title: icSHAPE from K562 (ENCLB577WZB)

description:
https://www.encodeproject.org/experiments/ENCSR803XFA/
***************
biological replicate number: 2
technical replicate number: 1
description: icSHAPE control (DMSO) on K562 immortalized cell line
experiment encode accession: ENCSR803XFA
assay title: icSHAPE
assembly: GRCh38
encode release date: 2019-05-13
lab: Rob Spitale, UCI
library encode accession: ENCLB577WZB
size range: >200

value: cell line

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Rob Spitale, UCI

value: ATCC

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical;

value: ENCBS453AZN at ENCODE; https://www.encodeproject.org/ENCBS453AZN/

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


title: Histone ChIP-seq from transverse colon (ENCLB242DED)

status: Public on Jan 06 2020

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/ENCSR413CHO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR413CHO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR651ISB
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB242DED
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 male adult (54 years) transverse colon tissue

tag: antibody

value: transverse colon

value: tissue

tag: description

value: EnTEX:Colon - Transverse

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 54 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: Kristin Ardlie

tag: link

value: ENCBS121FBL at ENCODE; https://www.encodeproject.org/ENCBS121FBL/

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


title: Control ChIP-seq from spleen (ENCLB282KOI)

description:
https://www.encodeproject.org/experiments/ENCSR803JPO/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR803JPO
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB282KOI
size range: 200-600

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

value: spleen

value: ENCBS949QWK at ENCODE; https://www.encodeproject.org/ENCBS949QWK/


title: Histone ChIP-seq from transverse colon (ENCLB699XTX)

description:
https://www.encodeproject.org/experiments/ENCSR792VLP/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR792VLP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR384KIB
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB699XTX
fragmentation methods: sonication (generic)
size range: 200-600

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

extract_protocol: not provided

value: female

value: 51 year

value: ENCBS515RIZ at ENCODE; https://www.encodeproject.org/ENCBS515RIZ/

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


title: Histone ChIP-seq from transverse colon (ENCLB106ELU)

description:
https://www.encodeproject.org/experiments/ENCSR413CHO/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR413CHO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR651ISB
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB106ELU
fragmentation methods: sonication (generic)
size range: 200-600

value: ENCBS633KVX at ENCODE; https://www.encodeproject.org/ENCBS633KVX/


title: Histone ChIP-seq from ovary (ENCLB907OBT)

description:
https://www.encodeproject.org/experiments/ENCSR440UCR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR440UCR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR509SEX
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB907OBT
fragmentation methods: sonication (generic)
size range: 200-600

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

value: ovary

value: 53 year

value: ENCBS760QKF at ENCODE; https://www.encodeproject.org/ENCBS760QKF/

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


title: Histone ChIP-seq from spleen (ENCLB503JXA)

description:
https://www.encodeproject.org/experiments/ENCSR787YHR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR787YHR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR803JPO
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB503JXA
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: male

value: adult


title: Histone ChIP-seq from transverse colon (ENCLB687BPS)

description:
https://www.encodeproject.org/experiments/ENCSR413CHO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR413CHO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR651ISB
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB687BPS
fragmentation methods: sonication (generic)
size range: 200-600

value: transverse colon

value: EnTEX:Colon - Transverse

value: 54 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: Histone ChIP-seq from transverse colon (ENCLB343IDX)

description:
https://www.encodeproject.org/experiments/ENCSR792VLP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR792VLP
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR384KIB
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB343IDX
fragmentation methods: sonication (generic)
size range: 200-600

value: female


title: Histone ChIP-seq from uterus (ENCLB713FBA)

description:
https://www.encodeproject.org/experiments/ENCSR448IJB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR448IJB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR979XBX
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB713FBA
fragmentation methods: sonication (generic)
size range: 200-600

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

value: uterus

value: ENCBS754FVJ at ENCODE; https://www.encodeproject.org/ENCBS754FVJ/


title: Control ChIP-seq from testis (ENCLB163UMV)

description:
https://www.encodeproject.org/experiments/ENCSR385ODY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR385ODY
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB163UMV
size range: 200-600

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

value: testis

value: ENCBS849BBS at ENCODE; https://www.encodeproject.org/ENCBS849BBS/

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


title: icSHAPE from K562 (ENCLB418JYU)

description:
https://www.encodeproject.org/experiments/ENCSR803XFA/
***************
biological replicate number: 1
technical replicate number: 1
description: icSHAPE control (DMSO) on K562 immortalized cell line
experiment encode accession: ENCSR803XFA
assay title: icSHAPE
assembly: GRCh38
encode release date: 2019-05-13
lab: Rob Spitale, UCI
library encode accession: ENCLB418JYU
size range: >200

library_source: transcriptomic

molecule: total RNA

source_name: Homo sapiens K562 cell line treated with dimethyl sulfoxide

tag: line

value: cell line

value: This sample corresponds to the untreated icSHAPE from the K562 cell line

tag: health state

value: chronic myelogenous leukemia (CML)

value: 53 year

value: Rob Spitale, UCI

value: ATCC

tag: treatments

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical;

value: ENCBS717VYS at ENCODE; https://www.encodeproject.org/ENCBS717VYS/

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


title: Control ChIP-seq from transverse colon (ENCLB381NHW)

description:
https://www.encodeproject.org/experiments/ENCSR384KIB/
***************
biological replicate number: 2
technical replicate number: 3
description:
experiment encode accession: ENCSR384KIB
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB381NHW
size range: 200-600

value: transverse colon

value: tissue

value: EnTEX:Colon - Transverse

value: adult

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS515RIZ at ENCODE; https://www.encodeproject.org/ENCBS515RIZ/

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


title: Histone ChIP-seq from transverse colon (ENCLB592OSR)

description:
https://www.encodeproject.org/experiments/ENCSR813ZEY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR813ZEY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB592OSR
fragmentation methods: sonication (generic)
size range: 200-600

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

value: male

value: 37 year

value: Kristin Ardlie

value: ENCBS990XOM at ENCODE; https://www.encodeproject.org/ENCBS990XOM/

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


title: Histone ChIP-seq from spleen (ENCLB932PMD)

description:
https://www.encodeproject.org/experiments/ENCSR787YHR/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR787YHR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR803JPO
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB932PMD
fragmentation methods: sonication (generic)
size range: 200-600

value: spleen

value: 54 year

value: ENCBS949QWK at ENCODE; https://www.encodeproject.org/ENCBS949QWK/

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


title: Histone ChIP-seq from heart left ventricle (ENCLB320WBA)

description:
https://www.encodeproject.org/experiments/ENCSR449FRQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR449FRQ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR178FVP
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB320WBA
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) heart left ventricle tissue

value: heart left ventricle

value: EnTEX:Heart - Left Ventricle

value: female

value: ENCBS684IAD at ENCODE; https://www.encodeproject.org/ENCBS684IAD/


title: Histone ChIP-seq from body of pancreas (ENCLB226UOI)

description:
https://www.encodeproject.org/experiments/ENCSR432DPY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR432DPY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR700CAX
encode release date: 2019-02-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB226UOI
fragmentation methods: sonication (generic)
size range: 200-600

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

value: body of pancreas

value: tissue

value: adult

value: 51 year

value: ENCBS535XPM at ENCODE; https://www.encodeproject.org/ENCBS535XPM/


title: Histone ChIP-seq from ovary (ENCLB793ODG)

description:
https://www.encodeproject.org/experiments/ENCSR440UCR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR440UCR
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR509SEX
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB793ODG
fragmentation methods: sonication (generic)
size range: 200-600

value: ovary

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS760QKF at ENCODE; https://www.encodeproject.org/ENCBS760QKF/

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


title: Histone ChIP-seq from adrenal gland (ENCLB901QQL)

description:
https://www.encodeproject.org/experiments/ENCSR379BVL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR379BVL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR234FYG
encode release date: 2018-12-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB901QQL
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) adrenal gland tissue

value: adrenal gland

value: EnTEX:Adrenal Gland

value: Kristin Ardlie

value: ENCBS458UEH at ENCODE; https://www.encodeproject.org/ENCBS458UEH/

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


title: Histone ChIP-seq from adrenal gland (ENCLB026RUK)

description:
https://www.encodeproject.org/experiments/ENCSR379BVL/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR379BVL
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR234FYG
encode release date: 2018-12-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB026RUK
fragmentation methods: none
size range: 200-600

value: female


title: Histone ChIP-seq from transverse colon (ENCLB310VNP)

description:
https://www.encodeproject.org/experiments/ENCSR413CHO/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR413CHO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR651ISB
encode release date: 2019-09-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB310VNP
fragmentation methods: sonication (generic)
size range: 200-600

value: transverse colon

value: EnTEX:Colon - Transverse

value: male

value: 54 year

value: ENCBS121FBL at ENCODE; https://www.encodeproject.org/ENCBS121FBL/

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


title: Histone ChIP-seq from testis (ENCLB735EYQ)

description:
https://www.encodeproject.org/experiments/ENCSR376JOC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR376JOC
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR215WNN
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB735EYQ
fragmentation methods: sonication (generic)
size range: 200-600

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

value: testis

value: tissue

value: adult

value: 37 year

value: ENCBS631HJF at ENCODE; https://www.encodeproject.org/ENCBS631HJF/

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


title: Control ChIP-seq from transverse colon (ENCLB678ZKI)

description:
https://www.encodeproject.org/experiments/ENCSR384KIB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR384KIB
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB678ZKI
size range: 200-600

value: 51 year

value: Bradley Bernstein, Broad

value: ENCBS555CAN at ENCODE; https://www.encodeproject.org/ENCBS555CAN/


title: Control ChIP-seq from transverse colon (ENCLB554JAR)

description:
https://www.encodeproject.org/experiments/ENCSR384KIB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR384KIB
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB554JAR
size range: 200-600

value: Kristin Ardlie

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


title: Histone ChIP-seq from transverse colon (ENCLB510VIZ)

description:
https://www.encodeproject.org/experiments/ENCSR749ABB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR749ABB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB510VIZ
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: transverse colon

value: ENCBS990XOM at ENCODE; https://www.encodeproject.org/ENCBS990XOM/


title: Control ChIP-seq from spleen (ENCLB010CLC)

description:
https://www.encodeproject.org/experiments/ENCSR711URW/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR711URW
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB010CLC
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

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

value: spleen

value: female

value: ENCBS892ESJ at ENCODE; https://www.encodeproject.org/ENCBS892ESJ/


title: Histone ChIP-seq from testis (ENCLB477ZIH)

description:
https://www.encodeproject.org/experiments/ENCSR376JOC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR376JOC
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR215WNN
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB477ZIH
fragmentation methods: sonication (generic)
size range: 200-600

value: male


title: Control ChIP-seq from testis (ENCLB882HQA)

description:
https://www.encodeproject.org/experiments/ENCSR385ODY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR385ODY
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-08
lab: Bradley Bernstein, Broad
library encode accession: ENCLB882HQA
size range: 200-600

value: testis

value: 54 year

value: ENCBS849BBS at ENCODE; https://www.encodeproject.org/ENCBS849BBS/

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


title: Histone ChIP-seq from transverse colon (ENCLB078JPU)

description:
https://www.encodeproject.org/experiments/ENCSR749ABB/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR749ABB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB078JPU
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: EnTEX:Colon - Transverse

value: adult

value: 37 year


title: Histone ChIP-seq from uterus (ENCLB986RNF)

description:
https://www.encodeproject.org/experiments/ENCSR354ZUG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR354ZUG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR979XBX
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB986RNF
fragmentation methods: sonication (generic)
size range: 200-600

value: uterus

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS754FVJ at ENCODE; https://www.encodeproject.org/ENCBS754FVJ/

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


title: Histone ChIP-seq from spleen (ENCLB675MRT)

description:
https://www.encodeproject.org/experiments/ENCSR709APF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR709APF
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR803JPO
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB675MRT
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: spleen

value: Kristin Ardlie

value: ENCBS949QWK at ENCODE; https://www.encodeproject.org/ENCBS949QWK/


title: icSHAPE from GM12878 (ENCLB827OJR)

description:
https://www.encodeproject.org/experiments/ENCSR836VQU/
***************
biological replicate number: 2
technical replicate number: 1
description: icSHAPE (NAi-N3) on GM12878 immortalized cell line
experiment encode accession: ENCSR836VQU
assay title: icSHAPE
assembly: GRCh38
possible controls: ENCSR052BBY
encode release date: 2019-05-13
lab: Rob Spitale, UCI
library encode accession: ENCLB827OJR
size range: >200

source_name: Homo sapiens GM12878 cell line treated with NAI-N3

value: cell line

value: This sample corresponds to the treated icSHAPE from GM12878 cell line

value: female

value: unknown

value: Rob Spitale, UCI

value: ATCC

value: ENCBS504ZJS at ENCODE; https://www.encodeproject.org/ENCBS504ZJS/

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


title: Histone ChIP-seq from uterus (ENCLB004OSL)

description:
https://www.encodeproject.org/experiments/ENCSR354ZUG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR354ZUG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR979XBX
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB004OSL
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: adult


title: Histone ChIP-seq from sigmoid colon (ENCLB451VHR)

description:
https://www.encodeproject.org/experiments/ENCSR343NWC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR343NWC
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR316ZPQ
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB451VHR
fragmentation methods: none
size range: 200-600

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

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: 51 year

value: ENCBS474RXX at ENCODE; https://www.encodeproject.org/ENCBS474RXX/

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


title: Control ChIP-seq from spleen (ENCLB070RKC)

description:
https://www.encodeproject.org/experiments/ENCSR711URW/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR711URW
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2019-02-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB070RKC
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: spleen

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS892ESJ at ENCODE; https://www.encodeproject.org/ENCBS892ESJ/


title: Histone ChIP-seq from spleen (ENCLB078ILN)

description:
https://www.encodeproject.org/experiments/ENCSR709APF/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR709APF
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR803JPO
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB078ILN
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: male

value: 54 year

value: ENCBS949QWK at ENCODE; https://www.encodeproject.org/ENCBS949QWK/

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


title: Histone ChIP-seq from tibial nerve (ENCLB054VCK)

description:
https://www.encodeproject.org/experiments/ENCSR338PGG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR338PGG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR059VTG
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB054VCK
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) tibial nerve tissue

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: female

value: ENCBS925LQY at ENCODE; https://www.encodeproject.org/ENCBS925LQY/


title: Histone ChIP-seq from coronary artery (ENCLB501GIA)

description:
https://www.encodeproject.org/experiments/ENCSR355GNZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR355GNZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR163XFK
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB501GIA
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) coronary artery tissue

value: coronary artery

value: tissue

value: EnTEX:Artery - Coronary

value: adult

value: ENCBS984LMH at ENCODE; https://www.encodeproject.org/ENCBS984LMH/


title: Histone ChIP-seq from sigmoid colon (ENCLB433SBQ)

description:
https://www.encodeproject.org/experiments/ENCSR343NWC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR343NWC
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR316ZPQ
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB433SBQ
fragmentation methods: sonication (generic)
size range: 200-600

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: 51 year

value: ENCBS474RXX at ENCODE; https://www.encodeproject.org/ENCBS474RXX/

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


title: Histone ChIP-seq from transverse colon (ENCLB076UOH)

description:
https://www.encodeproject.org/experiments/ENCSR643KID/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR643KID
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB076UOH
fragmentation methods: sonication (generic)
size range: 200-600

value: transverse colon

value: EnTEX:Colon - Transverse

value: male

value: 37 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS990XOM at ENCODE; https://www.encodeproject.org/ENCBS990XOM/

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


title: Control ChIP-seq from thyroid gland (ENCLB954QJI)

description:
https://www.encodeproject.org/experiments/ENCSR347VUG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR347VUG
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB954QJI
size range: 200-600

source_name: Homo sapiens female adult (51 year) thyroid gland tissue

value: thyroid gland

value: tissue

value: female

value: ENCBS541DMP at ENCODE; https://www.encodeproject.org/ENCBS541DMP/


title: Histone ChIP-seq from sigmoid colon (ENCLB065XDU)

description:
https://www.encodeproject.org/experiments/ENCSR333HMT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR333HMT
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR524NCH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB065XDU
fragmentation methods: sonication (generic)
size range: 200-600

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

value: sigmoid colon

value: adult

value: 54 year

value: ENCBS243UXH at ENCODE; https://www.encodeproject.org/ENCBS243UXH/

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


title: Histone ChIP-seq from upper lobe of left lung (ENCLB726HVY)

description:
https://www.encodeproject.org/experiments/ENCSR348FGT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR348FGT
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR774MLK
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB726HVY
fragmentation methods: sonication (generic)
size range: 200-600

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

value: upper lobe of left lung

value: ENCBS401SWW at ENCODE; https://www.encodeproject.org/ENCBS401SWW/


title: Histone ChIP-seq from transverse colon (ENCLB021FDL)

description:
https://www.encodeproject.org/experiments/ENCSR643KID/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR643KID
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB021FDL
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: transverse colon

value: EnTEX:Colon - Transverse

value: male


title: Control ChIP-seq from thyroid gland (ENCLB335DLR)

description:
https://www.encodeproject.org/experiments/ENCSR347VUG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR347VUG
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB335DLR
size range: 200-600

value: 51 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

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


title: Histone ChIP-seq from sigmoid colon (ENCLB293SJZ)

description:
https://www.encodeproject.org/experiments/ENCSR333HMT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR333HMT
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR524NCH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB293SJZ
fragmentation methods: none
size range: 200-600

value: tissue

value: EnTEX:Colon - Sigmoid


title: Histone ChIP-seq from tibial nerve (ENCLB987OLD)

description:
https://www.encodeproject.org/experiments/ENCSR338PGG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR338PGG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR059VTG
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB987OLD
fragmentation methods: sonication (generic)
size range: 200-600

value: tibial nerve

value: EnTEX:Nerve - Tibial

value: female

value: ENCBS925LQY at ENCODE; https://www.encodeproject.org/ENCBS925LQY/


title: Histone ChIP-seq from transverse colon (ENCLB341GJC)

description:
https://www.encodeproject.org/experiments/ENCSR640XRV/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR640XRV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-10-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB341GJC
fragmentation methods: sonication (generic)
size range: 200-600

value: adult

value: 37 year

value: ENCBS990XOM at ENCODE; https://www.encodeproject.org/ENCBS990XOM/

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


title: Histone ChIP-seq from transverse colon (ENCLB963MNY)

description:
https://www.encodeproject.org/experiments/ENCSR640XRV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR640XRV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-10-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB963MNY
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: transverse colon


title: Histone ChIP-seq from spleen (ENCLB202PFM)

description:
https://www.encodeproject.org/experiments/ENCSR635IRN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR635IRN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR803JPO
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB202PFM
fragmentation methods: sonication (generic)
size range: 200-600

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

value: spleen

value: 54 year

value: ENCBS949QWK at ENCODE; https://www.encodeproject.org/ENCBS949QWK/

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


title: Histone ChIP-seq from stomach (ENCLB810FAV)

description:
https://www.encodeproject.org/experiments/ENCSR330MAM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR330MAM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR948DNK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB810FAV
fragmentation methods: none
size range: 200-600

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

value: stomach

value: 51 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS633XWN at ENCODE; https://www.encodeproject.org/ENCBS633XWN/


title: TF ChIP-seq from thyroid gland (ENCLB790HOF)

description:
https://www.encodeproject.org/experiments/ENCSR331OGX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR331OGX
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR475NOQ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB790HOF
fragmentation methods: sonication (generic)
size range: 200-600

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

value: CTCF

value: thyroid gland

value: tissue

value: 53 year

value: ENCBS586UUR at ENCODE; https://www.encodeproject.org/ENCBS586UUR/

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


title: Histone ChIP-seq from coronary artery (ENCLB467HXM)

description:
https://www.encodeproject.org/experiments/ENCSR355GNZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR355GNZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR163XFK
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB467HXM
fragmentation methods: sonication (generic)
size range: 200-600

value: coronary artery

value: EnTEX:Artery - Coronary

value: female

value: adult

value: ENCBS984LMH at ENCODE; https://www.encodeproject.org/ENCBS984LMH/

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


title: Histone ChIP-seq from spleen (ENCLB251GGW)

description:
https://www.encodeproject.org/experiments/ENCSR635IRN/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR635IRN
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR803JPO
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB251GGW
fragmentation methods: sonication (generic)
size range: 200-600

value: spleen

value: male

value: 54 year

value: ENCBS949QWK at ENCODE; https://www.encodeproject.org/ENCBS949QWK/

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


title: TF ChIP-seq from transverse colon (ENCLB307YSC)

description:
https://www.encodeproject.org/experiments/ENCSR608WPS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR608WPS
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB307YSC
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: transverse colon

value: EnTEX:Colon - Transverse

value: 37 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS990XOM at ENCODE; https://www.encodeproject.org/ENCBS990XOM/

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


title: Control ChIP-seq from transverse colon (ENCLB231DEW)

description:
https://www.encodeproject.org/experiments/ENCSR651ISB/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR651ISB
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB231DEW
size range: 200-600

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

value: tissue

value: ENCBS989UNA at ENCODE; https://www.encodeproject.org/ENCBS989UNA/


title: TF ChIP-seq from spleen (ENCLB106KDZ)

description:
https://www.encodeproject.org/experiments/ENCSR601FEB/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR601FEB
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR189UPU
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB106KDZ
fragmentation methods: sonication (generic)
size range: 200-600

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

value: female

value: adult

value: 53 year

value: ENCBS793DBC at ENCODE; https://www.encodeproject.org/ENCBS793DBC/

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


title: Control ChIP-seq from sigmoid colon (ENCLB584ROV)

description:
https://www.encodeproject.org/experiments/ENCSR316ZPQ/
***************
biological replicate number: 1
technical replicate number: 4
description:
experiment encode accession: ENCSR316ZPQ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB584ROV
size range: 200-600

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: 51 year

value: ENCBS474RXX at ENCODE; https://www.encodeproject.org/ENCBS474RXX/

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


title: Histone ChIP-seq from upper lobe of left lung (ENCLB741OUC)

description:
https://www.encodeproject.org/experiments/ENCSR348FGT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR348FGT
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR774MLK
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB741OUC
fragmentation methods: sonication (generic)
size range: 200-600

value: upper lobe of left lung

value: male

value: 54 year

value: ENCBS401SWW at ENCODE; https://www.encodeproject.org/ENCBS401SWW/

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


title: TF ChIP-seq from spleen (ENCLB701PMN)

description:
https://www.encodeproject.org/experiments/ENCSR601FEB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR601FEB
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR189UPU
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB701PMN
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: spleen

value: tissue

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: Histone ChIP-seq from transverse colon (ENCLB655SZE)

description:
https://www.encodeproject.org/experiments/ENCSR516QFO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR516QFO
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB655SZE
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

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

value: transverse colon

value: EnTEX:Colon - Transverse

value: adult

value: 37 year

value: ENCBS990XOM at ENCODE; https://www.encodeproject.org/ENCBS990XOM/

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


title: TF ChIP-seq from thyroid gland (ENCLB854TYJ)

description:
https://www.encodeproject.org/experiments/ENCSR331OGX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR331OGX
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR475NOQ
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB854TYJ
fragmentation methods: sonication (generic)
size range: 200-600

value: thyroid gland

value: 53 year

value: female

value: ENCBS586UUR at ENCODE; https://www.encodeproject.org/ENCBS586UUR/

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


title: TF ChIP-seq from thyroid gland (ENCLB299HZM)

description:
https://www.encodeproject.org/experiments/ENCSR505ZGX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR505ZGX
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR777VQP
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB299HZM
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens thyroid gland tissue male adult (37 years)

value: male

value: ENCBS522TJW at ENCODE; https://www.encodeproject.org/ENCBS522TJW/


title: Control ChIP-seq from sigmoid colon (ENCLB309GUA)

description:
https://www.encodeproject.org/experiments/ENCSR316ZPQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR316ZPQ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB309GUA
size range: 200-600

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: 51 year

value: ENCBS474RXX at ENCODE; https://www.encodeproject.org/ENCBS474RXX/

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


title: Control ChIP-seq from transverse colon (ENCLB557NHH)

description:
https://www.encodeproject.org/experiments/ENCSR479HSY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR479HSY
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB557NHH
size range: 200-600

value: transverse colon

value: tissue

value: EnTEX:Colon - Transverse

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: TF ChIP-seq from thyroid gland (ENCLB105BCH)

description:
https://www.encodeproject.org/experiments/ENCSR505ZGX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR505ZGX
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR777VQP
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB105BCH
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: thyroid gland

value: adult

value: 37 year

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


title: Control ChIP-seq from transverse colon (ENCLB443HFG)

description:
https://www.encodeproject.org/experiments/ENCSR479HSY/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR479HSY
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB443HFG
size range: 200-600

value: male

value: ENCBS990XOM at ENCODE; https://www.encodeproject.org/ENCBS990XOM/


title: Control ChIP-seq from sigmoid colon (ENCLB262IIJ)

description:
https://www.encodeproject.org/experiments/ENCSR316ZPQ/
***************
biological replicate number: 1
technical replicate number: 3
description:
experiment encode accession: ENCSR316ZPQ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB262IIJ
size range: 200-600

value: sigmoid colon

value: female


title: TF ChIP-seq from spleen (ENCLB184HTV)

description:
https://www.encodeproject.org/experiments/ENCSR595BPR/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR595BPR
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR711URW
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB184HTV
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: spleen

value: 51 year

value: ENCBS892ESJ at ENCODE; https://www.encodeproject.org/ENCBS892ESJ/


title: Histone ChIP-seq from stomach (ENCLB719HAK)

description:
https://www.encodeproject.org/experiments/ENCSR330MAM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR330MAM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR948DNK
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB719HAK
fragmentation methods: sonication (generic)
size range: 200-600

value: stomach

value: ENCBS633XWN at ENCODE; https://www.encodeproject.org/ENCBS633XWN/

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


title: Histone ChIP-seq from transverse colon (ENCLB650OAV)

description:
https://www.encodeproject.org/experiments/ENCSR315EZG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR315EZG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR384KIB
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB650OAV
fragmentation methods: none
size range: 200-600

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

value: transverse colon

value: tissue

value: EnTEX:Colon - Transverse

value: Bradley Bernstein, Broad

value: ENCBS555CAN at ENCODE; https://www.encodeproject.org/ENCBS555CAN/


title: Histone ChIP-seq from tibial artery (ENCLB197GNE)

description:
https://www.encodeproject.org/experiments/ENCSR303BUB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR303BUB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR714GXC
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB197GNE
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) tibial artery tissue

value: tibial artery

value: EnTEX:Artery - Tibial

value: adult

value: Kristin Ardlie

value: ENCBS636NCW at ENCODE; https://www.encodeproject.org/ENCBS636NCW/


title: Histone ChIP-seq from transverse colon (ENCLB236SSM)

description:
https://www.encodeproject.org/experiments/ENCSR315EZG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR315EZG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR384KIB
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB236SSM
fragmentation methods: sonication (generic)
size range: 200-600

value: female


title: TF ChIP-seq from gastroesophageal sphincter (ENCLB893QXK)

description:
https://www.encodeproject.org/experiments/ENCSR298ZPF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR298ZPF
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR642QDW
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB893QXK
fragmentation methods: none
size range: 200-600

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

value: CTCF

value: gastroesophageal sphincter

value: EnTEX:Esophagus - Gastroesophageal Junction

value: ENCBS617FGB at ENCODE; https://www.encodeproject.org/ENCBS617FGB/


title: Histone ChIP-seq from transverse colon (ENCLB086LAE)

description:
https://www.encodeproject.org/experiments/ENCSR488YXS/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR488YXS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR384KIB
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB086LAE
fragmentation methods: sonication (generic)
size range: 200-600

value: 51 year

value: ENCBS515RIZ at ENCODE; https://www.encodeproject.org/ENCBS515RIZ/


title: Histone ChIP-seq from gastrocnemius medialis (ENCLB171KSP)

description:
https://www.encodeproject.org/experiments/ENCSR283BRU/
***************
biological replicate number: 2
technical replicate number: 3
description:
experiment encode accession: ENCSR283BRU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR138WRC
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB171KSP
fragmentation methods: none
size range: 200-600

source_name: Homo sapiens female adult (51 year) gastrocnemius medialis tissue

value: gastrocnemius medialis

value: i.e. REMC 6, 13, 14 and 15; EnTEX:Muscle - Skeletal also gastrocnemius medialis\n

value: ENCBS640TBC at ENCODE; https://www.encodeproject.org/ENCBS640TBC/

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


title: Histone ChIP-seq from transverse colon (ENCLB587TZB)

description:
https://www.encodeproject.org/experiments/ENCSR315EZG/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR315EZG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR384KIB
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB587TZB
fragmentation methods: sonication (generic)
size range: 200-600

value: transverse colon

value: tissue

value: EnTEX:Colon - Transverse

value: Bradley Bernstein, Broad


title: Histone ChIP-seq from gastrocnemius medialis (ENCLB099IIB)

description:
https://www.encodeproject.org/experiments/ENCSR283BRU/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR283BRU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR138WRC
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB099IIB
fragmentation methods: none
size range: 200-600

value: adult

value: Kristin Ardlie


title: Histone ChIP-seq from tibial artery (ENCLB754TZC)

description:
https://www.encodeproject.org/experiments/ENCSR303BUB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR303BUB
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR714GXC
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB754TZC
fragmentation methods: none
size range: 200-600

value: tibial artery

value: EnTEX:Artery - Tibial

value: female

value: ENCBS636NCW at ENCODE; https://www.encodeproject.org/ENCBS636NCW/


title: Histone ChIP-seq from gastrocnemius medialis (ENCLB655WMX)

description:
https://www.encodeproject.org/experiments/ENCSR283BRU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR283BRU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR138WRC
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB655WMX
fragmentation methods: none
size range: 200-600


title: TF ChIP-seq from spleen (ENCLB407PLO)

description:
https://www.encodeproject.org/experiments/ENCSR595BPR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR595BPR
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR711URW
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB407PLO
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

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

value: CTCF

value: spleen

value: ENCBS892ESJ at ENCODE; https://www.encodeproject.org/ENCBS892ESJ/


title: Histone ChIP-seq from vagina (ENCLB373HLL)

description:
https://www.encodeproject.org/experiments/ENCSR278TQE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR278TQE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR607UWA
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB373HLL
fragmentation methods: sonication (generic)
size range: 200-600

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

value: vagina

value: 51 year

value: ENCBS468YOF at ENCODE; https://www.encodeproject.org/ENCBS468YOF/


title: Control ChIP-seq from sigmoid colon (ENCLB347WZX)

description:
https://www.encodeproject.org/experiments/ENCSR316ZPQ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR316ZPQ
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB347WZX
size range: 200-600

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

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: ENCBS474RXX at ENCODE; https://www.encodeproject.org/ENCBS474RXX/

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


title: icSHAPE from HepG2 (ENCLB199MPN)

description:
https://www.encodeproject.org/experiments/ENCSR286LXS/
***************
biological replicate number: 1
technical replicate number: 1
description: icSHAPE control (DMSO) on HepG2 immortalized cell line
experiment encode accession: ENCSR286LXS
assay title: icSHAPE
assembly: GRCh38
encode release date: 2019-05-13
lab: Rob Spitale, UCI
library encode accession: ENCLB199MPN
size range: >200

source_name: Homo sapiens HepG2 cell line treated with dimethyl sulfoxide

value: cell line

value: This sample corresponds to the untreated icSHAPE from HepG2 cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 year

value: Rob Spitale, UCI

value: ATCC

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical;

value: ENCBS556YSM at ENCODE; https://www.encodeproject.org/ENCBS556YSM/

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


title: Histone ChIP-seq from vagina (ENCLB465FSC)

description:
https://www.encodeproject.org/experiments/ENCSR278TQE/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR278TQE
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR607UWA
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB465FSC
fragmentation methods: sonication (generic)
size range: 200-600

value: vagina

value: tissue

value: female

value: adult

value: 51 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: Histone ChIP-seq from sigmoid colon (ENCLB453WAH)

description:
https://www.encodeproject.org/experiments/ENCSR277SUG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR277SUG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR316ZPQ
encode release date: 2019-02-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB453WAH
fragmentation methods: sonication (generic)
size range: 200-600

value: sigmoid colon

value: EnTEX:Colon - Sigmoid

value: ENCBS474RXX at ENCODE; https://www.encodeproject.org/ENCBS474RXX/

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


title: Histone ChIP-seq from transverse colon (ENCLB475DOU)

description:
https://www.encodeproject.org/experiments/ENCSR315EZG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR315EZG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR384KIB
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB475DOU
fragmentation methods: sonication (generic)
size range: 200-600

value: transverse colon

value: EnTEX:Colon - Transverse

value: ENCBS515RIZ at ENCODE; https://www.encodeproject.org/ENCBS515RIZ/


title: Histone ChIP-seq from spleen (ENCLB020WFM)

description:
https://www.encodeproject.org/experiments/ENCSR272CIV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR272CIV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR711URW
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB020WFM
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: spleen

value: ENCBS892ESJ at ENCODE; https://www.encodeproject.org/ENCBS892ESJ/


title: Histone ChIP-seq from sigmoid colon (ENCLB238ATW)

description:
https://www.encodeproject.org/experiments/ENCSR277SUG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR277SUG
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR316ZPQ
encode release date: 2019-02-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB238ATW
fragmentation methods: sonication (generic)
size range: 200-600


title: Control ChIP-seq from transverse colon (ENCLB784IOH)

description:
https://www.encodeproject.org/experiments/ENCSR384KIB/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR384KIB
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB784IOH
size range: 200-600


title: Histone ChIP-seq from spleen (ENCLB223UVH)

description:
https://www.encodeproject.org/experiments/ENCSR272CIV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR272CIV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR711URW
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB223UVH
fragmentation methods: sonication (generic)
size range: 200-600

value: ENCBS363GBQ at ENCODE; https://www.encodeproject.org/ENCBS363GBQ/


title: Control ChIP-seq from transverse colon (ENCLB631DKN)

description:
https://www.encodeproject.org/experiments/ENCSR384KIB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR384KIB
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB631DKN
size range: 200-600


title: TF ChIP-seq from gastroesophageal sphincter (ENCLB554TCJ)

description:
https://www.encodeproject.org/experiments/ENCSR298ZPF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR298ZPF
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR642QDW
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB554TCJ
fragmentation methods: none
size range: 200-600

value: CTCF

value: gastroesophageal sphincter

value: EnTEX:Esophagus - Gastroesophageal Junction

value: ENCBS617FGB at ENCODE; https://www.encodeproject.org/ENCBS617FGB/


title: Histone ChIP-seq from spleen (ENCLB081MAU)

description:
https://www.encodeproject.org/experiments/ENCSR272CIV/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR272CIV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR711URW
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB081MAU
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

value: female

value: adult

value: 51 year


title: TF ChIP-seq from spleen (ENCLB886MPZ)

description:
https://www.encodeproject.org/experiments/ENCSR225YGX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR225YGX
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR803JPO
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB886MPZ
fragmentation methods: sonication (generic)
size range: 200-600

value: male

value: 54 year

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS949QWK at ENCODE; https://www.encodeproject.org/ENCBS949QWK/

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


title: TF ChIP-seq from spleen (ENCLB767KQK)

description:
https://www.encodeproject.org/experiments/ENCSR225YGX/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR225YGX
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR803JPO
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB767KQK
fragmentation methods: sonication (generic)
size range: 200-600

value: spleen


title: TF ChIP-seq from esophagus squamous epithelium (ENCLB859TMK)

description:
https://www.encodeproject.org/experiments/ENCSR266UTR/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR266UTR
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR514EZP
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB859TMK
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) esophagus squamous epithelium tissue

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa

value: ENCBS467KQD at ENCODE; https://www.encodeproject.org/ENCBS467KQD/

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


title: TF ChIP-seq from esophagus squamous epithelium (ENCLB384PMQ)

description:
https://www.encodeproject.org/experiments/ENCSR266UTR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR266UTR
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR514EZP
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB384PMQ
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF


title: Histone ChIP-seq from upper lobe of left lung (ENCLB144XVA)

description:
https://www.encodeproject.org/experiments/ENCSR263OXW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR263OXW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR422TGJ
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB144XVA
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens upper lobe of left lung tissue female adult (53 years)

value: upper lobe of left lung

value: 53 year

value: ENCBS684YJH at ENCODE; https://www.encodeproject.org/ENCBS684YJH/

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


title: Histone ChIP-seq from upper lobe of left lung (ENCLB626YPA)

description:
https://www.encodeproject.org/experiments/ENCSR263OXW/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR263OXW
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR422TGJ
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB626YPA
fragmentation methods: none
size range: 200-600

value: tissue

value: adult

value: female


title: Histone ChIP-seq from right atrium auricular region (ENCLB606FOV)

description:
https://www.encodeproject.org/experiments/ENCSR250AAV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR250AAV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR195BZZ
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB606FOV
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens right atrium auricular region tissue female adult (53 years)

value: right atrium auricular region

value: EnTEX:Heart - Atrial Appendage

value: Bradley Bernstein, Broad

value: ENCBS493WOF at ENCODE; https://www.encodeproject.org/ENCBS493WOF/


title: Histone ChIP-seq from transverse colon (ENCLB069MMO)

description:
https://www.encodeproject.org/experiments/ENCSR083DXD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR083DXD
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR479HSY
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB069MMO
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

value: transverse colon

value: EnTEX:Colon - Transverse

value: male

value: 37 year

value: Kristin Ardlie

value: ENCBS990XOM at ENCODE; https://www.encodeproject.org/ENCBS990XOM/

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


title: Histone ChIP-seq from uterus (ENCLB641FEP)

description:
https://www.encodeproject.org/experiments/ENCSR244ZKA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR244ZKA
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR979XBX
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB641FEP
fragmentation methods: sonication (generic)
size range: 200-600

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

value: uterus

value: 53 year

value: ENCBS754FVJ at ENCODE; https://www.encodeproject.org/ENCBS754FVJ/


title: Histone ChIP-seq from uterus (ENCLB125QQP)

description:
https://www.encodeproject.org/experiments/ENCSR244ZKA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR244ZKA
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR979XBX
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB125QQP
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue

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


title: icSHAPE from HepG2 (ENCLB458WVF)

description:
https://www.encodeproject.org/experiments/ENCSR286LXS/
***************
biological replicate number: 3
technical replicate number: 1
description: icSHAPE control (DMSO) on HepG2 immortalized cell line
experiment encode accession: ENCSR286LXS
assay title: icSHAPE
assembly: GRCh38
encode release date: 2019-05-13
lab: Rob Spitale, UCI
library encode accession: ENCLB458WVF
size range: >200

value: cell line

value: This sample corresponds to the untreated icSHAPE from HepG2 cell line

value: hepatocellular carcinoma

value: child

value: 15 year

value: Rob Spitale, UCI

value: ATCC

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical;

value: ENCBS208CBB at ENCODE; https://www.encodeproject.org/ENCBS208CBB/

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


title: icSHAPE from HepG2 (ENCLB272CLY)

description:
https://www.encodeproject.org/experiments/ENCSR286LXS/
***************
biological replicate number: 2
technical replicate number: 1
description: icSHAPE control (DMSO) on HepG2 immortalized cell line
experiment encode accession: ENCSR286LXS
assay title: icSHAPE
assembly: GRCh38
encode release date: 2019-05-13
lab: Rob Spitale, UCI
library encode accession: ENCLB272CLY
size range: >200

value: This sample corresponds to the untreated icSHAPE control from HepG2 cell line

value: male

value: ENCBS966ODK at ENCODE; https://www.encodeproject.org/ENCBS966ODK/


title: Histone ChIP-seq from right atrium auricular region (ENCLB945ZBH)

description:
https://www.encodeproject.org/experiments/ENCSR250AAV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR250AAV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR195BZZ
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB945ZBH
fragmentation methods: sonication (generic)
size range: 200-600

value: right atrium auricular region

value: EnTEX:Heart - Atrial Appendage

value: adult

value: Bradley Bernstein, Broad

value: 53 year

value: female

value: ENCBS493WOF at ENCODE; https://www.encodeproject.org/ENCBS493WOF/


title: icSHAPE from GM12878 (ENCLB659BXU)

description:
https://www.encodeproject.org/experiments/ENCSR052BBY/
***************
biological replicate number: 2
technical replicate number: 1
description: icSHAPE control (DMSO) on GM12878 immortalized cell line
experiment encode accession: ENCSR052BBY
assay title: icSHAPE
assembly: GRCh38
encode release date: 2019-05-13
lab: Rob Spitale, UCI
library encode accession: ENCLB659BXU
size range: >200

source_name: Homo sapiens GM12878 cell line treated with dimethyl sulfoxide

value: cell line

value: This sample corresponds to the untreated icSHAPE control from GM12878 cell line

value: unknown

value: ENCBS584ZED at ENCODE; https://www.encodeproject.org/ENCBS584ZED/

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


title: TF ChIP-seq from transverse colon (ENCLB790KRA)

description:
https://www.encodeproject.org/experiments/ENCSR236YGF/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR236YGF
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828XQV
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB790KRA
fragmentation methods: sonication (generic)
size range: 200-600

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

value: CTCF

value: transverse colon

value: tissue

value: EnTEX:Colon - Transverse

value: ENCBS765HGS at ENCODE; https://www.encodeproject.org/ENCBS765HGS/

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


title: TF ChIP-seq from transverse colon (ENCLB650NYA)

description:
https://www.encodeproject.org/experiments/ENCSR236YGF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR236YGF
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828XQV
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB650NYA
fragmentation methods: sonication (generic)
size range: 200-600


title: Control ChIP-seq from adrenal gland (ENCLB237WUX)

description:
https://www.encodeproject.org/experiments/ENCSR234FYG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR234FYG
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB237WUX
size range: 200-600

source_name: Homo sapiens female adult (51 year) adrenal gland tissue

value: adrenal gland

value: EnTEX:Adrenal Gland

value: 51 year

value: Kristin Ardlie

value: ENCBS458UEH at ENCODE; https://www.encodeproject.org/ENCBS458UEH/

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


title: Histone ChIP-seq from transverse colon (ENCLB636AGV)

description:
https://www.encodeproject.org/experiments/ENCSR047JMV/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR047JMV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828XQV
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB636AGV
fragmentation methods: sonication (generic)
size range: 200-600

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

value: female

value: adult

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS280DYM at ENCODE; https://www.encodeproject.org/ENCBS280DYM/


title: Histone ChIP-seq from spleen (ENCLB160VAZ)

description:
https://www.encodeproject.org/experiments/ENCSR272CIV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR272CIV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR711URW
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB160VAZ
fragmentation methods: sonication (generic)
size range: 200-600

value: spleen

value: ENCBS363GBQ at ENCODE; https://www.encodeproject.org/ENCBS363GBQ/


title: TF ChIP-seq from transverse colon (ENCLB775VMU)

description:
https://www.encodeproject.org/experiments/ENCSR236YGF/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR236YGF
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828XQV
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB775VMU
fragmentation methods: sonication (generic)
size range: 200-600

value: CTCF

value: transverse colon

value: tissue


title: D8b - day 8

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

description:
D8b
Timecourse_combined_dge.txt
Drop-Seq

data_processing:
Initial Drop-seq (Macosko et al., 2015) data processing was performed using Drop-seq_tools-1.0.1 following the protocol described by Nemesh)(seqAlignmentCookbook_v1.2Jan2016.pdf, http://mccarrolllab.com/dropseq).
Reads were aligned to the hg19 (Human) reference genome concatenated with ERCC annotations using STAR-2.5.3a with the Gencode21 (Human) as reference transcriptome.
Uniquely mapped reads, with ≤ 1 insertion or deletion, were used in quantification. Finally, the DigitalExpression tool was used to obtain the digital gene expression (DGE) matrix for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: DGE matrix in .txt format

molecule: polyA RNA

source_name: Endometrial stromal cells

extract_protocol:
Endometrial pipelle biopsies were dissociated as described previously (Barros, Brosens and Brighton (2016) Isolation and Primary Culture of Various Cell Types from Whole Human Endometrial Biopsies, Bio-Protocol: 6(22); DOI:   10.21769/BioProtoc.2028)
Cells in suspension were captured and lysed singly in nanoliter droplets, as described by Macosko et al (Cell. 2015 May 21;161(5):1202-1214. doi: 10.1016/j.cell.2015.05.002. PMID: 26000488).
Libraries were prepared as described by Macosko et al (Cell. 2015 May 21;161(5):1202-1214. doi: 10.1016/j.cell.2015.05.002. PMID: 26000488).

tag: tissue

value: Endometrial stromal cells

tag: patient id

tag: lh+

tag: bmi

tag: live-births

tag: 1st trimester losses

tag: sample type

value: Stromal cell culture

tag: sample processing

value: tissue dissociation, culture establishment and decidualisation


title: TF ChIP-seq from transverse colon (ENCLB415IEO)

description:
https://www.encodeproject.org/experiments/ENCSR236YGF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR236YGF
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828XQV
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB415IEO
fragmentation methods: sonication (generic)
size range: 200-600
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

tag: antibody

tag: description

value: EnTEX:Colon - Transverse

tag: biosample encode accession

tag: Sex

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


title: D2b - day 2

description:
D2b
Timecourse_combined_dge.txt
Drop-Seq

tag: age


title: Histone ChIP-seq from spleen (ENCLB385LMV)

description:
https://www.encodeproject.org/experiments/ENCSR272CIV/
***************
biological replicate number: 2
technical replicate number: 3
description:
experiment encode accession: ENCSR272CIV
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR711URW
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB385LMV
fragmentation methods: sonication (generic)
size range: 200-600

tag: dev stage

value: 51 year

tag: lab

tag: source

value: Kristin Ardlie

tag: link

value: ENCBS892ESJ at ENCODE; https://www.encodeproject.org/ENCBS892ESJ/


title: WD - withdrawal

description:
WD
Timecourse_combined_dge.txt
Drop-Seq

tag: tissue


title: D0a - day 0

description:
D0a
Timecourse_combined_dge.txt
Drop-Seq

tag: patient id


title: D2a - day 2

description:
D2a
Timecourse_combined_dge.txt
Drop-Seq

tag: lh+


title: Control ChIP-seq from adrenal gland (ENCLB801PJX)

description:
https://www.encodeproject.org/experiments/ENCSR234FYG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR234FYG
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2018-12-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB801PJX
size range: 200-600

value: adrenal gland

value: EnTEX:Adrenal Gland

value: female

value: adult

value: ENCBS458UEH at ENCODE; https://www.encodeproject.org/ENCBS458UEH/

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


title: TF ChIP-seq from spleen (ENCLB965DWZ)

description:
https://www.encodeproject.org/experiments/ENCSR225YGX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR225YGX
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR803JPO
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB965DWZ
fragmentation methods: sonication (generic)
size range: 200-600

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

value: CTCF

value: spleen

value: male

value: 54 year

value: Bradley Bernstein, Broad

value: ENCBS223WIE at ENCODE; https://www.encodeproject.org/ENCBS223WIE/

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


title: TF ChIP-seq from spleen (ENCLB479CHP)

description:
https://www.encodeproject.org/experiments/ENCSR225YGX/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR225YGX
assay title: TF ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR803JPO
encode release date: 2019-09-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB479CHP
fragmentation methods: none
size range: 200-600

value: tissue


title: D6 - day 6

description:
D6
Timecourse_combined_dge.txt
Drop-Seq

value: Endometrial stromal cells

tag: bmi

value: Stromal cell culture

value: tissue dissociation, culture establishment and decidualisation


title: D0b - day 0

description:
D0b
Timecourse_combined_dge.txt
Drop-Seq

tag: live-births


title: Histone ChIP-seq from breast epithelium (ENCLB646JPQ)

description:
https://www.encodeproject.org/experiments/ENCSR224STY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR224STY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR620GYX
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB646JPQ
fragmentation methods: sonication (generic)
size range: 200-600

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

value: breast epithelium

value: EnTEX:Breast - Mammary Tissue updated Feb 2019 with updated term name and ID from DCC.

value: 37 year

value: Kristin Ardlie

value: ENCBS706JPK at ENCODE; https://www.encodeproject.org/ENCBS706JPK/

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


title: icSHAPE from GM12878 (ENCLB052QDC)

description:
https://www.encodeproject.org/experiments/ENCSR052BBY/
***************
biological replicate number: 1
technical replicate number: 1
description: icSHAPE control (DMSO) on GM12878 immortalized cell line
experiment encode accession: ENCSR052BBY
assay title: icSHAPE
assembly: GRCh38
encode release date: 2019-05-13
lab: Rob Spitale, UCI
library encode accession: ENCLB052QDC
size range: >200

tag: line

value: cell line

value: This sample corresponds to the untreated icSHAPE control from GM12878 cell line

value: female

tag: health state

value: unknown

value: adult

value: Rob Spitale, UCI

value: ATCC

tag: treatments

value: treatment_term_id:CHEBI:28262; treatment_term_name:dimethyl sulfoxide; treatment_type:chemical;

value: ENCBS434ZBE at ENCODE; https://www.encodeproject.org/ENCBS434ZBE/

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


title: D0 - day 0

description:
D0
Timecourse_combined_dge.txt
Drop-Seq

value: Endometrial stromal cells

tag: 1st trimester losses

tag: sample type

value: Stromal cell culture

tag: sample processing

value: tissue dissociation, culture establishment and decidualisation


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB234PIW)

description:
https://www.encodeproject.org/experiments/ENCSR219QSM/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR219QSM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR728EIP
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB234PIW
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens male adult (54 years) gastroesophageal sphincter tissue

tag: antibody

value: gastroesophageal sphincter

value: tissue

tag: description

value: EnTEX:Esophagus - Gastroesophageal Junction

tag: biosample encode accession

tag: Sex

value: male

value: 54 year

value: Bradley Bernstein, Broad

value: ENCBS542QYP at ENCODE; https://www.encodeproject.org/ENCBS542QYP/

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


title: D2 - day 2

description:
D2
Timecourse_combined_dge.txt
Drop-Seq

tag: age


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB197SSJ)

description:
https://www.encodeproject.org/experiments/ENCSR219QSM/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR219QSM
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR728EIP
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB197SSJ
fragmentation methods: sonication (generic)
size range: 200-600

tag: dev stage

value: adult

tag: lab

tag: source

value: Kristin Ardlie

tag: link


title: Patient 6

description:
P6
Biopsy_combined_dge.txt
Drop-Seq

source_name: Endometrial biopsy

tag: tissue

value: Endometrial biopsy

tag: patient id

tag: lh+

tag: bmi

value: Freshly processed biopsy tissue

value: tissue dissociation


title: Patient 5

description:
P5
Biopsy_combined_dge.txt
Drop-Seq

tag: live-births


title: Histone ChIP-seq from breast epithelium (ENCLB406QGY)

description:
https://www.encodeproject.org/experiments/ENCSR224STY/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR224STY
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR620GYX
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB406QGY
fragmentation methods: sonication (generic)
size range: 200-600

value: breast epithelium

value: EnTEX:Breast - Mammary Tissue updated Feb 2019 with updated term name and ID from DCC.

value: 37 year

value: ENCBS706JPK at ENCODE; https://www.encodeproject.org/ENCBS706JPK/

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


title: Control ChIP-seq from testis (ENCLB710KBQ)

description:
https://www.encodeproject.org/experiments/ENCSR215WNN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR215WNN
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB710KBQ
size range: 200-600

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

value: testis

value: tissue

value: ENCBS631HJF at ENCODE; https://www.encodeproject.org/ENCBS631HJF/


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB425BGH)

description:
https://www.encodeproject.org/experiments/ENCSR204TAU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR204TAU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR514EZP
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB425BGH
fragmentation methods: none
size range: 200-600

value: esophagus squamous epithelium

value: EnTEX:Esophagus - Mucosa

value: female

value: 51 year

value: ENCBS821VGX at ENCODE; https://www.encodeproject.org/ENCBS821VGX/

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


title: Patient 4

description:
P4
Biopsy_combined_dge.txt
Drop-Seq

value: Endometrial biopsy

tag: 1st trimester losses


title: Control ChIP-seq from testis (ENCLB203NFL)

description:
https://www.encodeproject.org/experiments/ENCSR215WNN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR215WNN
assay title: Control ChIP-seq
assembly: GRCh38, hg19
encode release date: 2017-08-28
lab: Bradley Bernstein, Broad
library encode accession: ENCLB203NFL
size range: 200-600

value: male

value: adult

value: Bradley Bernstein, Broad

value: Kristin Ardlie


title: Patient 3

description:
P3
Biopsy_combined_dge.txt
Drop-Seq

tag: sample type

value: Freshly processed biopsy tissue

value: tissue dissociation


title: Histone ChIP-seq from stomach (ENCLB327JDY)

description:
https://www.encodeproject.org/experiments/ENCSR204OJS/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR204OJS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR962EJE
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB327JDY
fragmentation methods: sonication (generic)
size range: 200-600

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

value: stomach

value: 54 year

value: ENCBS443LLE at ENCODE; https://www.encodeproject.org/ENCBS443LLE/

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


title: Histone ChIP-seq from stomach (ENCLB176NYE)

description:
https://www.encodeproject.org/experiments/ENCSR204OJS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR204OJS
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR962EJE
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB176NYE
fragmentation methods: sonication (generic)
size range: 200-600

value: tissue


title: D4 - day 4

description:
D4
Timecourse_combined_dge.txt
Drop-Seq

value: Endometrial stromal cells

value: Stromal cell culture

tag: sample processing

value: tissue dissociation, culture establishment and decidualisation


title: Histone ChIP-seq from esophagus muscularis mucosa (ENCLB534SWF)

description:
https://www.encodeproject.org/experiments/ENCSR200AFX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR200AFX
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR545WFH
encode release date: 2019-08-01
lab: Bradley Bernstein, Broad
library encode accession: ENCLB534SWF
fragmentation methods: sonication (generic)
size range: 200-600

source_name: Homo sapiens female adult (51 year) esophagus muscularis mucosa tissue

tag: antibody

value: esophagus muscularis mucosa

value: EnTEX:Esophagus - Muscularis

value: female

value: 51 year

value: ENCBS955ZON at ENCODE; https://www.encodeproject.org/ENCBS955ZON/


title: Patient 1

description:
P1
Biopsy_combined_dge.txt
Drop-Seq

value: Endometrial biopsy


title: Histone ChIP-seq from esophagus squamous epithelium (ENCLB338ENB)

description:
https://www.encodeproject.org/experiments/ENCSR204TAU/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR204TAU
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR514EZP
encode release date: 2019-09-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB338ENB
fragmentation methods: sonication (generic)
size range: 200-600

value: esophagus squamous epithelium

tag: description

value: EnTEX:Esophagus - Mucosa

value: adult

value: Bradley Bernstein, Broad

value: Kristin Ardlie

value: ENCBS821VGX at ENCODE; https://www.encodeproject.org/ENCBS821VGX/

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


title: D8 - day 8

description:
D8
Timecourse_combined_dge.txt
Drop-Seq


title: Patient 2

description:
P2
Biopsy_combined_dge.txt
Drop-Seq

value: Freshly processed biopsy tissue

value: tissue dissociation


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB714BVB)

description:
https://www.encodeproject.org/experiments/ENCSR195JWZ/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR195JWZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR728EIP
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB714BVB
fragmentation methods: sonication (generic)
size range: 200-600

value: gastroesophageal sphincter

value: tissue

value: EnTEX:Esophagus - Gastroesophageal Junction

tag: biosample encode accession

value: male

value: 54 year

value: ENCBS542QYP at ENCODE; https://www.encodeproject.org/ENCBS542QYP/

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


title: ra1612_099

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

description:
102939-001-099
Mild asthmatic (after RV16)

data_processing:
The reference of ‘Homo_sapiens.GRCh37.75’ was used to align the reads. The mapping to the reference sequence was done using a short reader aligner based on Burrows-Wheeler transform.
Clustering and DNA sequencing were performed according to the manufacturer’s protocol using the Illumina NextSeq 500.
The reads were trimmed for adapter sequences using Trimmomatic v0.30 before the alignment.
The read counts were loaded into the DESeq2 package, a statistical package within the R/BioConductor platform to determine the differentially expressed genes (paired).
Image analysis, base calling and quality check were performed with Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.count.txt: Tab-delimited text files include curated counts of genes in each sample.

source_name: primary bronchial epithelial cells

extract_protocol:
The pellet was dissolved in 1 ml of TRIzol™ and stored at -80°C until RNA was isolated. After all samples were obtained, they were thawed at room temperature, and after 200 µl of chloroform was added, shaken vigorously for 30 seconds. The samples were kept at RT for 10 mins and centrifuged at 16,000g for 15 mins at 4°C. The aqueous phase was cleaned up and concentrated with protocol 5.3 using the Nucleospin® RNA XS extraction kit (Macherey-Nagel). No carrier RNA was added as it would interfere with RNA sequencing.
The NEBNext Ultra Directional RNA library prep kit for Illumina was used to process the samples. The samples preparation was performed according to the protocol “NEBNext Ultra Directional RNA Library Prep Kit for Illumina” (NEB #7420S/L). Briefly, oligo-dT magnetic beads were used to isolate mRNA from total RNA. cDNA synthesis was performed after fragmentation of this mRNA. This was used for ligation with sequencing adapters followed by PCR amplification of the resulting product. The quality and yield after sample preparation was measured with the fragment analyser. The size of the resulting products was consistent with the expected size distribution between 300-500 base pairs. To evaluate the quality of the library preparation and kits used, the raw data was sampled and mapped to annotated genomic references. Mapping positions were classified as intragenic, exonic, intergenic, intronic and rRNA. Clustering and DNA sequencing were performed according to the manufacturer’s protocol using the Illumina NextSeq 500. A concentration of 1.6pM was used as input. The reads were trimmed for adapter sequences using Trimmomatic v0.30 before the alignment. Presumed adapter sequences were removed from the read when the bases matched a sequence in the adapter sequence set (TruSeq adapters) with 2 or less mismatches and an alignment score of at least 12.

tag: cell type

value: primary bronchial epithelial cells

tag: collection method

value: direct bronchoscopy

tag: disease status

value: Mild asthmatic

tag: infection

value: rhinovirus (RV16)


title: Histone ChIP-seq from gastroesophageal sphincter (ENCLB840BOD)

description:
https://www.encodeproject.org/experiments/ENCSR195JWZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR195JWZ
assay title: Histone ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR728EIP
encode release date: 2019-02-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB840BOD
fragmentation methods: sonication (generic)
size range: 200-600

tag: Sex

tag: dev stage

value: adult

tag: age

tag: lab

value: Bradley Bernstein, Broad

tag: source


title: ra1612_097

description:
102939-001-097
Mild asthmatic (after RV16)