title: ChIP-seq from GM12878 (ENCLB163DKG)

description:
https://www.encodeproject.org/experiments/ENCSR142REC/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR142REC
assay title: ChIP-seq
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB163DKG
size range: 200-600

value: Control

value: immortalized cell line

value: adult

value: female

value: unknown

value: Bradley Bernstein, Broad

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


title: 4cell-1b

status: Public on Mar 09 2017

type: SRA

city: Boston

first: Xiaoji

last: Wu

state: MA

address: 149G Warren Alpert Building, 200 Longwood Avenue

department: PCMM

country: USA

institute: Boston Children's Hospital

library_source: genomic

data_processing:
Reads were trimmed by Trim Galore package.
Trimmed reads were aligned using Bismark package.
CpG sites containing SNPs were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: The processed bed files are tab-delimited data with the following eight columns: chromosome, start, end, level of signal (BS-seq or MAB-seq), C, T, strand, coverage.

molecule: genomic DNA

organism: Mus musculus

source_name: Single 4-cell blastomere

growth_protocol: Mice were maintained following the guidelines of the Institutional Animal Care and Use Committee at Harvard Medical School. Cell lines were maintained as discussed in methods and materials of the paper.

extract_protocol:
For scMAB-seq and liMAB-seq, the samples were lysed using lysis buffer. For regular MAB-seq and BS-seq, the starting material is purified genomic DNA.
MAB-seq samples were prepared using RRBS strategy or PBAT strategy. BS-seq samples of sperm and paternal pronuclei were prepared using RRBS strategy.

tag: tissue

value: Single mouse 4-cell blastomere

tag: genotype

value: Wild type


title: ChIP-seq from neural progenitor cell (ENCLB800FFW)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR139PIA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR139PIA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR603SVD
encode release date: 2016-06-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB800FFW
size range: 200-600
nucleic acid starting quantity: 10.8
nucleic acid starting quantity units: ng

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

organism: Homo sapiens

source_name: Homo sapiens neural progenitor in vitro differentiated cells female embryo (5 days) derived from H9

tag: antibody

value: neural progenitor cell

value: in vitro differentiated cells

tag: description

value: Frozen or fixed, in vitro specified neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

tag: biosample encode accession

tag: age

value: 5 day

tag: dev stage

value: embryonic

tag: Sex

tag: health state

value: healthy

tag: lab

value: Richard Myers, HAIB

tag: link

value: ENCBS018TPT at ENCODE; https://www.encodeproject.org/ENCBS018TPT/

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


title: 4cell-1a


title: 4cell-1c


title: ChIP-seq from radial glial cell (ENCLB460PBY)

description:
https://www.encodeproject.org/experiments/ENCSR136NUH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR136NUH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR689ICI
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB460PBY
size range: 200-600

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

value: radial glial cell

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

tag: passage number

value: ENCBS008AOU at ENCODE; https://www.encodeproject.org/ENCBS008AOU/


title: DnmtTKO-ESC-liMAB-rep2

source_name: Mouse embryonic stem cells

value: Around 100 mouse embryonic stem cells, J1

value: Dnmt TKO


title: 2cell-liMAB

source_name: 2-cell embryos

value: Around 50 mouse 2-cell embryos


title: 2cell-9a

source_name: Single 2-cell blastomere

value: Single mouse 2-cell blastomere


title: ChIP-seq from smooth muscle cell (ENCLB440JXQ)

description:
https://www.encodeproject.org/experiments/ENCSR130IMV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR130IMV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB440JXQ
size range: 200-600

source_name: Homo sapiens smooth muscle in vitro differentiated cells female embryo (5 days) derived from H9

value: smooth muscle cell

value: Frozen or fixed, in vitro differentiated smooth muscle cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: female

value: ENCBS899TTJ at ENCODE; https://www.encodeproject.org/ENCBS899TTJ/


title: ChIP-seq from smooth muscle cell (ENCLB275RJO)

description:
https://www.encodeproject.org/experiments/ENCSR130IMV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR130IMV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB275RJO
size range: 200-600
nucleic acid starting quantity: 77.25
nucleic acid starting quantity units: ng

value: in vitro differentiated cells

value: 5 day


title: 2cell-8a

value: Wild type


title: 4cell-2d-PBAT-MAB

value: Single mouse 4-cell blastomere


title: ChIP-seq from neural progenitor cell (ENCLB177VVW)

description:
https://www.encodeproject.org/experiments/ENCSR139PIA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR139PIA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR603SVD
encode release date: 2016-06-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB177VVW
size range: 200-600
nucleic acid starting quantity: 9.68
nucleic acid starting quantity units: ng

value: neural progenitor cell

value: Frozen or fixed, in vitro specified neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS018TPT at ENCODE; https://www.encodeproject.org/ENCBS018TPT/


title: 2cell-7a


title: 2cell-6a


title: 2cell-5b


title: ChIP-seq from Peyer's patch (ENCLB382FTZ)

description:
https://www.encodeproject.org/experiments/ENCSR124GAS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR124GAS
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB382FTZ
size range: 200-600

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

value: Control

value: Peyer's patch

value: tissue

value: EnTEX:Small Intestine - Terminal Ileum

value: adult

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS766ILR at ENCODE; https://www.encodeproject.org/ENCBS766ILR/

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


title: 2cell-4a

value: Single mouse 2-cell blastomere

value: Wild type


title: ChIP-seq from SK-N-SH (ENCLB442NJI)

description:
https://www.encodeproject.org/experiments/ENCSR121INC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR121INC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2017-01-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB442NJI
size range: 200-600

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

tag: line

value: SK-N-SH

value: immortalized cell line

value: 4 year

value: child

value: female

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

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

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


title: 2cell-3b


title: 2cell-3a


title: ChIP-seq from MM.1S (ENCLB510QDT)

description:
https://www.encodeproject.org/experiments/ENCSR120LGC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR120LGC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR264HOB
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB510QDT
size range: 300-600
nucleic acid starting quantity: 299.2
nucleic acid starting quantity units: ng

source_name: Homo sapiens MM.1S immortalized cell line

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

value: 42 year

value: immunoglobulin A lambda myeloma

value: ENCBS981ZAE at ENCODE; https://www.encodeproject.org/ENCBS981ZAE/

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

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


title: ChIP-seq from SK-N-SH (ENCLB463NVD)

description:
https://www.encodeproject.org/experiments/ENCSR121INC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR121INC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2017-01-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB463NVD
size range: 200-600

value: Bradley Bernstein, Broad

value: ENCBS018DDZ at ENCODE; https://www.encodeproject.org/ENCBS018DDZ/


title: 2cell-1b

value: Single mouse 2-cell blastomere

value: Wild type


title: 2cell-2a


title: ChIP-seq from SUDHL6 (ENCLB580RBM)

description:
https://www.encodeproject.org/experiments/ENCSR114GLZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR114GLZ
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR179YLS
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB580RBM
size range: 200-600

source_name: Homo sapiens SUDHL6 immortalized cell line

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

value: immortalized cell line

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

value: 43 year

value: adult

value: male

value: ENCBS136LHJ at ENCODE; https://www.encodeproject.org/ENCBS136LHJ/

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

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


title: 2cell-1a


title: ChIP-seq from mid-neurogenesis radial glial cells (ENCLB561NTM)

description:
https://www.encodeproject.org/experiments/ENCSR113LFZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR113LFZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR287XMW
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB561NTM
size range: 200-600

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

value: mid-neurogenesis radial glial cells

value: in vitro differentiated cells

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

value: embryonic

value: female

value: 5 day

value: healthy

value: ENCBS355KGI at ENCODE; https://www.encodeproject.org/ENCBS355KGI/

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


title: ChIP-seq from SK-N-MC (ENCLB361FKJ)

description:
https://www.encodeproject.org/experiments/ENCSR111QAW/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against H3K9ac using SK-N-MC cell line which was previously described as a neuroepithelioma (ATCC HTB-10). However recent evidence reveals it is Ewing's Sarcoma (www.ncbi.nlm.nih.gov/pubmed/15548687, www.ncbi.nlm.nih.gov/pubmed/25453903, www.ncbi.nlm.nih.gov/biosample/3151999).
experiment encode accession: ENCSR111QAW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR899XXQ
encode release date: 2017-01-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB361FKJ
size range: 200-600
nucleic acid starting quantity: 84
nucleic acid starting quantity units: ng

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

value: SK-N-MC

value: immortalized cell line

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

value: child

value: 14 year

value: Ewing's sarcoma

value: Bradley Bernstein, Broad

value: ENCBS273LIC at ENCODE; https://www.encodeproject.org/ENCBS273LIC/

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


title: ChIP-seq from smooth muscle cell (ENCLB201ZGA)

description:
https://www.encodeproject.org/experiments/ENCSR130IMV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR130IMV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB201ZGA
size range: 200-600

value: smooth muscle cell

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated smooth muscle cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: Richard Myers, HAIB

value: ENCBS780PCJ at ENCODE; https://www.encodeproject.org/ENCBS780PCJ/


title: ChIP-seq from SK-N-MC (ENCLB338VPC)

description:
https://www.encodeproject.org/experiments/ENCSR111QAW/
***************
biological replicate number: 2
technical replicate number: 2
description: ChIP-seq against H3K9ac using SK-N-MC cell line which was previously described as a neuroepithelioma (ATCC HTB-10). However recent evidence reveals it is Ewing's Sarcoma (www.ncbi.nlm.nih.gov/pubmed/15548687, www.ncbi.nlm.nih.gov/pubmed/25453903, www.ncbi.nlm.nih.gov/biosample/3151999).
experiment encode accession: ENCSR111QAW
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR899XXQ
encode release date: 2017-01-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB338VPC
size range: 200-600

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

value: female

value: ENCBS203EZT at ENCODE; https://www.encodeproject.org/ENCBS203EZT/

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


title: 2cell-18b

value: Single mouse 2-cell blastomere

value: Wild type


title: 2cell-5a


title: 2cell-17b


title: 2cell-18a


title: ChIP-seq from hepatocyte (ENCLB039ZAJ)

description:
https://www.encodeproject.org/experiments/ENCSR107PGG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR107PGG
assay title: ChIP-seq
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB039ZAJ
size range: 200-600

source_name: Homo sapiens hepatocyte in vitro differentiated cells female embryo (5 days) derived from H9

value: Control

value: hepatocyte

value: Frozen or fixed, in vitro differentiated hepatocyte-like cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: healthy

value: ENCBS077RUJ at ENCODE; https://www.encodeproject.org/ENCBS077RUJ/

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


title: ChIP-seq from hepatocyte (ENCLB565HMJ)

description:
https://www.encodeproject.org/experiments/ENCSR107PGG/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR107PGG
assay title: ChIP-seq
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB565HMJ
size range: 200-600

value: in vitro differentiated cells


title: 2cell-17a


title: ChIP-seq from SK-N-SH (ENCLB219ECM)

description:
https://www.encodeproject.org/experiments/ENCSR125IJY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR125IJY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2016-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB219ECM
size range: 200-600

value: SK-N-SH

value: immortalized cell line

value: 4 year

value: child

value: Bradley Bernstein, Broad

value: ENCBS500EWH at ENCODE; https://www.encodeproject.org/ENCBS500EWH/

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

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


title: ChIP-seq from neural cell (ENCLB520XPR)

description:
https://www.encodeproject.org/experiments/ENCSR124VOE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR124VOE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR308JFE
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB520XPR
size range: 200-600

source_name: Homo sapiens neural in vitro differentiated cells male embryo

value: neural cell

value: male

value: unknown

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

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


title: 2cell-15a

value: Single mouse 2-cell blastomere

value: Wild type


title: ChIP-seq from hepatocyte (ENCLB154QFW)

description:
https://www.encodeproject.org/experiments/ENCSR107PGG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR107PGG
assay title: ChIP-seq
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB154QFW
size range: 200-600

value: Control

value: hepatocyte

value: Frozen or fixed, in vitro differentiated hepatocyte-like cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

value: ENCBS520VFV at ENCODE; https://www.encodeproject.org/ENCBS520VFV/

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


title: 2cell-16a


title: ChIP-seq from neural progenitor cell (ENCLB913XSR)

description:
https://www.encodeproject.org/experiments/ENCSR105NMJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR105NMJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR603SVD
encode release date: 2016-06-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB913XSR
size range: 200-600
nucleic acid starting quantity: 104.94
nucleic acid starting quantity units: ng

value: neural progenitor cell

value: in vitro differentiated cells

value: Frozen or fixed, in vitro specified neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: ENCBS018TPT at ENCODE; https://www.encodeproject.org/ENCBS018TPT/


title: ChIP-seq from gastrocnemius medialis (ENCLB019XYQ)

description:
https://www.encodeproject.org/experiments/ENCSR105YNJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR105YNJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR897RRA
encode release date: 2016-10-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB019XYQ
size range: 200-600

source_name: Homo sapiens gastrocnemius medialis tissue male adult (54 years)

value: gastrocnemius medialis

value: tissue

value: i.e. REMC 6, 13, 14 and 15; EnTEX:Muscle - Skeletal

value: adult

value: male

value: 54 year

value: Bradley Bernstein, Broad

value: ENCBS693QTT at ENCODE; https://www.encodeproject.org/ENCBS693QTT/

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


title: 2cell-14a

value: Single mouse 2-cell blastomere

value: Wild type


title: ChIP-seq from gastrocnemius medialis (ENCLB218LEF)

description:
https://www.encodeproject.org/experiments/ENCSR105YNJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR105YNJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR897RRA
encode release date: 2016-10-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB218LEF
size range: 200-600


title: ChIP-seq from coronary artery (ENCLB498QZF)

description:
https://www.encodeproject.org/experiments/ENCSR122GIL/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR122GIL
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB498QZF
size range: 200-600

source_name: Homo sapiens coronary artery tissue female adult (53 years)

value: Control

value: coronary artery

value: EnTEX:Artery - Coronary

value: female

value: 53 year

value: ENCBS474IPU at ENCODE; https://www.encodeproject.org/ENCBS474IPU/

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


title: 2cell-2b


title: ChIP-seq from neural progenitor cell (ENCLB240HBB)

description:
https://www.encodeproject.org/experiments/ENCSR105NMJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR105NMJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR603SVD
encode release date: 2016-06-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB240HBB
size range: 200-600

value: neural progenitor cell

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated neural progenitor cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS044KWE at ENCODE; https://www.encodeproject.org/ENCBS044KWE/

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


title: ChIP-seq from radial glial cell (ENCLB376KNS)

description:
https://www.encodeproject.org/experiments/ENCSR104BSN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR104BSN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR689ICI
encode release date: 2017-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB376KNS
size range: 200-600

value: radial glial cell

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

value: Bradley Bernstein, Broad

value: ENCBS008AOU at ENCODE; https://www.encodeproject.org/ENCBS008AOU/


title: ChIP-seq from body of pancreas (ENCLB346ISX)

description:
https://www.encodeproject.org/experiments/ENCSR099LGH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR099LGH
assay title: ChIP-seq
encode release date: 2016-05-26
lab: Bradley Bernstein, Broad
library encode accession: ENCLB346ISX
size range: 200-600

source_name: Homo sapiens body of pancreas tissue male adult (54 years)

value: Control

value: body of pancreas

value: tissue

value: adult

value: male

value: 54 year

value: ENCBS209WBW at ENCODE; https://www.encodeproject.org/ENCBS209WBW/

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


title: RRBS_5AC_3

city: Olso

first: Jorke

last: Kamstra

address: Ullevålsveien 72

department: Basic Sciences and Aquatic Medicine

country: Norway

institute: Norwegian University of Life Sciences

description: processed data file: RRBSresults.xlsx

data_processing:
Trimming was performed with trim_galore (v0.4.0) with the following parameters:  RRBS: trim_galore --quality 20 --phred64 --paired --three_prime_clip_R1 10 --clip_R2 5 --three_prime_clip_R2 10 --fastqc –rrbs  BisPCR2:  trim_galore –fastqc --paired --clip_R1 20 --clip_R2 20
Bismark (0.14.5) mapping was performed with the following parameters:   bismark –bowtie2 -N 0 -L 30 --score_min L,0,-0,6
Sorted bismark.sam files were imported in MethylKit (v 0.9.2) with the read.bismark function, only allowing sequence reads with a phred score higher than 20 and minimum 5 reads per CpG. Next, samples were filtered by excluding reads above the 99.9 percentile, since these reads are either mapped against repeat elements or have very high PCR bias. Two strategies were taken to assess differential methylation. First, differentially methylated regions (DMRs) were found by dividing the genome in regions of 300 bp, with at least 4 Cs analyzed with at least 5 reads. With this analysis, DMRs were detected using a FDR cut off of 1% and a methylation difference of at least 10%. These probes were used for downstream analysis pathway analysis (see supplemental excel files CvsMEHP.xlsx and Cvs5AC.xlsx).
Data from Bismark methylation extractor loaded into Seqmonk (v0.33) genome browser. (used to feature enrichment)
BisPCR2:Data from Bismark methylation extractor loaded into Seqmonk (v0.33) genome browser. Used the logistic regression filter in R to assess differential methylation
Genome_build: GRCz10
Supplementary_files_format_and_content: Processed data files are in excel format. They represent differential methylated sites or regions, as analyzed by Seqmonk or MethylKit.

organism: Danio rerio

source_name: 6 dpf whole zebrafish embryos

extract_protocol:
Precipitation and purification of genomic DNA was performed with the Gentra puregene tissue DNA extraction kit (Qiagen, Germany). Pools of zebrafish (10 and 2 embryos, for 6 and 15 dpf, respectively) and tissues were snap frozen in liquid nitrogen. Prior to DNA extraction the pools of zebrafish embryos and tissues were disrupted in 300 µL lysis buffer with a 20G needle, followed by an overnight incubation at 65°C with 1.5 µL of proteinase K (Qiagen, Germany) and 1.5 µL of RNAse A (20 mg/mL) (Life Technologies, Germany). After the incubation an extra 1.5 µL of RNAse was added and samples were incubated at room temperature for 1 hour. Proteins were precipitated with protein precipitation buffer (Qiagen, Germany) and DNA was precipitated by adding 0.5 mL isopropanol and 90 µL 3M NaAc (pH 5.3). After centrifugation (1 min, 13000 rpm), the pellet was washed twice with 70% ethanol, followed by rehydration in TE buffer. Samples were stored at -20°C until further analysis. Quality of DNA was assessed by gel electroforeses for fragmentation and RNA contamination, and quantity and purity by nanodrop (ND-1000, Thermo Scientific, Germany).
Genomic DNA was measured with the Quant-it Picogreen dsDNA assay (Thermo Fischer) and 1 µg total genomic DNA was digested overnight with MSP1 at 37°C. Digestions were terminated by adding 0.5M EDTA and digested DNA was purified on a GeneJET PCR purification column (Thermo Fischer). Libraries were made using the NEBNext Ultra DNA library preparation kit for Illumina, including methylated index adapters. Adapter ligated fragments were bisulfite converted using the zymo EZ DNA Methylation Gold kit (Zymo Research, US), followed by 14 cycles of PCR. PCR products were purified suing AMPure XP beads and quality was assessed on a Bioanalyzer (Agilent, Belgium), using a High sensitivity DNA chip (Agilent, Belgium). Concentrations of the library were measured by QPCR. Samples were pooled in equal concentrations and sequencing was performed on an Illumina HiSeq2500 in paired end (2x100pb)
We developed primers for a random subset of DMCs. We used the recently developed bisPCR2 method which uses two rounds of PCR [1]. One round is used for amplifying PCR products with primers with illumina adapter overhangs. In a second PCR all amplicons of one sample are pooled in equal amounts (gel electrophoresis intensity bands) and are subjected to PCR with specific indices and standard illumina library primers. Bernstein et al reported 48 primer indices in their method, which we all used. We followed the method with slight deviations. First we developed primers using bisearch (http://bisearch.enzim.hu/), added the overhangs and optimized and checked the products with the type-it HRM kit (Qiagen, Germany). We checked the right product size, the Cq value of the product and the efficiency of the PCR with unmethylated to methylated control material. To produce unmethylated DNA, we subjected 50 ng of 6 dpf zebrafish genomic DNA to a whole genome amplification reaction with the repli-G kit (Qiagen, Germany) according to the manufacturer’s recommendations. Furthermore we subjected 1 µg of the same DNA sample to an M.SssI CpG methylase reaction (New England Biolabs, USA) to produce fully methylated DNA using 2 µl of NEB2 buffer, 0.5 µL of 32 mM SAM, 4 U of M.SssI in a 20 µL reaction. After 2 hr incubation at 37 ºC another 0.5 µL of SAM and 4 U of M.SssI was added to the sample and the mixture was incubated for another 4 hrs. Samples were bisulfite converted with the epitect bisulfite kit according to the manufacturer (Qiagen, Germany) and measured on nanodrop (ND-1000, Thermo Scientific) in ssDNA mode for an estimation of the concentration. Samples were diluted to 5 ng/µL and mixed in different ratios (0, 25, 50, 75 and 100%). Type-IT HRM reactions, which is the same family of TAQ as the pyromark kit (used in the  bisPCR2 method), were performed in 10 µL buffer, 700 nM primer mix and 10 ng template in 20 µL reactions. All PCR reactions were performed with a 5 min hot start and cycling condition of 95ºC 30 s, Ta 30 s, 63, 2 min (45 cycles). The optimized Ta is shown in supplementary table $$. Following PCR#1 optimization, the protocol of Bernstein et al [1] was followed using the pyromark PCR kit (Qiagen, Germany), using optimized annealing temperatures and an extension temperature of 63 ºC, which greatly enhanced Cq values and unbiased the PCR reactions with regard to methylated or unmethylated DNA. PCR#1 reactions were performed with the pyromark PCR kit (Qiagen, Germany) in 20 µL reactions (10 µL buffer, 700 nM primer mix, 20 ng DNA template) with a 15 min hot start, followed by 45 cycles of 95 ºC 30s, TaºC 30s and 63ºC for 1 min and a final extension of 10 min. After all PCR reactions were performed, amplicons were pooled. PCR#1 pools were purified using the Qiagen PCR purification kit (Qiagen, Germany) and concentrations were measured on nanodrop (ND-1000, Thermo Scientific). PCR#2 reactions were performed with index specific primers in 20 µL reactions consisting of 10 µL pyromark buffer, 700 nM index primer, 700 nM library primer and 1 ng of pooled PCR#1 product, with 15 min hot start, followed by 10 cycles of 95 ºC 30 s, 56 ºC 30 s and 63 ºC for 2 min followed by a final extension of 10 min. PCR#2 samples were purified with AMPure XP beads (Beckman Coulter, USA) according to manufacturer. Concentrations were measured using the Qubit fluorimeter (Life technologies, Norway) and calculated to nM using the formula:   c (nM) =(Qubit conc (ng/µL)*1000000)/(660*average length)  A subset of PCR#2 samples was analyzed on agilent 2100 bioanalyzer and highly comparable profiles were observed between analyzed samples (data not shown). PCR#2 samples were diluted in equimolar portions to 2 nM and next generation sequencing was performed as described earlier by Bernstein et al. After sequencing the samples were analyzed as described above. Differential methylation was calculated using logistic regression with BH FDR multiple comparisons and sites with a difference of more than 10% methylation were considered biologically relevant differences.    1. Bernstein DL, Kameswaran V, Le Lay JE, Sheaffer KL, Kaestner KH. The BisPCR2 method for targeted bisulfite sequencing. Epigenetics Chromatin. 2015;8:27.

value: whole embryos

tag: strain

value: AB strain

tag: Stage

value: 6 dpf

tag: generation

tag: treatment


title: 2cell-12a

tag: tissue

value: Single mouse 2-cell blastomere

value: Wild type


title: RRBS_5AC_4

description: processed data file: RRBSresults.xlsx


title: RRBS_5AC_2

description: processed data file: RRBSresults.xlsx


title: 2cell-11a

tag: genotype


title: ChIP-seq from MM.1S (ENCLB927FOD)

description:
https://www.encodeproject.org/experiments/ENCSR094VCE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR094VCE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR264HOB
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB927FOD
size range: 300-600
nucleic acid starting quantity: 156.74
nucleic acid starting quantity units: ng

tag: antibody

value: immortalized cell line

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

value: female

value: 42 year

value: immunoglobulin A lambda myeloma

value: ENCBS241TLI at ENCODE; https://www.encodeproject.org/ENCBS241TLI/

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

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


title: RRBS_5AC_5

description: processed data file: RRBSresults.xlsx


title: RRBS_MEHP_5

description: processed data file: RRBSresults.xlsx

value: MEHP (30 µM)


title: RRBS_MEHP_3

description: processed data file: RRBSresults.xlsx


title: ChIP-seq from HCT116 (ENCLB744LEJ)

description:
https://www.encodeproject.org/experiments/ENCSR093SHE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR093SHE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2016-12-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB744LEJ
size range: 200-600
nucleic acid starting quantity: 63.5
nucleic acid starting quantity units: ng

source_name: Homo sapiens HCT116 immortalized cell line

tag: description

value: cells obtained from ATCC; http://www.ncbi.nlm.nih.gov/pubmed?cmd=Retrieve&list_uids=7214343&dopt=AbstractPlus

value: unknown

value: male

value: colorectal carcinoma

value: Bradley Bernstein, Broad

value: ENCBS851PYB at ENCODE; https://www.encodeproject.org/ENCBS851PYB/

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

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


title: RRBS_MEHP_4

description: processed data file: RRBSresults.xlsx

value: whole embryos

value: AB strain

value: 6 dpf


title: ChIP-seq from MM.1S (ENCLB396PYS)

description:
https://www.encodeproject.org/experiments/ENCSR094VCE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR094VCE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR264HOB
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB396PYS
size range: 300-600
nucleic acid starting quantity: 88.4
nucleic acid starting quantity units: ng

value: immortalized cell line

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

tag: biosample encode accession

value: adult

value: female

value: 42 year

value: ENCBS981ZAE at ENCODE; https://www.encodeproject.org/ENCBS981ZAE/


title: 2cell-11b

value: Single mouse 2-cell blastomere

value: Wild type


title: RRBS_5AC_1

description: processed data file: RRBSresults.xlsx


title: 2cell-10a


title: RRBS_MEHP_1

description: processed data file: RRBSresults.xlsx

value: MEHP (30 µM)


title: RRBS_MEHP_2

description: processed data file: RRBSresults.xlsx


title: RRBS_Control_2

description: processed data file: RRBSresults.xlsx

value: Control (0.01% DMSO)


title: RRBS_Control_4

description: processed data file: RRBSresults.xlsx


title: 2cell-13b


title: RRBS_Control_3

description: processed data file: RRBSresults.xlsx


title: ChIP-seq from HCT116 (ENCLB571FUG)

description:
https://www.encodeproject.org/experiments/ENCSR091QXP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR091QXP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2016-12-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB571FUG
size range: 200-600

value: cells obtained from ATCC

tag: age

value: unknown

value: male

value: colorectal carcinoma

value: Bradley Bernstein, Broad

value: ENCBS847SOB at ENCODE; https://www.encodeproject.org/ENCBS847SOB/

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


title: 2cell-13a


title: ChIP-seq from smooth muscle cell (ENCLB443HPI)

description:
https://www.encodeproject.org/experiments/ENCSR090QTV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR090QTV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB443HPI
size range: 200-600

value: smooth muscle cell

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated smooth muscle cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

tag: dev stage

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS780PCJ at ENCODE; https://www.encodeproject.org/ENCBS780PCJ/

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


title: H3S10P_MEF_TPA_replicate1

city: London

first: Francesco

last: Gualdrini

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Francis Crick Institute

description: Chip-Seq

data_processing:
Wig files are those generated by MACS at 1bp resolution and a set normalised to 30 million mapped reads and to the assessed scaling factors are additionally provided.
Genome_build: MM9
Supplementary_files_format_and_content: ChipSeq: Wig files are those generated by MACS at 1bp resolution and a set normalised to 30 million mapped reads and to the assessed scaling factors are additionally provided.

source_name: Cultured MEFs (Mouse Embryonic fibroblasts)

growth_protocol: The different types of MEFs were cultured in Dulbecco modified Eagles medium (DMEM) supplemented with 10% fetal calf serum (FCS), 100 IU/ml penicillin, and 100 μ/ml streptomycin.

extract_protocol: Chip-Seq: DNA samples were end repaired, poly-A tailed and Illumina single end adapters were ligated following the standard Illumina protocol with minor adjustments. Agencourt AMPure XP beads at 0.8x ratio were used to size select out adapter dimers after adapter ligation.  The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix. Post PCR, AMPure XP beads were used at a 1:1 ratio to maintain size integrity and to allow size select on 2%Agarose gel.  Samples were finally purified with QAIquick gel extraction kit and quality controlled on the DNA 1000 BioAnalyser 2100 chip. Samples have been multiplexed and run on Hi-seq 2000/1000 (6 samples per multiplexed lane).

treatment_protocol: Cells were  starved for 48h in 0.3%FCS. Where indicated, cells were stimulated for 5 or 15 minutes minutes with 12-O-tetradecanoyl phorbol-13-acetate (Sigma TPA, 50 ng/ml).

value: normal

tag: chip antibody

value: H3S10P (Millipore, cat# 04-817)

tag: scaling factor used (reads*scaling factor)


title: ChIP-seq from smooth muscle cell (ENCLB938CUO)

description:
https://www.encodeproject.org/experiments/ENCSR090QTV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR090QTV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB938CUO
size range: 200-600

tag: Sex

value: female

tag: health state

tag: lab

value: ENCBS899TTJ at ENCODE; https://www.encodeproject.org/ENCBS899TTJ/


title: H3S10P_15min_replicate1

description: Chip-Seq


title: RRBS_Control_1

description: processed data file: RRBSresults.xlsx

value: whole embryos

value: AB strain

value: 6 dpf

value: Control (0.01% DMSO)


title: H3S10P_MEF_TPA_replicate2

description: Chip-Seq


title: ChIP-seq from MM.1S (ENCLB827VML)

description:
https://www.encodeproject.org/experiments/ENCSR086YIH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR086YIH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR264HOB
encode release date: 2016-06-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB827VML
size range: 300-600
nucleic acid starting quantity: 339.32
nucleic acid starting quantity units: ng

extract_protocol:
extraction method: see document
general protocol: https://www.encodeproject.org/documents/18f0d330-5799-45f7-babe-7728dfbd1103/@@download/attachment/Epigenomics_Mag%20Bead_ChIP_Protocol_v01.4_exp.pdf

tag: line

value: immortalized cell line

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

value: adult

value: 42 year

value: immunoglobulin A lambda myeloma

value: Bradley Bernstein, Broad

tag: link

value: ENCBS241TLI at ENCODE; https://www.encodeproject.org/ENCBS241TLI/

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

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


title: H3S10P_5min_replicate2

description: Chip-Seq

value: normal


title: H3S10P_MEF_03_replicate1

description: Chip-Seq

value: H3S10P (Millipore, cat# 04-817)


title: fkh1-dsm fkh2Δ 4C-Seq rep2

city: Los Angeles

first: Andrew

middle: Zachary

last: Ostrow

state: California

address: 1050 Childs Way

department: Biological Sciences

institute: University of Southern California

description: 4C genomic DNA

data_processing:
Barcode-splitting was performed with ea-utils.1.1.2-806
Genome alignment was performed with Bowtie2-2.2.5
Filtering and conversion of sam files to bam files was performed with samtools-0.1.19
Conversion of bam files to bed files was performed with bedtools2-2.24.0
Binning of data was performed with bedtools-2.24.0
Genome_build: Saccharomyces cerevisiae S288c; note=R64-1-1
Supplementary_files_format_and_content: Barcode-splitting was performed with ea-utils.1.1.2-806; Genome alignment was performed with Bowtie2-2.2.5; Filtering and conversion of sam files to bam files was performed with samtools-0.1.19; Conversion of bam files to bed files was performed with bedtools2-2.24.0; Binning of data was performed with bedtools-2.24.0.

organism: Saccharomyces cerevisiae

source_name: Liquid cultured S. cerevisiae

extract_protocol:
see characteristic: extract protocol
Libaries were constructed using NEBNext DNA Library Prep Kit for Illumina (NEB, E7370) following manufacturer's protocol and using standard Illumina sequences, as described in Ostrow et al., 2017 and Peace et al., 2016.

tag: cell cycle

value: Late G1-phase

tag: strain

tag: library strategy

value: OTHER

tag: extract protocol

value: 4C DNA was created by arresting cells with alpha factor, crosslinking with formaldehyde, isolating intact chromatin, digesting with XbaI, ligating with T4 DNA Ligase, digesting with MseI, ligating with T4 DNA Ligase, performing PCR with primers adjacent to and emanating from ARS305, and sonicating with Covaris S2, as described in Knott et al., 2012 and Ostrow et al., 2017.


title: H3S10P_MEF_03_replicate2

description: Chip-Seq

tag: genotype


title: H3S10P_0min_replicate1

description: Chip-Seq


title: ChIP-seq from OCI-LY1 (ENCLB642REN)

description:
https://www.encodeproject.org/experiments/ENCSR076JBA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR076JBA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB642REN
size range: 200-600

source_name: Homo sapiens OCI-LY1 immortalized cell line

tag: antibody

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

value: 44 year

value: male

value: B cell lymphoma

value: ENCBS729LWO at ENCODE; https://www.encodeproject.org/ENCBS729LWO/

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

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


title: ChIP-seq from NCI-H929 (ENCLB665NED)

description:
https://www.encodeproject.org/experiments/ENCSR082NQB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR082NQB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR409FGC
encode release date: 2016-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB665NED
size range: 200-600

source_name: Homo sapiens NCI-H929 immortalized cell line

value: immortalized cell line

tag: description

value: human multiple myeloma established from the pleural effusion of a 62-year-old white woman with myeloma (IgAkappa) at relapse; cells were described as follows:cells synthesize high amounts of immunoglobulin, c-myc proto-oncogene is rearranged and c-myc RNA is expressed, cells are EBV-negative;

value: adult

value: female

value: 62 year

value: multiple myeloma

value: ENCBS571AQH at ENCODE; https://www.encodeproject.org/ENCBS571AQH/

value: Derived from ENCODE donor ENCDO220OYR; https://www.encodeproject.org/ENCDO220OYR/


title: H3S10P_0min_replicate2

description: Chip-Seq

value: normal

value: H3S10P (Millipore, cat# 04-817)


title: fkh1-dsm fkh2Δ 4C-Seq rep1

description: 4C genomic DNA

value: Late G1-phase

value: OTHER

value: 4C DNA was created by arresting cells with alpha factor, crosslinking with formaldehyde, isolating intact chromatin, digesting with XbaI, ligating with T4 DNA Ligase, digesting with MseI, ligating with T4 DNA Ligase, performing PCR with primers adjacent to and emanating from ARS305, and sonicating with Covaris S2, as described in Knott et al., 2012 and Ostrow et al., 2017.


title: ChIP-seq from MM.1S (ENCLB959AIK)

description:
https://www.encodeproject.org/experiments/ENCSR086YIH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR086YIH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR264HOB
encode release date: 2016-06-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB959AIK
size range: 300-600
nucleic acid starting quantity: 238.34
nucleic acid starting quantity units: ng

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

tag: biosample encode accession

value: 42 year

value: immunoglobulin A lambda myeloma

value: Bradley Bernstein, Broad

value: ENCBS981ZAE at ENCODE; https://www.encodeproject.org/ENCBS981ZAE/

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

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


title: ChIP-seq from NCI-H929 (ENCLB943KMV)

description:
https://www.encodeproject.org/experiments/ENCSR082NQB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR082NQB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR409FGC
encode release date: 2016-10-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB943KMV
size range: 200-600

value: immortalized cell line

value: human multiple myeloma established from the pleural effusion of a 62-year-old white woman with myeloma (IgAkappa) at relapse; cells were described as follows:cells synthesize high amounts of immunoglobulin, c-myc proto-oncogene is rearranged and c-myc RNA is expressed, cells are EBV-negative;

value: adult

value: female

tag: age

value: ENCBS197CBA at ENCODE; https://www.encodeproject.org/ENCBS197CBA/


title: RRBS_Control_5

description: processed data file: RRBSresults.xlsx

tag: tissue

value: whole embryos

value: AB strain

tag: Stage

value: 6 dpf

tag: generation

tag: treatment

value: Control (0.01% DMSO)


title: fkh2Δ 4C-Seq rep2

description: 4C genomic DNA

value: Late G1-phase

value: OTHER

value: 4C DNA was created by arresting cells with alpha factor, crosslinking with formaldehyde, isolating intact chromatin, digesting with XbaI, ligating with T4 DNA Ligase, digesting with MseI, ligating with T4 DNA Ligase, performing PCR with primers adjacent to and emanating from ARS305, and sonicating with Covaris S2, as described in Knott et al., 2012 and Ostrow et al., 2017.


title: ChIP-seq from OCI-LY1 (ENCLB295YEN)

description:
https://www.encodeproject.org/experiments/ENCSR076JBA/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR076JBA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR569IIN
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB295YEN
size range: 200-600

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

value: 44 year

tag: dev stage

tag: Sex

value: male

tag: health state

value: B cell lymphoma

value: ENCBS729LWO at ENCODE; https://www.encodeproject.org/ENCBS729LWO/

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

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


title: H3K4ME3_15min_replicate2

description: Chip-Seq

value: normal

tag: chip antibody

value: H3K4me3 ( Abcam Cat# Ab1012 Lot# GR56209-1)

tag: scaling factor used (reads*scaling factor)


title: H3K4ME3_15min_replicate1

description: Chip-Seq


title: fkh1Δ fkh2Δ RNA-Seq rep2

description: RNA

library_source: transcriptomic

molecule: total RNA

tag: cell cycle

value: asynchronous

tag: strain

value: RNA-Seq

value: total RNA was isolated from 10 mL cultures grown in YEPD to OD600 ~1 using Ribopure Yeast Kit (ThermoFisher AM1926). cDNA libraries were created using SuperScript III First-Strand Synthesis (ThermoFisher #18080051) with oligo dT primers followed by NEBNext Second Strand Synthesis (NEB E6111S).


title: fkh2Δ 4C-Seq rep1

description: 4C genomic DNA

tag: library strategy

tag: extract protocol


title: H3K4ME3_5min_replicate2

description: Chip-Seq

tag: genotype


title: fkh2-dsm fkh1Δ RNA-Seq rep2

description: RNA

tag: antibody


title: ChIP-seq from ACC112 (ENCLB487IFL)

description:
https://www.encodeproject.org/experiments/ENCSR059MVB/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR059MVB
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR836XKP
encode release date: 2014-09-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB487IFL
size range: 200-600

source_name: Homo sapiens ACC112 immortalized cell line

tag: line

value: immortalized cell line

tag: description

value: adenoid cystic carcinoma cell line supplied by Lurdes Queimado, M.D., Ph.D.Phone:405-271-4232 (office); 405-271-4279 (lab); cells immortalized by infection with a retrovirus expressing HPV16 E6 and E7

tag: biosample encode accession

value: adult

value: 70 year

value: submaxillar tumor

tag: lab

value: Bradley Bernstein, Broad

tag: link

value: ENCBS827JIC at ENCODE; https://www.encodeproject.org/ENCBS827JIC/

value: Derived from ENCODE donor ENCDO085ZKK; https://www.encodeproject.org/ENCDO085ZKK/

value: ENCODE dbxrefs Cellosaurus CVCL_Y492; http://web.expasy.org/cellosaurus/CVCL_Y492


title: ChIP-seq from SK-N-SH (ENCLB104CEU)

description:
https://www.encodeproject.org/experiments/ENCSR074TRC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR074TRC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2017-01-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB104CEU
size range: 200-600

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

value: SK-N-SH

tag: age

value: 4 year

value: child

value: female

value: ENCBS500EWH at ENCODE; https://www.encodeproject.org/ENCBS500EWH/

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

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


title: fkh1Δ fkh2Δ RNA-Seq rep1

description: RNA

value: asynchronous

value: RNA-Seq

value: total RNA was isolated from 10 mL cultures grown in YEPD to OD600 ~1 using Ribopure Yeast Kit (ThermoFisher AM1926). cDNA libraries were created using SuperScript III First-Strand Synthesis (ThermoFisher #18080051) with oligo dT primers followed by NEBNext Second Strand Synthesis (NEB E6111S).


title: ChIP-seq from SK-N-SH (ENCLB375XUA)

description:
https://www.encodeproject.org/experiments/ENCSR074TRC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR074TRC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR185OHN
encode release date: 2017-01-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB375XUA
size range: 200-600

value: immortalized cell line

tag: dev stage

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


title: H3K4ME3_0min_replicate2

description: Chip-Seq

value: normal

value: H3K4me3 ( Abcam Cat# Ab1012 Lot# GR56209-1)


title: fkh2-dsm fkh1Δ RNA-Seq rep1

description: RNA


title: H3K4ME3_5min_replicate1

description: Chip-Seq


title: ChIP-seq from ACC112 (ENCLB923ITE)

description:
https://www.encodeproject.org/experiments/ENCSR059MVB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR059MVB
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR836XKP
encode release date: 2014-09-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB923ITE
size range: 200-600

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

value: adenoid cystic carcinoma cell line supplied by Lurdes Queimado, M.D., Ph.D.Phone:405-271-4232 (office); 405-271-4279 (lab); cells immortalized by infection with a retrovirus expressing HPV16 E6 and E7

value: adult

tag: Sex

value: male

value: 70 year

value: submaxillar tumor

value: Bradley Bernstein, Broad

value: ENCBS726UUU at ENCODE; https://www.encodeproject.org/ENCBS726UUU/


title: H3K4ME3_0min_replicate1

description: Chip-Seq


title: ChIP-seq from ACC112 (ENCLB459BIM)

description:
https://www.encodeproject.org/experiments/ENCSR059MVB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR059MVB
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR836XKP
encode release date: 2014-09-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB459BIM
size range: 200-600

tag: health state

value: ENCBS827JIC at ENCODE; https://www.encodeproject.org/ENCBS827JIC/

value: Derived from ENCODE donor ENCDO085ZKK; https://www.encodeproject.org/ENCDO085ZKK/

value: ENCODE dbxrefs Cellosaurus CVCL_Y492; http://web.expasy.org/cellosaurus/CVCL_Y492


title: H3K9ACS10P_15min_replicate2

description: Chip-Seq

tag: chip antibody


title: fkh1Δ RNA-Seq rep2

description: RNA

value: asynchronous


title: ChIP-seq from neutrophil (ENCLB830WEQ)

description:
https://www.encodeproject.org/experiments/ENCSR058FCG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR058FCG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR557RDB
encode release date: 2016-11-16
lab: Bradley Bernstein, Broad
library encode accession: ENCLB830WEQ
size range: 200-600

source_name: Homo sapiens neutrophil primary cell

value: neutrophil

value: primary cell

value: Neutrophils were isolated by centrifuging heparinized venous blood over Histopaque 1119 (Sigma-Aldrich) and subsequently over a discontinuous Percoll (Amersham Biosciences) gradient.  Cells provided by Max Planck Institute for Infection Biology, Berlin

value: unknown

value: not collected

value: ENCBS360EQL at ENCODE; https://www.encodeproject.org/ENCBS360EQL/

value: Derived from ENCODE donor ENCDO055UKA; https://www.encodeproject.org/ENCDO055UKA/


title: ChIP-seq from Karpas-422 (ENCLB948BXD)

description:
https://www.encodeproject.org/experiments/ENCSR058SHN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR058SHN
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB948BXD
size range: 200-600

source_name: Homo sapiens Karpas-422 immortalized cell line

value: immortalized cell line

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: adult

value: female

value: human B cell non-Hodgkin's lymphoma

value: ENCBS171YVY at ENCODE; https://www.encodeproject.org/ENCBS171YVY/

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

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


title: fkh1Δ RNA-Seq rep1

description: RNA

value: asynchronous

value: RNA-Seq

value: total RNA was isolated from 10 mL cultures grown in YEPD to OD600 ~1 using Ribopure Yeast Kit (ThermoFisher AM1926). cDNA libraries were created using SuperScript III First-Strand Synthesis (ThermoFisher #18080051) with oligo dT primers followed by NEBNext Second Strand Synthesis (NEB E6111S).


title: fkh2Δ RNA-Seq rep2

description: RNA


title: H3K9ACS10P_5min_replicate1

description: Chip-Seq

value: normal

tag: scaling factor used (reads*scaling factor)


title: H3K9ACS10P_15min_replicate1

description: Chip-Seq


title: H3K9ACS10P_5min_replicate2

description: Chip-Seq


title: ChIP-seq from neutrophil (ENCLB225HSR)

description:
https://www.encodeproject.org/experiments/ENCSR058FCG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR058FCG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR557RDB
encode release date: 2016-11-16
lab: Bradley Bernstein, Broad
library encode accession: ENCLB225HSR
size range: 200-600

value: neutrophil

value: primary cell

value: Neutrophils were isolated by centrifuging heparinized venous blood over Histopaque 1119 (Sigma-Aldrich) and subsequently over a discontinuous Percoll (Amersham Biosciences) gradient.  Cells provided by Max Planck Institute for Infection Biology, Berlin

value: unknown

value: Bradley Bernstein, Broad

value: ENCBS462VZJ at ENCODE; https://www.encodeproject.org/ENCBS462VZJ/


title: H3K9ACS10P_0min_replicate2

description: Chip-Seq


title: H3K9ACS10P_0min_replicate1

description: Chip-Seq


title: fkh2-dsm fkh1Δ BrdU-IP-Seq rep1

description: BrdU-incorporated IP DNA

tag: cell cycle

value: Late G1-phase

value: OTHER

value: BrdU-IP DNA was obtained by arresting cells with alpha-factor to OD ~0.5 in YEPD, releasing into YEPD, hydroxyurea, and BrdU. DNA was extracted and sonicated using Covaris S2, and BrdU-incorporated DNA was incubated with anti-BrdU to obtain BrdU-IP material, as described in Ostrow et al., 2017.

value: anti-BrdU


title: ChIP-seq from MCF-7 (ENCLB269UER)

description:
https://www.encodeproject.org/experiments/ENCSR057MWG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR057MWG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2016-11-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB269UER
size range: 200-600

source_name: Homo sapiens MCF-7 immortalized cell line

value: immortalized cell line

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

value: 69 year

value: adult

value: female

value: breast cancer (adenocarcinoma)

tag: passage number

value: ENCBS967MVZ at ENCODE; https://www.encodeproject.org/ENCBS967MVZ/

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

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

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


title: fkh2Δ RNA-Seq rep1

description: RNA

value: asynchronous

tag: strain

tag: library strategy

value: RNA-Seq

value: total RNA was isolated from 10 mL cultures grown in YEPD to OD600 ~1 using Ribopure Yeast Kit (ThermoFisher AM1926). cDNA libraries were created using SuperScript III First-Strand Synthesis (ThermoFisher #18080051) with oligo dT primers followed by NEBNext Second Strand Synthesis (NEB E6111S).


title: fkh1-dsm fkh2Δ BrdU-IP-Seq rep2

description: BrdU-incorporated IP DNA

value: Late G1-phase

tag: extract protocol


title: fkh1-dsm fkh2Δ RNA-Seq rep2

description: RNA

tag: antibody


title: fkh2-dsm fkh1Δ BrdU-IP-Seq rep2

description: BrdU-incorporated IP DNA

value: OTHER


title: ChIP-seq from GM12878 (ENCLB973TBZ)

description:
https://www.encodeproject.org/experiments/ENCSR057BWO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR057BWO
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR142REC
encode release date: 2016-11-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB973TBZ
size range: 200-600

source_name: Homo sapiens GM12878 immortalized cell line

tag: line

value: unknown

value: Bradley Bernstein, Broad

value: ENCBS978YID at ENCODE; https://www.encodeproject.org/ENCBS978YID/

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

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


title: H3K4ME3_NONA_TPA

description: Chip-Seq

data_processing:
ChipSeq: Wig files are those generated by MACS at 1bp resolution and a set normalised to 30 million mapped reads and to the assessed scaling factors are additionally provided.
Genome_build: MM9
Supplementary_files_format_and_content: wig files

extract_protocol: Chip-Seq: DNA samples were end repaired, poly-A tailed and Illumina single end adapters were ligated following the standard Illumina protocol with minor adjustments. Agencourt AMPure XP beads at 0.8x ratio were used to size select out adapter dimers after adapter ligation.  The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix. Post PCR, AMPure XP beads were used at a 1:1 ratio to maintain size integrity and to allow size select on 2%Agarose gel.  Samples were finally purified with QAIquick gel extraction kit and quality controlled on the DNA 1000 BioAnalyser 2100 chip.

treatment_protocol: Cells were  starved for 48h in 0.3%FCS. Where indicated, cells were stimulated for 30 minutes with 12-O-tetradecanoyl phorbol-13-acetate (Sigma TPA, 50 ng/ml).

tag: genotype

value: TKO recon pMY Elk-1 nonA mutant

value: H3K4me3 ( Abcam Cat# Ab1012 Lot# GR56209-1)


title: fkh1-dsm fkh2Δ RNA-Seq rep1

description: RNA


title: H3K4ME3_NONA_03

description: Chip-Seq


title: ChIP-seq from GM12878 (ENCLB736ZLR)

description:
https://www.encodeproject.org/experiments/ENCSR057BWO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR057BWO
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR142REC
encode release date: 2016-11-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB736ZLR
size range: 200-600

value: immortalized cell line

tag: description

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

tag: biosample encode accession

value: adult

value: female

value: ENCBS830CIQ at ENCODE; https://www.encodeproject.org/ENCBS830CIQ/

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

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


title: fkh1-dsm fkh2Δ BrdU-IP-Seq rep1

description: BrdU-incorporated IP DNA

value: BrdU-IP DNA was obtained by arresting cells with alpha-factor to OD ~0.5 in YEPD, releasing into YEPD, hydroxyurea, and BrdU. DNA was extracted and sonicated using Covaris S2, and BrdU-incorporated DNA was incubated with anti-BrdU to obtain BrdU-IP material, as described in Ostrow et al., 2017.

value: anti-BrdU


title: ChIP-seq from HepG2 (ENCLB062JEV)

description:
https://www.encodeproject.org/experiments/ENCSR055XHN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR055XHN
assay title: ChIP-seq
encode release date: 2017-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB062JEV
size range: 200-600

source_name: Homo sapiens HepG2 immortalized cell line

extract_protocol: not provided

value: Control

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

value: child

value: male

value: 15 year

value: hepatocellular carcinoma

tag: lab

tag: link

value: ENCBS777VZC at ENCODE; https://www.encodeproject.org/ENCBS777VZC/

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


title: ChIP-seq from HepG2 (ENCLB162WSO)

description:
https://www.encodeproject.org/experiments/ENCSR055XHN/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR055XHN
assay title: ChIP-seq
encode release date: 2017-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB162WSO
size range: 200-600

value: immortalized cell line

tag: dev stage

tag: age

value: Bradley Bernstein, Broad

value: ENCBS467HWM at ENCODE; https://www.encodeproject.org/ENCBS467HWM/


title: ChIP-seq from HepG2 (ENCLB123IGA)

description:
https://www.encodeproject.org/experiments/ENCSR055XHN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR055XHN
assay title: ChIP-seq
encode release date: 2017-02-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB123IGA
size range: 200-600

tag: Sex

tag: health state


title: fkh2Δ BrdU-IP-Seq rep2

description: BrdU-incorporated IP DNA

value: Late G1-phase

value: OTHER


title: ChIP-seq from adrenal gland (ENCLB092WWL)

description:
https://www.encodeproject.org/experiments/ENCSR053PIY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR053PIY
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR754WVA
encode release date: 2016-10-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB092WWL
size range: 200-600

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

value: adrenal gland

value: tissue

value: EnTEX:Adrenal Gland

value: adult

value: 37 year

value: ENCBS137LDS at ENCODE; https://www.encodeproject.org/ENCBS137LDS/

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


title: fkh1Δ BrdU-IP-Seq rep1

description: BrdU-incorporated IP DNA

value: BrdU-IP DNA was obtained by arresting cells with alpha-factor to OD ~0.5 in YEPD, releasing into YEPD, hydroxyurea, and BrdU. DNA was extracted and sonicated using Covaris S2, and BrdU-incorporated DNA was incubated with anti-BrdU to obtain BrdU-IP material, as described in Ostrow et al., 2017.

value: anti-BrdU


title: ChIP-seq from MCF-7 (ENCLB272LZL)

description:
https://www.encodeproject.org/experiments/ENCSR056UBA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR056UBA
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR768LHG
encode release date: 2017-01-13
lab: Bradley Bernstein, Broad
library encode accession: ENCLB272LZL
size range: 200-600

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

value: 69 year

value: female

value: breast cancer (adenocarcinoma)

value: ENCBS967MVZ at ENCODE; https://www.encodeproject.org/ENCBS967MVZ/

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

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

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


title: ChIP-seq from GM12878 (ENCLB559JXA)

description:
https://www.encodeproject.org/experiments/ENCSR000BVP/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq protocol v042211.1 on human GM12878
experiment encode accession: ENCSR000BVP
assay title: ChIP-seq
encode release date: 2012-09-10
lab: Richard Myers, HAIB
library encode accession: ENCLB559JXA

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

value: Control

value: immortalized cell line

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

value: unknown

value: Richard Myers, HAIB

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

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

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

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

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


title: ChIP-seq from HeLa-S3 (ENCLB695AHK)

description:
https://www.encodeproject.org/experiments/ENCSR000AOB/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on human HeLa-S3
experiment encode accession: ENCSR000AOB
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AHK

source_name: Homo sapiens HeLa-S3 immortalized cell line

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

value: adult

value: 31 year

value: cervical adenocarcinoma

value: Bradley Bernstein, Broad

value: ENCBS655ARO at ENCODE; https://www.encodeproject.org/ENCBS655ARO/

value: Derived from ENCODE donor ENCDO000AAB; https://www.encodeproject.org/ENCDO000AAB/

value: ENCODE dbxrefs Cellosaurus CVCL_0058; http://web.expasy.org/cellosaurus/CVCL_0058


title: fkh1Δ BrdU-IP-Seq rep2

description: BrdU-incorporated IP DNA

value: Late G1-phase

value: OTHER

value: BrdU-IP DNA was obtained by arresting cells with alpha-factor to OD ~0.5 in YEPD, releasing into YEPD, hydroxyurea, and BrdU. DNA was extracted and sonicated using Covaris S2, and BrdU-incorporated DNA was incubated with anti-BrdU to obtain BrdU-IP material, as described in Ostrow et al., 2017.

value: anti-BrdU


title: ChIP-seq from adrenal gland (ENCLB559KSD)

description:
https://www.encodeproject.org/experiments/ENCSR053PIY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR053PIY
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR754WVA
encode release date: 2016-10-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB559KSD
size range: 200-600

value: adrenal gland

value: tissue

value: EnTEX:Adrenal Gland

value: male

value: 37 year

value: ENCBS137LDS at ENCODE; https://www.encodeproject.org/ENCBS137LDS/

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


title: H3K4ME3_WT_TPA

description: Chip-Seq

value: TKO recon pMY Elk-1 wt

tag: chip antibody

value: H3K4me3 ( Abcam Cat# Ab1012 Lot# GR56209-1)

tag: scaling factor used (reads*scaling factor)


title: H3K4ME3_WT_03

description: Chip-Seq


title: fkh2Δ BrdU-IP-Seq rep1

description: BrdU-incorporated IP DNA

tag: cell cycle


title: ChIP-seq from HeLa-S3 (ENCLB695AHL)

description:
https://www.encodeproject.org/experiments/ENCSR000AOB/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human HeLa-S3
experiment encode accession: ENCSR000AOB
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AHL

value: Control

value: immortalized cell line

value: adult

value: female

value: 31 year

value: cervical adenocarcinoma

value: Bradley Bernstein, Broad

value: ENCBS075PNA at ENCODE; https://www.encodeproject.org/ENCBS075PNA/


title: ChIP-seq from keratinocyte (ENCLB695AIA)

description:
https://www.encodeproject.org/experiments/ENCSR000ALS/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on human NHEK
experiment encode accession: ENCSR000ALS
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AIA

source_name: Homo sapiens keratinocyte primary cell female

value: keratinocyte

value: primary cell

value: epidermal keratinocytes

value: unknown

value: ENCBS585ENC at ENCODE; https://www.encodeproject.org/ENCBS585ENC/

value: Derived from ENCODE donor ENCDO268AAA; https://www.encodeproject.org/ENCDO268AAA/

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

value: Lonza  sample source; http://www.lonza.com


title: ChIP-seq from hepatocyte (ENCLB161XYT)

description:
https://www.encodeproject.org/experiments/ENCSR034BEQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR034BEQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR107PGG
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB161XYT
size range: 200-600
nucleic acid starting quantity: 890
nucleic acid starting quantity units: ng

source_name: Homo sapiens hepatocyte in vitro differentiated cells female embryo (5 days) derived from H9

value: hepatocyte

value: in vitro differentiated cells

value: Frozen or fixed, in vitro differentiated hepatocyte-like cells from ES WA09 (H9) by the SESCC for use by the ENCODE consortia

value: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

value: ENCBS520VFV at ENCODE; https://www.encodeproject.org/ENCBS520VFV/

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


title: H3K4ME3_FW_TPA

description: Chip-Seq

value: TKO recon pMY Elk-1 FW mutant

value: H3K4me3 ( Abcam Cat# Ab1012 Lot# GR56209-1)


title: ChIP-seq from hepatocyte (ENCLB780JMR)

description:
https://www.encodeproject.org/experiments/ENCSR034BEQ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR034BEQ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR107PGG
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB780JMR
size range: 200-600

value: female

value: ENCBS077RUJ at ENCODE; https://www.encodeproject.org/ENCBS077RUJ/


title: ChIP-seq from endothelial cell of umbilical vein (ENCLB695AUC)

description:
https://www.encodeproject.org/experiments/ENCSR000ALG/
***************
biological replicate number: 1
technical replicate number: 2
description: Control ChIP-seq on human endothelial cell of umbilical vein
experiment encode accession: ENCSR000ALG
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AUC

source_name: Homo sapiens endothelial of umbilical vein primary cell newborn

value: Control

value: endothelial cell of umbilical vein

value: primary cell

value: umbilical vein endothelial cells

value: newborn

value: not collected

value: unknown

value: Bradley Bernstein, Broad

value: ENCBS717AAA at ENCODE; https://www.encodeproject.org/ENCBS717AAA/

value: Derived from ENCODE donor ENCDO000AAS; https://www.encodeproject.org/ENCDO000AAS/

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


title: Actin KO4

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Mus musculus GRCm38.p4 genome using tophat2 v2.1.0 with the parameters “–no-novel-junctions” and “–G” when specifying the genome file
Cufflinks v2.2.1 was used to derive FPKM (Fragments Per Kilobase of transcript per Million mapped reads)
Differential gene expression was analyzed by Cuffdiff
Genome_build: Mus musculus GRCm38.p4 genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, tab-delimited text files include fold change and p-values of each comparison

source_name: connective tissue

growth_protocol: Dulbecco’s modified Eagle medium (DMEM) with high glucose (Sigma), 10% fetal bovine serum (Sigma) and 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma), in a humidified incubator with 5% CO2 at 37 Deg.

extract_protocol:
Total RNA was extracted from 70% confluent cells using TRI Reagent according to the manufacturer protocol (Sigma-Aldrich).
Library construction according to the SciLife lab guideline using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer protocol

tag: tissue

value: embryonic fibroblasts

tag: strain

value: BALB/c

tag: developmental stage

value: 10.5 day old embryos

value: Actb -/-


title: H3ME3_ESNTPA_replicate2

description: Chip-Seq

source_name: Cultured MEFs (Mouse Embryonic fibroblasts)

value: TCF KO (TKO)

value: H3K4me3 ( Abcam Cat# Ab1012 Lot# GR56209-1)


title: H3K4ME3_FW_03

description: Chip-Seq

value: TKO recon pMY Elk-1 FW mutant


title: H3ME3_ESNTPA_replicate1

description: Chip-Seq


title: Actin KO3


title: Actin Hetero4

value: Actb +/-


title: H3ME3_ESN_03_replicate2

description: Chip-Seq


title: ChIP-seq from thoracic aorta (ENCLB015LAO)

description:
https://www.encodeproject.org/experiments/ENCSR015GFK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR015GFK
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR158PLZ
encode release date: 2016-11-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB015LAO
size range: 200-600
nucleic acid starting quantity: 12.32
nucleic acid starting quantity units: ng

source_name: Homo sapiens thoracic aorta tissue male adult (37 years)

tag: antibody

value: thoracic aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult

value: male

value: 37 year

value: ENCBS543OJU at ENCODE; https://www.encodeproject.org/ENCBS543OJU/

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


title: ChIP-seq from PC-9 (ENCLB539LMN)

description:
https://www.encodeproject.org/experiments/ENCSR011GWK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR011GWK
assay title: ChIP-seq
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB539LMN
size range: 200-600

source_name: Homo sapiens PC-9 immortalized cell line

value: Control

tag: line

value: immortalized cell line

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

value: unknown

value: not collected

value: Bradley Bernstein, Broad

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

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

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


title: H3ME3_ESN_03_replicate1

description: Chip-Seq

tag: genotype

value: TCF KO (TKO)

value: H3K4me3 ( Abcam Cat# Ab1012 Lot# GR56209-1)


title: H3ME3_MEFTPA_replicate2

description: Chip-Seq

value: normal


title: ChIP-seq from NCI-H929 (ENCLB460RPX)

description:
https://www.encodeproject.org/experiments/ENCSR011CSR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR011CSR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR409FGC
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB460RPX
size range: 200-600

source_name: Homo sapiens NCI-H929 immortalized cell line

tag: description

value: human multiple myeloma established from the pleural effusion of a 62-year-old white woman with myeloma (IgAkappa) at relapse; cells were described as follows:cells synthesize high amounts of immunoglobulin, c-myc proto-oncogene is rearranged and c-myc RNA is expressed, cells are EBV-negative;

value: adult

value: female

value: 62 year

value: multiple myeloma

value: ENCBS571AQH at ENCODE; https://www.encodeproject.org/ENCBS571AQH/

value: Derived from ENCODE donor ENCDO220OYR; https://www.encodeproject.org/ENCDO220OYR/


title: H3ME3_MEF_03_replicate2

description: Chip-Seq


title: Actin Hetero1

value: embryonic fibroblasts

value: BALB/c

value: 10.5 day old embryos

value: Actb +/-


title: ChIP-seq from gastrocnemius medialis (ENCLB592NMU)

description:
https://www.encodeproject.org/experiments/ENCSR001UFN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR001UFN
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB592NMU
size range: 200-600

source_name: Homo sapiens gastrocnemius medialis tissue female adult (53 years)

value: Control

value: gastrocnemius medialis

value: tissue

value: i.e. REMC 6, 13, 14 and 15; EnTEX:Muscle - Skeletal

tag: biosample encode accession

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS866HOM at ENCODE; https://www.encodeproject.org/ENCBS866HOM/

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


title: H3K4ME3_EMPTY_03

description: Chip-Seq

value: TKO recon pMY Empty

value: H3K4me3 ( Abcam Cat# Ab1012 Lot# GR56209-1)


title: Actin Hetero2


title: ChIP-seq from NCI-H929 (ENCLB575BDT)

description:
https://www.encodeproject.org/experiments/ENCSR011CSR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR011CSR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR409FGC
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB575BDT
size range: 200-600

value: immortalized cell line

value: human multiple myeloma established from the pleural effusion of a 62-year-old white woman with myeloma (IgAkappa) at relapse; cells were described as follows:cells synthesize high amounts of immunoglobulin, c-myc proto-oncogene is rearranged and c-myc RNA is expressed, cells are EBV-negative;

value: adult

value: female

value: 62 year

value: multiple myeloma

tag: lab

value: ENCBS197CBA at ENCODE; https://www.encodeproject.org/ENCBS197CBA/


title: ChIP-seq from bipolar spindle neuron (ENCLB483DUI)

description:
https://www.encodeproject.org/experiments/ENCSR001KCX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR001KCX
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB483DUI
size range: 200-600

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

value: Control

value: bipolar spindle neuron

value: in vitro differentiated cells

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

value: male

value: Thomas Gingeras, CSHL

tag: link

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

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


title: ChIP-seq from SUDHL6 (ENCLB904QMV)

description:
https://www.encodeproject.org/experiments/ENCSR018LUP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR018LUP
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR179YLS
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB904QMV
size range: 200-600

source_name: Homo sapiens SUDHL6 immortalized cell line

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

value: 43 year

tag: dev stage

value: Bradley Bernstein, Broad

value: ENCBS136LHJ at ENCODE; https://www.encodeproject.org/ENCBS136LHJ/

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

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


title: ChIP-seq from thoracic aorta (ENCLB196SNK)

description:
https://www.encodeproject.org/experiments/ENCSR015GFK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR015GFK
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR158PLZ
encode release date: 2016-11-15
lab: Bradley Bernstein, Broad
library encode accession: ENCLB196SNK
size range: 200-600
nucleic acid starting quantity: 15.175
nucleic acid starting quantity units: ng

value: thoracic aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult

tag: age

value: 37 year

value: ENCBS543OJU at ENCODE; https://www.encodeproject.org/ENCBS543OJU/

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


title: Actin Wt3

value: embryonic fibroblasts

value: BALB/c

value: 10.5 day old embryos

value: Actb +/+


title: H3K9K14AC_NONA_TPA

description: Chip-Seq

value: TKO recon pMY Elk-1 nonA mutant

value: H3K9acK14ac ( Millipore Cat# 06-599 Lot# 1969119)


title: H3ME3_MEF_03_replicate1

description: Chip-Seq

value: normal

value: H3K4me3 ( Abcam Cat# Ab1012 Lot# GR56209-1)


title: Actin Wt2


title: H3K9K14AC_NONA_03

description: Chip-Seq


title: ChIP-seq from bipolar spindle neuron (ENCLB472FIM)

description:
https://www.encodeproject.org/experiments/ENCSR001KCX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR001KCX
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB472FIM
size range: 200-600

value: Control

value: bipolar spindle neuron

value: in vitro differentiated cells

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

value: 53 year

tag: Sex

value: male

value: Thomas Gingeras, CSHL

value: ENCBS374AAA at ENCODE; https://www.encodeproject.org/ENCBS374AAA/

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


title: H3K9K14AC_FW_TPA

description: Chip-Seq

value: TKO recon pMY Elk-1 FW mutant


title: ChIP-seq from PC-9 (ENCLB216AGC)

description:
https://www.encodeproject.org/experiments/ENCSR011GWK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR011GWK
assay title: ChIP-seq
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB216AGC
size range: 200-600

value: immortalized cell line

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

value: unknown

value: not collected

value: Bradley Bernstein, Broad

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

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

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


title: Actin Hetero3

value: embryonic fibroblasts

value: BALB/c

value: 10.5 day old embryos

value: Actb +/-


title: ChIP-seq from cardiac muscle cell (ENCLB165PXM)

description:
https://www.encodeproject.org/experiments/ENCSR000NPF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR000NPF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR867SJE
encode release date: 2016-11-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB165PXM
size range: 200-600

source_name: Homo sapiens cardiac muscle in vitro differentiated cells fetal

value: cardiac muscle cell

value: in vitro differentiated cells

value: fetal

value: John Stamatoyannopoulos, UW

value: ENCBS343AKO at ENCODE; https://www.encodeproject.org/ENCBS343AKO/

value: Derived from ENCODE donor ENCDO924HBJ; https://www.encodeproject.org/ENCDO924HBJ/


title: H3K9K14AC_FW_03

description: Chip-Seq

value: TKO recon pMY Elk-1 FW mutant

value: H3K9acK14ac ( Millipore Cat# 06-599 Lot# 1969119)


title: H3K4ME3_EMPTY_TPA

description: Chip-Seq

value: TKO recon pMY Empty

value: H3K4me3 ( Abcam Cat# Ab1012 Lot# GR56209-1)


title: ChIP-seq from H1-hESC (ENCLB197SAE)

description:
https://www.encodeproject.org/experiments/ENCSR000AMI/
***************
biological replicate number: 2
technical replicate number: 3
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR000AMI
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB197SAE
size range: 300-600

source_name: Homo sapiens H1-hESC stem cell male embryo

value: Control

value: stem cell

value: embryonic

value: male

value: unknown

tag: health state

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS011NFB at ENCODE; https://www.encodeproject.org/ENCBS011NFB/

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

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771


title: ChIP-seq from cardiac muscle cell (ENCLB528QAP)

description:
https://www.encodeproject.org/experiments/ENCSR000NPF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR000NPF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR867SJE
encode release date: 2016-11-12
lab: Bradley Bernstein, Broad
library encode accession: ENCLB528QAP
size range: 200-600

value: cardiac muscle cell

value: in vitro differentiated cells

value: fetal

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS806KLM at ENCODE; https://www.encodeproject.org/ENCBS806KLM/


title: Actin Wt1

value: embryonic fibroblasts

value: BALB/c

value: 10.5 day old embryos

value: Actb +/+


title: H3K9K14AC_WT_TPA

description: Chip-Seq

value: TKO recon pMY Elk-1 wt

tag: chip antibody

value: H3K9acK14ac ( Millipore Cat# 06-599 Lot# 1969119)


title: SmallRNA-seq-DcrKO-Control-12hr

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

country: Japan

institute: Nagoya University

data_processing:
Small RNA-seq samples were analyzed by Illumina HiSeq 2000
Sequences from the Illumina HiSeq 2000 Sequencing system were processed for adaptor removal and size exclusion of sequences < 15 nt with Cutadapt.
Filtered reads were mapped to mm9 assembly with bowtie 1.0.1 (Langmead et al., 2009), allowing two mismatches.
Pre-miRNA expression levels were computed as the number of reads that mapped to pre-miRNA in miRBase v18..
Genome_build: mm9
Supplementary_files_format_and_content: Bw files were produced in a rpm scale.

source_name: Dicer knockout embryonic stem cells

growth_protocol: mESCs were cultured in mES media.

extract_protocol:
Small RNA fraction from Dicer KO mESCs was extracted by miRNeasy Mini Kit (Qiagen).
Small RNA fraction was subjected to library preparation using the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs), and analyzed by Illumina HiSeq 2000.

treatment_protocol: Cells were treated with DMSO or JQ1 (500 nM) for 6 or 12 hrs.

tag: cell type

value: Embryonic stem cells

value: Dicer KO

tag: treatment

value: Control 12 hr


title: ChIP-seq from H1-hESC (ENCLB701ZDL)

description:
https://www.encodeproject.org/experiments/ENCSR000AMI/
***************
biological replicate number: 2
technical replicate number: 7
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR000AMI
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB701ZDL
size range: 200-600

value: Control

value: stem cell

value: embryonic

value: male

value: unknown

value: healthy

value: Bradley Bernstein, Broad

value: ENCBS011NFB at ENCODE; https://www.encodeproject.org/ENCBS011NFB/

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


title: H3K9K14AC_WT_03

description: Chip-Seq

tag: scaling factor used (reads*scaling factor)


title: SmallRNA-seq-DcrKO-JQ1-6hr


title: SmallRNA-seq-DcrKO-Control-6hr

value: Control 6 hr


title: Actin Wt4

tag: tissue

value: embryonic fibroblasts

tag: strain

value: BALB/c

value: 10.5 day old embryos


title: ChIP-seq from H1-hESC (ENCLB778YWY)

description:
https://www.encodeproject.org/experiments/ENCSR000AMI/
***************
biological replicate number: 2
technical replicate number: 5
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR000AMI
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB778YWY
size range: 300-600

tag: antibody

value: ENCODE dbxrefs Cellosaurus CVCL_9771; http://web.expasy.org/cellosaurus/CVCL_9771


title: ChIP-seq from H1-hESC (ENCLB997SYN)

description:
https://www.encodeproject.org/experiments/ENCSR000AMI/
***************
biological replicate number: 2
technical replicate number: 1
description: Control ChIP-seq on human H1-hESC
experiment encode accession: ENCSR000AMI
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB997SYN
size range: 300-600


title: H3K9K14AC_EMPTY_03

description: Chip-Seq

value: TKO recon pMY Empty

value: H3K9acK14ac ( Millipore Cat# 06-599 Lot# 1969119)


title: H3ME3_MEFTPA_replicate1

description: Chip-Seq

value: normal

value: H3K4me3 ( Abcam Cat# Ab1012 Lot# GR56209-1)


title: H3K9K14AC_ESNTPA_replicate2

description: Chip-Seq

value: TCF KO (TKO)