15 year

value: hepatocellular carcinoma

value: ENCBS297BHJ at ENCODE; https://www.encodeproject.org/ENCBS297BHJ/

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


title: Histone ChIP-seq from MCF-7 (ENCLB682BPE)

description:
https://www.encodeproject.org/experiments/ENCSR059ICA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR059ICA
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2017-01-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB682BPE
fragmentation methods: sonication (generic)
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: 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: total RNA-seq from T-cell (ENCLB270TBA)

description:
https://www.encodeproject.org/experiments/ENCSR631FXT/
***************
biological replicate number: 1
technical replicate number: 2
description: Allcells15824 inactive T-cells
experiment encode accession: ENCSR631FXT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-03-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB270TBA
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (38 years) T-cell primary cell

value: T-cell

value: primary cell

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS824ZOO at ENCODE; https://www.encodeproject.org/ENCBS824ZOO/

value: Derived from ENCODE donor ENCDO923WRX; https://www.encodeproject.org/ENCDO923WRX/


title: Histone ChIP-seq from KOPT-K1 (ENCLB374RGX)

description:
https://www.encodeproject.org/experiments/ENCSR630IBN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR630IBN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR255BOF
encode release date: 2018-03-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB374RGX
fragmentation methods: sonication (generic)
size range: 200-600

value: cell line

value: cells from Birgit; a human T-ALL cell line with a chromosome translocation breakpoint at t(11;14)(p13;q11) affecting the putative oncoprotein

value: unknown

value: not collected

value: ENCBS345YKN at ENCODE; https://www.encodeproject.org/ENCBS345YKN/

value: Derived from ENCODE donor ENCDO568LPD; https://www.encodeproject.org/ENCDO568LPD/

value: ENCODE dbxrefs Cellosaurus CVCL_4965; http://web.expasy.org/cellosaurus/CVCL_4965


title: Histone ChIP-seq from MCF-7 (ENCLB900USU)

description:
https://www.encodeproject.org/experiments/ENCSR610IYQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR610IYQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2017-01-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB900USU
fragmentation methods: sonication (generic)
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


title: total RNA-seq from T-cell (ENCLB054LLJ)

description:
https://www.encodeproject.org/experiments/ENCSR631FXT/
***************
biological replicate number: 1
technical replicate number: 1
description: Allcells15824 inactive T-cells
experiment encode accession: ENCSR631FXT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-03-09
lab: Barbara Wold, Caltech
library encode accession: ENCLB054LLJ
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: T-cell

value: primary cell

value: male

value: adult

value: 38 year

value: John Stamatoyannopoulos, UW

value: AllCells

value: ENCBS824ZOO at ENCODE; https://www.encodeproject.org/ENCBS824ZOO/


title: total RNA-seq from Panc1 (ENCLB972WVN)

description:
https://www.encodeproject.org/experiments/ENCSR128CYL/
***************
biological replicate number: 1
technical replicate number: 1
description: Panc1_rep2
experiment encode accession: ENCSR128CYL
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB972WVN
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens Panc1 cell line

value: cell line

value: 56 year

value: Mats Ljungman, UMichigan

value: ATCC

value: pancreatic carcinoma

value: ENCBS777OZT at ENCODE; https://www.encodeproject.org/ENCBS777OZT/

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


title: total RNA-seq from activated T-cell (ENCLB013DOU)

description:
https://www.encodeproject.org/experiments/ENCSR111PSY/
***************
biological replicate number: 1
technical replicate number: 1
description: Allcells6054 activated T-cells
experiment encode accession: ENCSR111PSY
assay title: total RNA-seq
assembly: GRCh38
possible controls: ENCSR306IAW
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB013DOU
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens male adult (42 years) activated T-cell primary cell

value: activated T-cell

value: 42 year

value: ENCBS501IVR at ENCODE; https://www.encodeproject.org/ENCBS501IVR/

value: Derived from ENCODE donor ENCDO833KUM; https://www.encodeproject.org/ENCDO833KUM/


title: TF ChIP-seq from K562 (ENCLB879NSI)

description:
https://www.encodeproject.org/experiments/ENCSR109SJT/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-SMAD4 ChIP-seq on human K562
experiment encode accession: ENCSR109SJT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2021-04-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB879NSI
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting SMAD4

value: female

value: 53 year

value: Michael Snyder, Stanford

value: Kevin White

value: chronic myelogenous leukemia (CML)

value: ENCBS118MRE at ENCODE; https://www.encodeproject.org/ENCBS118MRE/

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


title: TF ChIP-seq from K562 (ENCLB161GQQ)

description:
https://www.encodeproject.org/experiments/ENCSR109SJT/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-SMAD4 ChIP-seq on human K562
experiment encode accession: ENCSR109SJT
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR328FYU
encode release date: 2021-04-16
lab: Michael Snyder, Stanford
library encode accession: ENCLB161GQQ
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: adult

value: ENCBS837LKW at ENCODE; https://www.encodeproject.org/ENCBS837LKW/


title: TF ChIP-seq from HepG2 (ENCLB731ELF)

description:
https://www.encodeproject.org/experiments/ENCSR660ENW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR660ENW
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR693GOR
encode release date: 2020-07-08
lab: Richard Myers, HAIB
library encode accession: ENCLB731ELF
fragmentation methods: sonication (generic)

value: male

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS284RXP at ENCODE; https://www.encodeproject.org/ENCBS284RXP/

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


title: TF ChIP-seq from HepG2 (ENCLB082UPU)

description:
https://www.encodeproject.org/experiments/ENCSR623RFC/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR623RFC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR042HRU, ENCSR856RWG
encode release date: 2021-04-22
lab: Richard Myers, HAIB
library encode accession: ENCLB082UPU
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting SP110

value: ENCBS419YDL at ENCODE; https://www.encodeproject.org/ENCBS419YDL/


title: TF ChIP-seq from HepG2 (ENCLB168TMU)

description:
https://www.encodeproject.org/experiments/ENCSR623RFC/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR623RFC
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR042HRU, ENCSR856RWG
encode release date: 2021-04-22
lab: Richard Myers, HAIB
library encode accession: ENCLB168TMU
fragmentation methods: sonication (generic)

value: ENCBS194LLE at ENCODE; https://www.encodeproject.org/ENCBS194LLE/


title: TF ChIP-seq from HepG2 (ENCLB920RYU)

description:
https://www.encodeproject.org/experiments/ENCSR075PWK/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR075PWK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR730QNM
encode release date: 2020-08-17
lab: Richard Myers, HAIB
library encode accession: ENCLB920RYU
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting ZNF225

value: ENCBS349ILB at ENCODE; https://www.encodeproject.org/ENCBS349ILB/


title: TF ChIP-seq from K562 (ENCLB164NIH)

description:
https://www.encodeproject.org/experiments/ENCSR603REQ/
***************
biological replicate number: 1
technical replicate number: 1
description: PCBP2 ChIP-seq in K562
experiment encode accession: ENCSR603REQ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR440JAU
encode release date: 2018-01-16
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB164NIH
size range: 200-400
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens K562 cell line

value: PCBP2 ChIP-seq in K562

value: female

value: 53 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS531SJK at ENCODE; https://www.encodeproject.org/ENCBS531SJK/


title: TF ChIP-seq from HepG2 (ENCLB326IFE)

description:
https://www.encodeproject.org/experiments/ENCSR075PWK/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR075PWK
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR730QNM
encode release date: 2020-08-17
lab: Richard Myers, HAIB
library encode accession: ENCLB326IFE
fragmentation methods: sonication (generic)

value: cell line

value: male

value: child

value: ENCBS197YOX at ENCODE; https://www.encodeproject.org/ENCBS197YOX/


title: TF ChIP-seq from K562 (ENCLB821XDF)

description:
https://www.encodeproject.org/experiments/ENCSR052PTN/
***************
biological replicate number: 1
technical replicate number: 1
description: PCBP1 ChIP-seq in K562
experiment encode accession: ENCSR052PTN
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR440JAU
encode release date: 2018-01-16
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB821XDF
size range: 200-400
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: PCBP1 ChIP-seq in K562

value: adult

value: ENCBS789RGF at ENCODE; https://www.encodeproject.org/ENCBS789RGF/

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


title: TF ChIP-seq from K562 (ENCLB011URI)

description:
https://www.encodeproject.org/experiments/ENCSR052PTN/
***************
biological replicate number: 2
technical replicate number: 1
description: PCBP1 ChIP-seq in K562
experiment encode accession: ENCSR052PTN
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR440JAU
encode release date: 2018-01-16
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB011URI
size range: 200-400
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: ENCBS031KNX at ENCODE; https://www.encodeproject.org/ENCBS031KNX/


title: TF ChIP-seq from K562 (ENCLB305QUM)

description:
https://www.encodeproject.org/experiments/ENCSR603REQ/
***************
biological replicate number: 2
technical replicate number: 1
description: PCBP2 ChIP-seq in K562
experiment encode accession: ENCSR603REQ
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR440JAU
encode release date: 2018-01-16
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB305QUM
size range: 200-400

value: ENCBS739OBP at ENCODE; https://www.encodeproject.org/ENCBS739OBP/


title: total RNA-seq from foreskin keratinocyte (ENCLB819WTD)

description:
https://www.encodeproject.org/experiments/ENCSR034RPU/
***************
biological replicate number: 1
technical replicate number: 1
description: RiboZero RNA-seq on primary keratinocytes in day 0 of differentiation
experiment encode accession: ENCSR034RPU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB819WTD
size range: >200

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell

extract_protocol:
general protocol: https://www.encodeproject.org/documents/9021cb71-35b1-4a9a-9fcc-38c6df5e9fea/@@download/attachment/ggr.keratinocyte.snyder-lab.rna_assays.pdf
extraction method: Qiagen RNA extraction

value: foreskin keratinocyte

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, grown in 2D culture, day 0.0

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari

value: Healthy

value: ENCBS666IIR at ENCODE; https://www.encodeproject.org/ENCBS666IIR/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: TF ChIP-seq from K562 (ENCLB618WQQ)

description:
https://www.encodeproject.org/experiments/ENCSR014RCS/
***************
biological replicate number: 2
technical replicate number: 1
description: HNRNPK ChIP-seq in K562
experiment encode accession: ENCSR014RCS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR814UCX
encode release date: 2018-01-19
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB618WQQ
size range: 200-400
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: HNRNPK

value: cell line

value: HNRNPK ChIP-seq in K562

value: female

value: 53 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: chronic myelogenous leukemia (CML)

value: ENCBS937TYX at ENCODE; https://www.encodeproject.org/ENCBS937TYX/


title: total RNA-seq from K562 (ENCLB067SQT)

description:
https://www.encodeproject.org/experiments/ENCSR615EEK/
***************
biological replicate number: 1
technical replicate number: 1
description: K562_rep2
experiment encode accession: ENCSR615EEK
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB067SQT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

value: adult

value: Mats Ljungman, UMichigan

value: ENCBS206PUV at ENCODE; https://www.encodeproject.org/ENCBS206PUV/

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


title: total RNA-seq from foreskin keratinocyte (ENCLB575CLO)

description:
https://www.encodeproject.org/experiments/ENCSR034RPU/
***************
biological replicate number: 2
technical replicate number: 1
description: RiboZero RNA-seq on primary keratinocytes in day 0 of differentiation
experiment encode accession: ENCSR034RPU
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB575CLO
size range: >200

value: foreskin keratinocyte

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 0.0

value: male

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari

value: ENCBS538XZS at ENCODE; https://www.encodeproject.org/ENCBS538XZS/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: TF ChIP-seq from K562 (ENCLB949HLM)

description:
https://www.encodeproject.org/experiments/ENCSR014RCS/
***************
biological replicate number: 1
technical replicate number: 1
description: HNRNPK ChIP-seq in K562
experiment encode accession: ENCSR014RCS
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR814UCX
encode release date: 2018-01-19
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB949HLM
size range: 200-400
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: HNRNPK

value: cell line

value: HNRNPK ChIP-seq in K562

value: female

value: 53 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: ENCBS967ZYE at ENCODE; https://www.encodeproject.org/ENCBS967ZYE/


title: TF ChIP-seq from WTC11 (ENCLB812AHW)

description:
https://www.encodeproject.org/experiments/ENCSR547WSB/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-TRERF1 ChIP-seq on human WTC11
experiment encode accession: ENCSR547WSB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR764ZNN
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB812AHW
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting TRERF1

value: adult

value: 30 year

value: Michael Snyder, Stanford

value: Richard Myers

value: ENCBS717QHI at ENCODE; https://www.encodeproject.org/ENCBS717QHI/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from K562 (ENCLB574TUK)

description:
https://www.encodeproject.org/experiments/ENCSR008DOU/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-SNAPC5 ChIP-seq on human K562
experiment encode accession: ENCSR008DOU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR766WPH
encode release date: 2021-03-31
lab: Michael Snyder, Stanford
library encode accession: ENCLB574TUK
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting SNAPC5

value: chronic myelogenous leukemia (CML)

value: ENCBS399JTJ at ENCODE; https://www.encodeproject.org/ENCBS399JTJ/

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


title: TF ChIP-seq from WTC11 (ENCLB700FDD)

description:
https://www.encodeproject.org/experiments/ENCSR547WSB/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-TRERF1 ChIP-seq on human WTC11
experiment encode accession: ENCSR547WSB
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR764ZNN
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB700FDD
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: male

value: ENCBS706GIE at ENCODE; https://www.encodeproject.org/ENCBS706GIE/


title: total RNA-seq from foreskin keratinocyte (ENCLB409CBC)

description:
https://www.encodeproject.org/experiments/ENCSR527SSD/
***************
biological replicate number: 1
technical replicate number: 1
description: RiboZero RNA-seq on primary keratinocytes in day 6 of differentiation
experiment encode accession: ENCSR527SSD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB409CBC
size range: >200

source_name: Homo sapiens male newborn (2-4 days) foreskin keratinocyte primary cell treated with 1.2 mM calcium for 5.5 days

value: foreskin keratinocyte

value: primary cell

value: Primary foreskin keratinocyte cells from a newborn healthy male donor, differentiated in 2D culture, day 6.0

value: newborn

value: 2-4 day

value: Paul Khavari, Stanford

value: Paul Khavari

tag: treatments

value: treatment_term_id:CHEBI:86158; treatment_term_name:calcium; treatment_type:chemical; duration:5.5; duration_units:day;

value: Healthy

value: ENCBS389AUD at ENCODE; https://www.encodeproject.org/ENCBS389AUD/

value: Derived from ENCODE donor ENCDO615NVN; https://www.encodeproject.org/ENCDO615NVN/


title: total RNA-seq from foreskin keratinocyte (ENCLB764HOA)

description:
https://www.encodeproject.org/experiments/ENCSR527SSD/
***************
biological replicate number: 2
technical replicate number: 1
description: RiboZero RNA-seq on primary keratinocytes in day 6 of differentiation
experiment encode accession: ENCSR527SSD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2017-10-10
lab: Michael Snyder, Stanford
library encode accession: ENCLB764HOA
size range: >200

value: ENCBS135YLX at ENCODE; https://www.encodeproject.org/ENCBS135YLX/

value: Derived from ENCODE donor ENCDO005EGE; https://www.encodeproject.org/ENCDO005EGE/


title: TF ChIP-seq from neural cell (ENCLB152YMT)

description:
https://www.encodeproject.org/experiments/ENCSR511CUH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR511CUH
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR308JFE
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB152YMT
fragmentation methods: sonication (generic)
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: total RNA-seq from upper lobe of left lung (ENCLB600ZWE)

description:
https://www.encodeproject.org/experiments/ENCSR589EBT/
***************
biological replicate number: 1
technical replicate number: 1
description: W80_upper_lobe_of_left_lung
experiment encode accession: ENCSR589EBT
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB600ZWE
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (61 years) upper lobe of left lung tissue, preserved by flash-freezing

value: upper lobe of left lung

value: tissue

value: female

value: DM:no; HTN:no; CAD:no; lungs with moderate emphysema

value: adult

value: 61 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS468BRF at ENCODE; https://www.encodeproject.org/ENCBS468BRF/

value: Derived from ENCODE donor ENCDO186XRB; https://www.encodeproject.org/ENCDO186XRB/


title: TF ChIP-seq from HepG2 (ENCLB528TIL)

description:
https://www.encodeproject.org/experiments/ENCSR519QAA/
***************
biological replicate number: 2
technical replicate number: 1
description: HNRNPK ChIP-seq on HepG2
experiment encode accession: ENCSR519QAA
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR561BTA
encode release date: 2018-01-16
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB528TIL
size range: 200-400
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Homo sapiens HepG2 cell line

value: HNRNPK

value: cell line

value: HNRNPK ChIP-seq on HepG2 cells

value: male

value: child

value: 15 year

value: Xiang-Dong Fu, UCSD

value: ATCC

value: hepatocellular carcinoma

value: ENCBS271WON at ENCODE; https://www.encodeproject.org/ENCBS271WON/

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


title: TF ChIP-seq from WTC11 (ENCLB610JLP)

description:
https://www.encodeproject.org/experiments/ENCSR004HEA/
***************
biological replicate number: 2
technical replicate number: 1
description: eGFP-OTX2 ChIP-seq on human WTC11
experiment encode accession: ENCSR004HEA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR764ZNN
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB610JLP
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting OTX2

value: adult

value: 30 year

value: Richard Myers

value: ENCBS048CCX at ENCODE; https://www.encodeproject.org/ENCBS048CCX/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from HepG2 (ENCLB623PGQ)

description:
https://www.encodeproject.org/experiments/ENCSR005WGY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR005WGY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR019ZGX
encode release date: 2020-08-28
lab: Richard Myers, HAIB
library encode accession: ENCLB623PGQ
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting ZNF407

value: Richard Myers, HAIB

value: ENCBS785UBU at ENCODE; https://www.encodeproject.org/ENCBS785UBU/


title: TF ChIP-seq from HepG2 (ENCLB993VKX)

description:
https://www.encodeproject.org/experiments/ENCSR005WGY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR005WGY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR019ZGX
encode release date: 2020-08-28
lab: Richard Myers, HAIB
library encode accession: ENCLB993VKX
fragmentation methods: sonication (generic)

value: cell line

value: ENCBS948ZQP at ENCODE; https://www.encodeproject.org/ENCBS948ZQP/


title: TF ChIP-seq from HepG2 (ENCLB181UZG)

description:
https://www.encodeproject.org/experiments/ENCSR519QAA/
***************
biological replicate number: 1
technical replicate number: 1
description: HNRNPK ChIP-seq on HepG2
experiment encode accession: ENCSR519QAA
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR561BTA
encode release date: 2018-01-16
lab: Xiang-Dong Fu, UCSD
library encode accession: ENCLB181UZG
size range: 200-400

value: HNRNPK

value: HNRNPK ChIP-seq on HepG2 cells

value: male

value: ENCBS747KOI at ENCODE; https://www.encodeproject.org/ENCBS747KOI/


title: TF ChIP-seq from HepG2 (ENCLB303LRU)

description:
https://www.encodeproject.org/experiments/ENCSR517HGZ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR517HGZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR524BHN
encode release date: 2020-08-28
lab: Richard Myers, HAIB
library encode accession: ENCLB303LRU
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting ZNF781

value: child

value: 15 year

value: ENCBS075SFY at ENCODE; https://www.encodeproject.org/ENCBS075SFY/


title: Sertoli Hi-C rep2 (P7)

status: Public on May 20 2021

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
processed data file:
Sertoli_AB_Compartments_P7.bigWig
Supplementary_Table_2.xlsx

data_processing:
For each of the experiments, reads were trimmed using Trim Galore (v0.6.0) and cutadapt (v1.18) and assessed for quality with FastQC (v0.11.8). STAR (v2.7.2a), BWA mem (v0.7.12) and HiC-Pro (v2.11.4) were used to map transcriptomic (RNA-seq), genomic (ChIP-seq, ATAC-seq) and 3D (Hi-C) trimmed reads to the GRCm38 (mm10) genome respectively
The GENCODE M23 gene annotation set was used to estimate strand-specific gene expression data in the RNA-seq data with the Bioconductor package RSubread (v1.28.1) and to assign the locations of nearby genes in the ATAC-seq datasets. For ChIP-seq and ATAC-seq experiments, duplicated reads were removed with Picard MarkDuplicates (v2.17.10) and low quality reads (MAPQ < 55) or reads that mapped to the mitochondrial genome were removed with SAMtools (v1.0).
MACS2 (v2.1.1.20160309) was used to call peaks in the ChIP-seq and ATAC-seq datasets using the parameters ‘-call-summits -m 2 20’ and ‘--nomodel –broad’ respectively
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tables of expression values and fold changes in gene expression, bigWig Coverage files and called peaks.

organism: Mus musculus

source_name: Sertoli Cells

extract_protocol: Hi-C were performed for each cell type on  about 1 million primary Sertoli cells using the Arima Hi-C Kit (#A510008).  Cells were fixed in 2% methanol-free formaldehyde in PBS at RT for ten min. with occasional mixing then quenched by addition of glycine to 0.125M with occasional mixing for 5 min.. Cells were placed on ice for 15 min. prior to washing with 1X PBS and stored at -80o C.  Hi-C was performed according to Arima Genomics (Document part # A160134 v00).  Sequencing libraries were prepared using the KAPA Hyper Prep Kit and xGen Duplex Seq adapters (Integrated DNA Techologies) according to Arima Genomics (Document part # A160139 v00).

tag: genoype

value: CAG-Stopflox-tdTomato; Dhh-Cre

tag: strain background

value: Mixed 129Sv and C57Bl/6J

tag: tamoxifen time point

value: 7 days


title: total RNA-seq from pancreas (ENCLB802COO)

description:
https://www.encodeproject.org/experiments/ENCSR523RGW/
***************
biological replicate number: 1
technical replicate number: 1
description: W71_pancreas
experiment encode accession: ENCSR523RGW
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB802COO
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (47 years) pancreas tissue, preserved by flash-freezing

value: pancreas

value: tissue

value: female

value: DM:yes; HTN:yes; CAD:no

value: adult

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS441SQC at ENCODE; https://www.encodeproject.org/ENCBS441SQC/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: total RNA-seq from adrenal gland (ENCLB755ACC)

description:
https://www.encodeproject.org/experiments/ENCSR003BTD/
***************
biological replicate number: 1
technical replicate number: 1
description: W71_adrenal_gland
experiment encode accession: ENCSR003BTD
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB755ACC
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (47 years) adrenal gland tissue, preserved by flash-freezing

value: adrenal gland

value: ENCBS450CEG at ENCODE; https://www.encodeproject.org/ENCBS450CEG/


title: total RNA-seq from colonic mucosa (ENCLB426QJG)

description:
https://www.encodeproject.org/experiments/ENCSR516BJM/
***************
biological replicate number: 1
technical replicate number: 1
description: W62_colonic_mucosa
experiment encode accession: ENCSR516BJM
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB426QJG
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female child (16 years) colonic mucosa tissue, preserved by flash-freezing

value: colonic mucosa

value: DM:no; HTN:no; CAD:no

value: child

value: 16 year

value: ENCBS562DVH at ENCODE; https://www.encodeproject.org/ENCBS562DVH/

value: Derived from ENCODE donor ENCDO575EGL; https://www.encodeproject.org/ENCDO575EGL/


title: ChIPseq_ESC_tko_IgG_r2

status: Public on May 17 2021

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Illumina RTA 1.18.64 (HiSeq 2500) or RTA 2.4.1 (MiSeq) and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. ChIP-seq samples were aligned to the mm10/hg19 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters, allowing only for uniquely mapping reads.
Genome_build: mm10/hg19
wig files were generated using the qExportWig function from the QuasR package with default parameters except scaling=1e6 and setting shift to the inferred shifts (Methods). The scores in the wig file therefore represent the number of shifted alignments per 100bp window and per million reads in the library. Peaks were identified using MACS2 using default parameters, except for the option -g, which was set to the mappable genome size for mm10 and hg19 respectively. For the mouse samples, MACS2 was run using the IgG samples as a control, for the human samples, no control was used. Resulting peaks were then filtered for mappability, whereby only peaks that were at least 80% mappable were retained for further analysis. Mappability was defined as the fraction of all possible 50mers contained in a given region that were mappable using the same alignment parameters as used to map the ChIP-seq data. For all downstream analysis, only reproducible peaks, i.e. peaks that occured in all replicates, were used. Scores in the bed files correspond to log2 enrichment over IgG for mouse or log2 read counts for human samples.
Banp motif matches for mm10 and hg19 (PredictedBanpMotifs_withChIPsignal_mm10.csv, PredictedBanpMotifs_withChIPsignal_hg19.csv) were defined as matches to the Banp weight matrix with a log2-odds score (versus a uniform background) of at least 12.5 (Methods). ChIP signal was calculated in a 201 bp window centered on each motif. File columns described in file header.

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma). The human cancer cell lines (HCT116 and HCC1954) were cultured in DMEM medium supplemented with 10% fetal calf serum, 1× nonessential amino acids and 1× L-glutamine (37°C, 7% CO2).

extract_protocol:
DNA was purified by Phenol:Chloroform extraction.
Immunoprecipitated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina). In the library preparation protocol, samples were amplified using 10 PCR cycles.

treatment_protocol: Cells (1x107) were seeded into 10 cm plates the day before the experiment. Chromatin Immunoprecipitation (ChIP) was carried out as previously described (Lienert, F. et al. Nat. Genet., 2011) with following modifications: (1) chromatin was sonicated for ~22 cycles of 20 sec. on and 40 sec. off using a Diagenode Bioruptor Pico, (2) 75-200ug of chromatin was used per IP, (3) protein A/G magnetic Dynabeads (Thermo Fisher Scientific) were used.

tag: cell type

value: embryonic stem cells

tag: genotype

value: Dnmt triple knock-out

tag: strain

tag: chip antibody

value: AbCam, ab72076


title: ChIPseq_ESC_wt_IgG_r1

value: wild type


title: ChIPseq_ESC_wt_IgG_r3


title: ChIPseq_ESC_tko_Banp_r2


title: ChIPseq_ESC_tko_IgG_r3


title: ChIPseq_ESC_tko_IgG_r1


title: ChIPseq_ESC_tko_Banp_r1


title: TF ChIP-seq from HepG2 (ENCLB264GGW)

description:
https://www.encodeproject.org/experiments/ENCSR517HGZ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR517HGZ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR524BHN
encode release date: 2020-08-28
lab: Richard Myers, HAIB
library encode accession: ENCLB264GGW
fragmentation methods: sonication (generic)

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

value: male

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: hepatocellular carcinoma

value: ENCBS579PTY at ENCODE; https://www.encodeproject.org/ENCBS579PTY/

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


title: ChIPseq_ESC_tko_Banp_r3


title: ChIPseq_ESC_wt_Banp_r2


title: total RNA-seq from lung (ENCLB180FNT)

description:
https://www.encodeproject.org/experiments/ENCSR045GTF/
***************
biological replicate number: 1
technical replicate number: 1
description: W71_lung
experiment encode accession: ENCSR045GTF
assay title: total RNA-seq
assembly: GRCh38
encode release date: 2021-01-04
lab: Barbara Wold, Caltech
library encode accession: ENCLB180FNT
spikeins used: ERCC spike profile for stranded Ribo reduced libraries 2019 December
nucleic acid starting quantity: 300
nucleic acid starting quantity units: ng

source_name: Homo sapiens female adult (47 years) lung tissue, preserved by flash-freezing

value: lung

value: tissue

tag: Sex

value: female

value: DM:yes; HTN:yes; CAD:no

tag: dev stage

value: adult

tag: age

value: 47 year

value: Michael Snyder, Stanford

value: Yiing Lin, MD, PhD

value: ENCBS806SDX at ENCODE; https://www.encodeproject.org/ENCBS806SDX/

value: Derived from ENCODE donor ENCDO528BHB; https://www.encodeproject.org/ENCDO528BHB/


title: ChIPseq_ESC_wt_Banp_r1

value: embryonic stem cells

value: wild type

value: AbCam, ab72076


title: ChIPseq_HCC1954_wt_Banp_r2

tag: cell line


title: ChIPseq_HCC1954_wt_Banp_r1


title: ChIPseq_HCT116_wt_Banp_r2


title: ChIPseq_HCT116_wt_Banp_r1


title: TF ChIP-seq from WTC11 (ENCLB781VYF)

description:
https://www.encodeproject.org/experiments/ENCSR004HEA/
***************
biological replicate number: 1
technical replicate number: 1
description: eGFP-OTX2 ChIP-seq on human WTC11
experiment encode accession: ENCSR004HEA
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR764ZNN
encode release date: 2021-04-06
lab: Michael Snyder, Stanford
library encode accession: ENCLB781VYF
fragmentation methods: sonication (Bioruptor Pico)
size range: 250-450

value: cell line

value: male

value: 30 year

tag: lab

tag: source

value: Richard Myers

tag: link

value: ENCBS888MUA at ENCODE; https://www.encodeproject.org/ENCBS888MUA/

value: Derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: ChIPseq_ESC_wt_IgG_r2