title: ChIP-seq from induced pluripotent stem cell (ENCLB562PGD)

description:
https://www.encodeproject.org/experiments/ENCSR293NAJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR293NAJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2017-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB562PGD
size range: 200-600

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

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

tag: description

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

tag: biosample encode accession

value: 53 year

tag: dev stage

value: adult

value: male

value: Thomas Gingeras, CSHL

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

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

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

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


title: ChIP-seq from hepatocyte (ENCLB914RRW)

status: Public on Mar 09 2017

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR289TGF/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR289TGF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR107PGG
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB914RRW
size range: 200-600

library_source: genomic

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

molecule: genomic DNA

organism: Homo sapiens

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

tag: antibody

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

tag: age

value: 5 day

value: embryonic

tag: Sex

value: female

tag: health state

value: healthy

tag: lab

value: Richard Myers, HAIB

tag: link

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

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


title: ChIP-seq from mid-neurogenesis radial glial cells (ENCLB057GFS)

description:
https://www.encodeproject.org/experiments/ENCSR287XMW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR287XMW
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB057GFS
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: Control

value: mid-neurogenesis radial glial cells

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

tag: passage number

value: Bradley Bernstein, Broad

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


title: ChIP-seq from hepatocyte (ENCLB231KWG)

description:
https://www.encodeproject.org/experiments/ENCSR289TGF/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR289TGF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR107PGG
encode release date: 2016-12-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB231KWG
size range: 200-600

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


title: PARCLiP-hnRNPG-METTL14KD-repl1

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description:
Sample 9
m6A sites recruiting HNRNPG

library_source: transcriptomic

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

molecule: total RNA

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

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

tag: cell line

value: embryonic kidney cell line HEK293T

tag: genotype

value: METTL14 Knockdown

tag: par-clip antibody

value: HNRNPG (sc-14581, Santa Cruz, lot# K0614)


title: PARCLiP-hnRNPG-METTL14KD-repl2

description:
Sample 10
m6A sites recruiting HNRNPG


title: mRNAseq-hnRNPG-Control-repl2

description:
Sample 12
DEXSeq_exons in HC-m6A-containing genes

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

source_name: mRNAseq-hnRNPG-Control

value: wild type


title: PARCLiP-hnRNPG-METTL3KD-repl2

description:
Sample 8
m6A sites recruiting HNRNPG

value: METTL3 Knockdown


title: PARCLiP-hnRNPG-Control-repl2

description:
Sample 6
m6A sites recruiting HNRNPG

source_name: PARCLiP-hnRNPG-Control


title: PARCLiP-hnRNPG-METTL3KD-repl1

description:
Sample 7
m6A sites recruiting HNRNPG


title: PARCLiP-meRIP-IP-repl2

description:
Sample 4
m6A sites recruiting HNRNPG

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

source_name: PARCLiP-meRIP-IP

tag: m6a ip antibody

value: anti-m6A (Synaptic Systems, 202003)


title: ChIP-seq from mid-neurogenesis radial glial cells (ENCLB027AOW)

description:
https://www.encodeproject.org/experiments/ENCSR290EHP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR290EHP
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR287XMW
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB027AOW
size range: 200-600

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

value: in vitro differentiated cells

value: embryonic

value: female

value: 5 day

value: ENCBS908BQA at ENCODE; https://www.encodeproject.org/ENCBS908BQA/


title: ChIP-seq from SK-N-MC (ENCLB118XRD)

description:
https://www.encodeproject.org/experiments/ENCSR287VPM/
***************
biological replicate number: 3
technical replicate number: 1
description: ChIP-seq against H3K4me3 using SK-N-MC cell line which was previously described as a neuroepithelioma (ATCC HTB-10). However recent evidence reveals it is Ewing's Sarcoma (www.ncbi.nlm.nih.gov/pubmed/15548687, www.ncbi.nlm.nih.gov/biosample/3151999, www.ncbi.nlm.nih.gov/pubmed/25453903).
experiment encode accession: ENCSR287VPM
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR899XXQ
encode release date: 2016-11-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB118XRD
size range: 200-600
nucleic acid starting quantity: 235
nucleic acid starting quantity units: ng

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

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

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


title: ChIP-seq from right lobe of liver (ENCLB365QEI)

description:
https://www.encodeproject.org/experiments/ENCSR276SJT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR276SJT
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB365QEI
size range: 200-600

source_name: Homo sapiens right lobe of liver tissue female adult (53 years)

value: Control

value: right lobe of liver

value: tissue

value: i.e. REMC 2,3,4,5 and 16; EnTEX:Liver

value: adult

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS536THV at ENCODE; https://www.encodeproject.org/ENCBS536THV/

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


title: ChIP-seq from radial glial cell (ENCLB257MZJ)

description:
https://www.encodeproject.org/experiments/ENCSR279HKO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR279HKO
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR689ICI
encode release date: 2016-05-20
lab: Bradley Bernstein, Broad
library encode accession: ENCLB257MZJ
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: in vitro differentiated cells

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

value: embryonic

value: female

value: 5 day

value: healthy

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

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


title: PARCLiP-meRIP-IP-repl1

description:
Sample 3
m6A sites recruiting HNRNPG

value: embryonic kidney cell line HEK293T

value: wild type

value: anti-m6A (Synaptic Systems, 202003)

value: HNRNPG (sc-14581, Santa Cruz, lot# K0614)


title: ChIP-seq from cardiac muscle cell (ENCLB292OOJ)

description:
https://www.encodeproject.org/experiments/ENCSR276OLB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR276OLB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR867SJE
encode release date: 2017-01-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB292OOJ
size range: 200-600

source_name: Homo sapiens cardiac muscle in vitro differentiated cells fetal

value: cardiac muscle cell

value: unknown

value: fetal

value: not collected

value: John Stamatoyannopoulos, UW

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

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


title: ChIP-seq from cardiac muscle cell (ENCLB871ZTL)

description:
https://www.encodeproject.org/experiments/ENCSR276OLB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR276OLB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR867SJE
encode release date: 2017-01-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB871ZTL
size range: 200-600

value: in vitro differentiated cells

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


title: PARCLiP-meRIP-Input-repl1

description:
Sample 1
m6A sites recruiting HNRNPG

source_name: PARCLiP-meRIP-Input


title: PARCLiP-meRIP-Input-repl2

description:
Sample 2
m6A sites recruiting HNRNPG


title: PARCLiP-hnRNPG-Control-repl1

description:
Sample 5
m6A sites recruiting HNRNPG


title: mRNAseq-hnRNPG-Control-repl1

description:
Sample 11
DEXSeq_exons in HC-m6A-containing genes


title: mRNAseq-hnRNPG-KD1-repl2

description:
Sample 14
DEXSeq_exons in HC-m6A-containing genes

value: HNRNPG Knockdown


title: ChIP-seq from keratinocyte (ENCLB695AIB)

description:
https://www.encodeproject.org/experiments/ENCSR000ALS/
***************
biological replicate number: 4
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: ENCLB695AIB

source_name: Homo sapiens keratinocyte primary cell female

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

value: Control

value: keratinocyte

value: primary cell

value: female

value: Bradley Bernstein, Broad

value: ENCBS574ILP at ENCODE; https://www.encodeproject.org/ENCBS574ILP/

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


title: ChIP-seq from endothelial cell of umbilical vein (ENCLB695AUB)

description:
https://www.encodeproject.org/experiments/ENCSR000ALG/
***************
biological replicate number: 1
technical replicate number: 5
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: ENCLB695AUB

source_name: Homo sapiens endothelial of umbilical vein primary cell newborn

value: endothelial cell of umbilical vein

value: umbilical vein endothelial cells

value: newborn

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: ChIP-seq from PC-3 (ENCLB629HBR)

description:
https://www.encodeproject.org/experiments/ENCSR275NCH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR275NCH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB629HBR
size range: 300-600
nucleic acid starting quantity: 70.38
nucleic acid starting quantity units: ng

source_name: Homo sapiens PC-3 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: prostate cancer cell line

value: adult

value: male

value: 62 year

value: grade IV, adenocarcinoma

value: ENCBS596CTT at ENCODE; https://www.encodeproject.org/ENCBS596CTT/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: ChIP-seq from neural progenitor cell (ENCLB755YGZ)

description:
https://www.encodeproject.org/experiments/ENCSR274OIJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR274OIJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR603SVD
encode release date: 2016-11-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB755YGZ
size range: 200-600
nucleic acid starting quantity: 144.76
nucleic acid starting quantity units: ng

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

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: 5 day

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

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

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


title: ChIP-seq from induced pluripotent stem cell (ENCLB125FMJ)

description:
https://www.encodeproject.org/experiments/ENCSR293NAJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR293NAJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2017-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB125FMJ
size range: 200-600

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

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

value: 53 year

value: adult

value: male

value: Thomas Gingeras, CSHL

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

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

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

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


title: ChIP-seq from neural progenitor cell (ENCLB452SDT)

description:
https://www.encodeproject.org/experiments/ENCSR274OIJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR274OIJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR603SVD
encode release date: 2016-11-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB452SDT
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: ENCBS044KWE at ENCODE; https://www.encodeproject.org/ENCBS044KWE/


title: ChIP-seq from K562 (ENCLB695AJV)

description:
https://www.encodeproject.org/experiments/ENCSR000AKY/
***************
biological replicate number: 1
technical replicate number: 1
description: Control ChIP-seq on human K562
experiment encode accession: ENCSR000AKY
assay title: ChIP-seq
encode release date: 2011-02-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB695AJV

source_name: Homo sapiens K562 immortalized cell line

value: Control

value: immortalized cell line

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

value: female

value: chronic myelogenous leukemia (CML)

value: Bradley Bernstein, Broad

value: ENCBS639AAA at ENCODE; https://www.encodeproject.org/ENCBS639AAA/

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

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

value: ENCODE dbxrefs K562; http://genome.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&term=K562

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


title: ChIP-seq from cardiac muscle cell (ENCLB940GTB)

description:
https://www.encodeproject.org/experiments/ENCSR269ULZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR269ULZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR867SJE
encode release date: 2017-01-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB940GTB
size range: 200-600

value: cardiac muscle cell

value: unknown

value: fetal

value: not collected

value: John Stamatoyannopoulos, UW

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

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


title: ChIP-seq from neutrophil (ENCLB121LXT)

description:
https://www.encodeproject.org/experiments/ENCSR267YXV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR267YXV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR557RDB
encode release date: 2016-11-16
lab: Bradley Bernstein, Broad
library encode accession: ENCLB121LXT
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: ENCBS360EQL at ENCODE; https://www.encodeproject.org/ENCBS360EQL/

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


title: ChIP-seq from neutrophil (ENCLB181PNQ)

description:
https://www.encodeproject.org/experiments/ENCSR267YXV/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR267YXV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR557RDB
encode release date: 2016-11-16
lab: Bradley Bernstein, Broad
library encode accession: ENCLB181PNQ
size range: 200-600

value: Bradley Bernstein, Broad

value: ENCBS921VGK at ENCODE; https://www.encodeproject.org/ENCBS921VGK/


title: ChIP-seq from cardiac muscle cell (ENCLB789WSZ)

description:
https://www.encodeproject.org/experiments/ENCSR269ULZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR269ULZ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR867SJE
encode release date: 2017-01-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB789WSZ
size range: 200-600

value: in vitro differentiated cells

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


title: ChIP-seq from thoracic aorta (ENCLB494EAW)

description:
https://www.encodeproject.org/experiments/ENCSR266XMB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR266XMB
assay title: ChIP-seq
encode release date: 2016-06-30
lab: Bradley Bernstein, Broad
library encode accession: ENCLB494EAW
size range: 200-600

source_name: Homo sapiens thoracic aorta tissue male adult (54 years)

value: Control

value: thoracic aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult

value: male

value: 54 year

value: ENCBS703OTV at ENCODE; https://www.encodeproject.org/ENCBS703OTV/

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


title: ChIP-seq from neutrophil (ENCLB642JUJ)

description:
https://www.encodeproject.org/experiments/ENCSR267YXV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR267YXV
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR557RDB
encode release date: 2016-11-16
lab: Bradley Bernstein, Broad
library encode accession: ENCLB642JUJ
size range: 200-600

value: neutrophil

value: primary cell

value: unknown

value: not collected


title: ChIP-seq from endothelial cell of umbilical vein (ENCLB695AUA)

description:
https://www.encodeproject.org/experiments/ENCSR000ALG/
***************
biological replicate number: 1
technical replicate number: 4
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: ENCLB695AUA

value: endothelial cell of umbilical vein

value: umbilical vein endothelial cells

value: newborn

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: WT_minimal_ribosome

city: San Francisco

first: Natalie

last: Baggett

address: 600 16th Street, S376

department: Microbiology and Immunology

institute: UCSF

description:
ribosome protected RNA fragments
Growth in MOPS minimal plus glucose media

data_processing:
Remaining linker-1 reads (CTGTAGGCACCATCAAT) were removed from fastq files using fastx_clipper
Reads were aligned to E.coli rRNA and tRNA using Bowtie v.0.12.0 allowing for one mismatch and reads aligning to more than one position in the genome were randomly assigned to one of those positions
The remaining reads were aligned to genome using Bowtie v.0.12.0 allowing for one mismatch and reads aligning in more than one position in the genome were discarded
The aligned reads were converted to BAM files and sorted and indexed using SAMtools
Wiggle files were created by center mapping the reads between 20-40bps. Using a 10bp trim on either side of the read then mapping the read across the remaining location using Plastid.
Genome_build: NC_000913
Supplementary_files_format_and_content: Bedgraph wiggle files were created for each sample and replicate for all reads aligned to the genome after computational rRNA and tRNA subtraction

organism: Escherichia coli

source_name: whole cell lysate

growth_protocol: All strains were grown shaking at 37°C  in 200mL cultures of MOPS complete-glucose liquid media (unless otherwise annotated) in 1L flasks and cells were harvested at OD(420nm) between 0.4 - 0.6

extract_protocol:
Whole cell lysates were clarified by brief centrifugation. Ribosome footprints were created using Mnase digestion (45 enzyme units per absorbance unit of lysate at 260nm). Using sucrose gradients the monosome fraction of lysate was isolated and footprints were size selected and converted to a cDNA library. Total RNA was extracted from purified lysate for a simultaneous RNA-seq library production for total RNA samples. Small RNA and ribosomal RNA subtraction was performed in total RNA samples using MEGAClear (ThermoFisher) and MicrobExpress (ThermoFisher) kits. Subtracted total RNA was then subjected to alkaline fragmentation prior to library preparation.
A Linker-1 adapter (IDT) was ligated onto the 3' end of size selected RNA fragments, either ribosome footprints or fragmented total RNA. A cDNA library was created using Superscript III (ThermoFisher). After gel purification of the cDNA library all ssDNA fragments were circularized using CircLigase (Epicentre). For ribosome profiling samples rRNA containing circles were depleted using oligo-biotin  and streptavidin coupled Dynabeads (ThermoFisher) subtraction. A PCR amplification off the circles using HF Phusion (NEB) completed the libraries by adding Illumina Tru-Seq adapters and a unique index for each sample.

treatment_protocol: Cells from each strain were rapidly harvested by filtration and lysate was produced by pulverization of liquid nitrogen cooled samples.

tag: strain


title: ChIP-seq from thyroid gland (ENCLB426TAS)

description:
https://www.encodeproject.org/experiments/ENCSR266EYO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR266EYO
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR777VQP
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB426TAS
size range: 200-600

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

value: thyroid gland

value: tissue

value: 37 year

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

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


title: ChIP-seq from Loucy (ENCLB247EMC)

description:
https://www.encodeproject.org/experiments/ENCSR267UCE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR267UCE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR648HLP
encode release date: 2016-11-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB247EMC
size range: 200-600
nucleic acid starting quantity: 6.6
nucleic acid starting quantity units: ng

source_name: Homo sapiens Loucy immortalized cell line

value: Loucy

value: immortalized cell line

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

value: adult

value: female

value: 38 year

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

value: ENCBS170DPY at ENCODE; https://www.encodeproject.org/ENCBS170DPY/

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

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

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


title: ∆RF3_minimal_ribosome

value: K12 MG1655 deltaprfC


title: WT_minimal_mRNA

description:
total RNA
Growth in MOPS minimal plus glucose media


title: RF2*∆RF3_exp3_ribosome

description: ribosome protected RNA fragments

value: K12 MG1655 prfB-Bstrain allele deltaprfC


title: RF2*∆RF3_exp4_repA_ribosome

description: ribosome protected RNA fragments


title: ChIP-seq from thyroid gland (ENCLB216QPS)

description:
https://www.encodeproject.org/experiments/ENCSR266EYO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR266EYO
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR777VQP
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB216QPS
size range: 200-600

value: thyroid gland

value: tissue

value: male

value: Bradley Bernstein, Broad


title: RF2*∆RF3_exp2_repA_ribosome

description: ribosome protected RNA fragments


title: RF2*∆RF3_exp2_repB_ribosome

description: ribosome protected RNA fragments


title: RF2*∆RF3_exp4_repB_ribosome

description: ribosome protected RNA fragments


title: RF2*_exp3_ribosome

description: ribosome protected RNA fragments

value: K12 MG1655 prfB-Bstrain allele


title: RF2*_exp1_ribosome

description: ribosome protected RNA fragments


title: ChIP-seq from MM.1S (ENCLB019PEH)

description:
https://www.encodeproject.org/experiments/ENCSR264HOB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR264HOB
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB019PEH
size range: 300-600

source_name: Homo sapiens MM.1S immortalized cell line

value: Control

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: 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: ∆RF3_exp3_ribosome

description: ribosome protected RNA fragments


title: ChIP-seq from MM.1S (ENCLB955OVO)

description:
https://www.encodeproject.org/experiments/ENCSR264HOB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR264HOB
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB955OVO
size range: 300-600

value: adult

value: female

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


title: ChIP-seq from neural progenitor cell (ENCLB251ALY)

description:
https://www.encodeproject.org/experiments/ENCSR274OIJ/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR274OIJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR603SVD
encode release date: 2016-11-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB251ALY
size range: 200-600
nucleic acid starting quantity: 144.76
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: 5 day

value: embryonic

value: healthy

value: Richard Myers, HAIB

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

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


title: ChIP-seq from vagina (ENCLB229OXA)

description:
https://www.encodeproject.org/experiments/ENCSR258UUX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR258UUX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR620XWM
encode release date: 2016-11-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB229OXA
size range: 200-600

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

value: vagina

value: tissue

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS047TWL at ENCODE; https://www.encodeproject.org/ENCBS047TWL/

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


title: ∆RF3_exp1_ribosome

description: ribosome protected RNA fragments

value: K12 MG1655 deltaprfC


title: ∆RF3_minimal_mRNA


title: ChIP-seq from vagina (ENCLB189VIG)

description:
https://www.encodeproject.org/experiments/ENCSR258UUX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR258UUX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR620XWM
encode release date: 2016-11-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB189VIG
size range: 200-600

value: adult

value: female


title: WT_exp2_ribosome

description: ribosome protected RNA fragments


title: WT_exp4_ribosome

description: ribosome protected RNA fragments


title: ChIP-seq from neural progenitor cell (ENCLB536PES)

description:
https://www.encodeproject.org/experiments/ENCSR256KTR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR256KTR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR603SVD
encode release date: 2016-11-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB536PES
size range: 200-600
nucleic acid starting quantity: 116.75
nucleic acid starting quantity units: ng

value: neural progenitor cell

value: in vitro differentiated cells


title: ChIP-seq from neural progenitor cell (ENCLB460ZVK)

description:
https://www.encodeproject.org/experiments/ENCSR256KTR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR256KTR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR603SVD
encode release date: 2016-11-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB460ZVK
size range: 200-600

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


title: ChIP-seq from induced pluripotent stem cell (ENCLB102RMQ)

description:
https://www.encodeproject.org/experiments/ENCSR249YGG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR249YGG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB102RMQ
size range: 200-600

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

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

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

value: male

value: Thomas Gingeras, CSHL

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

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

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

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


title: RF2*∆RF3_exp4_repA_mRNA

description: total RNA

value: K12 MG1655 prfB-Bstrain allele deltaprfC


title: WT_exp1_ribosome

description: ribosome protected RNA fragments


title: ChIP-seq from MM.1S (ENCLB004TFB)

description:
https://www.encodeproject.org/experiments/ENCSR264HOB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR264HOB
assay title: ChIP-seq
encode release date: 2015-08-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB004TFB
size range: 300-600

value: Control

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

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: ChIP-seq from bipolar spindle neuron (ENCLB528LON)

description:
https://www.encodeproject.org/experiments/ENCSR247PYK/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR247PYK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR001KCX
encode release date: 2016-05-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB528LON
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: bipolar spindle neuron

value: in vitro differentiated cells

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

value: 53 year

value: male

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


title: ChIP-seq from induced pluripotent stem cell (ENCLB757FNZ)

description:
https://www.encodeproject.org/experiments/ENCSR236YPE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR236YPE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB757FNZ
size range: 200-600

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

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

value: Thomas Gingeras, CSHL

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

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

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

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


title: RF2*_exp3_mRNA

description: total RNA

value: K12 MG1655 prfB-Bstrain allele


title: ChIP-seq from induced pluripotent stem cell (ENCLB755YHD)

description:
https://www.encodeproject.org/experiments/ENCSR236YPE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR236YPE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB755YHD
size range: 200-600

value: adult

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


title: ChIP-seq from induced pluripotent stem cell (ENCLB674TUZ)

description:
https://www.encodeproject.org/experiments/ENCSR249YGG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR249YGG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2016-05-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB674TUZ
size range: 200-600


title: RF2*∆RF3_exp2_repB_mRNA

description: total RNA

value: K12 MG1655 prfB-Bstrain allele deltaprfC


title: RF2*∆RF3_exp4_repB_mRNA

description: total RNA


title: ChIP-seq from bipolar spindle neuron (ENCLB839RKP)

description:
https://www.encodeproject.org/experiments/ENCSR247PYK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR247PYK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR001KCX
encode release date: 2016-05-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB839RKP
size range: 200-600

value: bipolar spindle neuron

value: in vitro differentiated cells

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


title: ChIP-seq from breast epithelium (ENCLB612VTX)

description:
https://www.encodeproject.org/experiments/ENCSR247XFQ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR247XFQ
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB612VTX
size range: 200-600

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

value: Control

value: breast epithelium

value: tissue

value: EnTEX:Breast - Mammary Tissue

value: female

value: 53 year

value: Bradley Bernstein, Broad

value: ENCBS433LAO at ENCODE; https://www.encodeproject.org/ENCBS433LAO/

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


title: RF2*_exp1_mRNA

description: total RNA


title: ChIP-seq from thyroid gland (ENCLB661MLR)

description:
https://www.encodeproject.org/experiments/ENCSR225VCV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR225VCV
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR777VQP
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB661MLR
size range: 200-600

value: thyroid gland

value: male

value: 37 year

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

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


title: RF2*∆RF3_exp2_repA_mRNA

description: total RNA

value: K12 MG1655 prfB-Bstrain allele deltaprfC


title: ∆RF3_exp3_mRNA

description: total RNA

value: K12 MG1655 deltaprfC


title: RF2*∆RF3_exp3_mRNA

description: total RNA


title: ∆RF3_exp1_mRNA

description: total RNA


title: ChIP-seq from thyroid gland (ENCLB734PTL)

description:
https://www.encodeproject.org/experiments/ENCSR225VCV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR225VCV
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR777VQP
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB734PTL
size range: 200-600

value: adult


title: WT_exp3_mRNA

description: total RNA


title: ChIP-seq from HCT116 (ENCLB447JUQ)

description:
https://www.encodeproject.org/experiments/ENCSR227XNT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR227XNT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2017-01-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB447JUQ
size range: 200-600

source_name: Homo sapiens HCT116 immortalized cell line

value: immortalized cell line

value: cells obtained from ATCC

value: unknown

value: colorectal carcinoma

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

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

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

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


title: ChIP-seq from hepatocyte (ENCLB244HLM)

description:
https://www.encodeproject.org/experiments/ENCSR220XCD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR220XCD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR107PGG
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB244HLM
size range: 200-600

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: 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: ChIP-seq from HCT116 (ENCLB843PKP)

description:
https://www.encodeproject.org/experiments/ENCSR227XNT/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR227XNT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2017-01-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB843PKP
size range: 200-600

value: immortalized cell line

value: cells obtained from ATCC

value: male

value: Bradley Bernstein, Broad

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


title: WT_exp4_mRNA

description: total RNA


title: WT_exp3_ribosome

description: ribosome protected RNA fragments


title: WT_exp1_mRNA

description: total RNA


title: ChIP-seq from smooth muscle cell (ENCLB060LLH)

description:
https://www.encodeproject.org/experiments/ENCSR210ZPC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR210ZPC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB060LLH
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: ENCBS780PCJ at ENCODE; https://www.encodeproject.org/ENCBS780PCJ/


title: WT_exp2_mRNA

description: total RNA


title: ChIP-seq from smooth muscle cell (ENCLB891RKX)

description:
https://www.encodeproject.org/experiments/ENCSR210ZPC/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR210ZPC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB891RKX
size range: 200-600
nucleic acid starting quantity: 60.06
nucleic acid starting quantity units: ng

value: in vitro differentiated cells

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


title: ChIP-seq from smooth muscle cell (ENCLB902XMZ)

description:
https://www.encodeproject.org/experiments/ENCSR210ZPC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR210ZPC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB902XMZ
size range: 200-600
nucleic acid starting quantity: 68.5
nucleic acid starting quantity units: ng

value: 5 day


title: TetTKO-ESC-liMAB-rep1

city: Boston

first: Xiaoji

last: Wu

state: MA

address: 149G Warren Alpert Building, 200 Longwood Avenue

department: PCMM

institute: Boston Children's Hospital

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.

organism: Mus musculus

source_name: Mouse embryonic stem cells

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: Around 100 mouse embryonic stem cells, E14

value: Tet TKO


title: ChIP-seq from gastrocnemius medialis (ENCLB151TWB)

description:
https://www.encodeproject.org/experiments/ENCSR206STN/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR206STN
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR775IMI
encode release date: 2016-11-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB151TWB
size range: 200-600
nucleic acid starting quantity: 100.54
nucleic acid starting quantity units: ng

source_name: Homo sapiens gastrocnemius medialis tissue male adult (37 years)

value: gastrocnemius medialis

value: tissue

tag: description

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

value: adult

value: 37 year

value: ENCBS861DVK at ENCODE; https://www.encodeproject.org/ENCBS861DVK/

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


title: ChIP-seq from gastrocnemius medialis (ENCLB793PYA)

description:
https://www.encodeproject.org/experiments/ENCSR206STN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR206STN
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR775IMI
encode release date: 2016-11-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB793PYA
size range: 200-600
nucleic acid starting quantity: 100.54
nucleic acid starting quantity units: ng

tag: biosample encode accession

value: male

value: Bradley Bernstein, Broad


title: Sperm-regularMAB-rep2

source_name: Sperm

value: Purified sperm DNA

value: Wild type


title: ChIP-seq from gastrocnemius medialis (ENCLB970DHJ)

description:
https://www.encodeproject.org/experiments/ENCSR206STN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR206STN
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR775IMI
encode release date: 2016-11-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB970DHJ
size range: 200-600
nucleic acid starting quantity: 297
nucleic acid starting quantity units: ng

tag: dev stage


title: Sperm-regularMAB-rep1


title: ChIP-seq from thyroid gland (ENCLB643AYL)

description:
https://www.encodeproject.org/experiments/ENCSR203KCB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR203KCB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR164POT
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB643AYL
size range: 200-600
nucleic acid starting quantity: 135.8
nucleic acid starting quantity units: ng

source_name: Homo sapiens thyroid gland tissue male adult (54 years)

tag: antibody

value: thyroid gland

value: 54 year

value: ENCBS050AKF at ENCODE; https://www.encodeproject.org/ENCBS050AKF/

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


title: ChIP-seq from thyroid gland (ENCLB858CWL)

description:
https://www.encodeproject.org/experiments/ENCSR203KCB/
***************
biological replicate number: 2
technical replicate number: 4
description:
experiment encode accession: ENCSR203KCB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR164POT
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB858CWL
size range: 200-600
nucleic acid starting quantity: 135.8
nucleic acid starting quantity units: ng

tag: age


title: TetTKO-ESC-liMAB-PBAT-MAB

source_name: TetTKO-ESC-liMAB-PBAT-MAB

value: Around 100 mouse embryonic stem cells, E14


title: ChIP-seq from thyroid gland (ENCLB953TBZ)

description:
https://www.encodeproject.org/experiments/ENCSR203KCB/
***************
biological replicate number: 1
technical replicate number: 2
description:
experiment encode accession: ENCSR203KCB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR164POT
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB953TBZ
size range: 200-600
nucleic acid starting quantity: 131.6
nucleic acid starting quantity units: ng

tag: Sex


title: shTdg-ESC-regularMAB

value: shTdg


title: Sperm-regularBS-rep1


title: ChIP-seq from thyroid gland (ENCLB289VGQ)

description:
https://www.encodeproject.org/experiments/ENCSR203KCB/
***************
biological replicate number: 2
technical replicate number: 3
description:
experiment encode accession: ENCSR203KCB
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR164POT
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB289VGQ
size range: 200-600
nucleic acid starting quantity: 131.6
nucleic acid starting quantity units: ng


title: ChIP-seq from hepatocyte (ENCLB976TQV)

description:
https://www.encodeproject.org/experiments/ENCSR220XCD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR220XCD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR107PGG
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB976TQV
size range: 200-600

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: female

tag: health state

value: healthy

value: Richard Myers, HAIB

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

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


title: sc-TetTKO7-PBAT-MAB

value: Single mouse embryonic stem cells, E14

value: Tet TKO


title: ChIP-seq from OCI-LY7 (ENCLB576ISW)

description:
https://www.encodeproject.org/experiments/ENCSR199KHR/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR199KHR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR063AUO
encode release date: 2016-10-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB576ISW
size range: 200-600

source_name: Homo sapiens OCI-LY7 immortalized cell line

value: immortalized cell line

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

value: 48 year

value: adult

value: male

value: B cell lymphoma

tag: lab

value: Bradley Bernstein, Broad

value: ENCBS304FAI at ENCODE; https://www.encodeproject.org/ENCBS304FAI/

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

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


title: shTdg-ESC-liMAB-PBAT-MAB

source_name: shTdg-ESC-liMAB-PBAT-MAB

value: Around 100 mouse embryonic stem cells, E14

value: shTdg


title: ChIP-seq from GM12878 (ENCLB931QSZ)

description:
https://www.encodeproject.org/experiments/ENCSR199WXF/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on GM12878-human
experiment encode accession: ENCSR199WXF
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR890ZMI, ENCSR136WQZ
encode release date: 2016-03-30
lab: Richard Myers, HAIB
library encode accession: ENCLB931QSZ

source_name: Homo sapiens GM12878 immortalized cell line

value: EED

value: GM12878, B-lymphocyte, lymphoblastoid.

value: female

value: unknown

value: Richard Myers, HAIB

tag: link

value: ENCBS083XJQ at ENCODE; https://www.encodeproject.org/ENCBS083XJQ/

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

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

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


title: sc-TetTKO6-PBAT-MAB

value: Single mouse embryonic stem cells, E14

value: Tet TKO


title: ChIP-seq from OCI-LY7 (ENCLB428SHK)

description:
https://www.encodeproject.org/experiments/ENCSR199KHR/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR199KHR
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR063AUO
encode release date: 2016-10-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB428SHK
size range: 200-600
nucleic acid starting quantity: 18.32
nucleic acid starting quantity units: ng

value: immortalized cell line

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

value: 48 year

value: adult

value: male

value: B cell lymphoma

value: Bradley Bernstein, Broad

value: ENCBS699NWP at ENCODE; https://www.encodeproject.org/ENCBS699NWP/


title: TetTKO-ESC-liMAB-rep2

value: Around 100 mouse embryonic stem cells, E14


title: ChIP-seq from PC-3 (ENCLB921NJR)

description:
https://www.encodeproject.org/experiments/ENCSR197QXT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR197QXT
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR328AHC
encode release date: 2016-11-09
lab: Bradley Bernstein, Broad
library encode accession: ENCLB921NJR
size range: 300-600
nucleic acid starting quantity: 18.496
nucleic acid starting quantity units: ng

source_name: Homo sapiens PC-3 immortalized cell line

value: prostate cancer cell line

value: 62 year

value: grade IV, adenocarcinoma

tag: passage number

value: ENCBS596CTT at ENCODE; https://www.encodeproject.org/ENCBS596CTT/

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

value: ENCODE dbxrefs Cellosaurus CVCL_0035; http://web.expasy.org/cellosaurus/CVCL_0035

value: ATCC sample source; http://www.atcc.org/products/all/CRL-1435.aspx


title: ChIP-seq from gastrocnemius medialis (ENCLB737OGT)

description:
https://www.encodeproject.org/experiments/ENCSR206STN/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR206STN
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR775IMI
encode release date: 2016-11-17
lab: Bradley Bernstein, Broad
library encode accession: ENCLB737OGT
size range: 200-600
nucleic acid starting quantity: 297
nucleic acid starting quantity units: ng

value: gastrocnemius medialis

value: tissue

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

value: 37 year

value: ENCBS861DVK at ENCODE; https://www.encodeproject.org/ENCBS861DVK/

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


title: sc-TetTKO5-PBAT-MAB

value: Single mouse embryonic stem cells, E14

value: Tet TKO


title: Sperm-regularBS-rep2

value: Purified sperm DNA

value: Wild type


title: ChIP-seq from smooth muscle cell (ENCLB938LRC)

description:
https://www.encodeproject.org/experiments/ENCSR189XIE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR189XIE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-11-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB938LRC
size range: 200-600
nucleic acid starting quantity: 16.65
nucleic acid starting quantity units: ng

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

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

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

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


title: sc-TetTKO3

source_name: Single mouse embryonic stem cell


title: sc-TetTKO4


title: sc-shTdg7

value: shTdg


title: ChIP-seq from Loucy (ENCLB651GRG)

description:
https://www.encodeproject.org/experiments/ENCSR183CQK/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR183CQK
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR648HLP
encode release date: 2014-09-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB651GRG
size range: 200-600

source_name: Homo sapiens Loucy immortalized cell line

value: Loucy

value: immortalized cell line

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

value: adult

value: 38 year

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

value: Bradley Bernstein, Broad

value: ENCBS170DPY at ENCODE; https://www.encodeproject.org/ENCBS170DPY/

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

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

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


title: sc-TetTKO2

value: Single mouse embryonic stem cells, E14

value: Tet TKO


title: shTdg-ESC-liMAB-rep1

value: Around 100 mouse embryonic stem cells, E14


title: sc-TetTKO1


title: ChIP-seq from smooth muscle cell (ENCLB837WBU)

description:
https://www.encodeproject.org/experiments/ENCSR189XIE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR189XIE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-11-07
lab: Bradley Bernstein, Broad
library encode accession: ENCLB837WBU
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

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

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


title: ChIP-seq from HCT116 (ENCLB245ENB)

description:
https://www.encodeproject.org/experiments/ENCSR179BUC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR179BUC
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR198WIH
encode release date: 2017-01-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB245ENB
size range: 200-600

value: immortalized cell line

value: cells obtained from ATCC

value: unknown

value: male

value: colorectal carcinoma

value: Bradley Bernstein, Broad

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

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

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

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


title: shTdg-ESC-liMAB-rep2

value: Around 100 mouse embryonic stem cells, E14

value: shTdg


title: ChIP-seq from gastroesophageal sphincter (ENCLB795YAL)

description:
https://www.encodeproject.org/experiments/ENCSR178MWD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR178MWD
assay title: ChIP-seq
encode release date: 2016-11-03
lab: Bradley Bernstein, Broad
library encode accession: ENCLB795YAL
size range: 200-600

source_name: Homo sapiens gastroesophageal sphincter tissue female adult (53 years)

value: Control

value: gastroesophageal sphincter

value: tissue

value: EnTEX:Esophagus - Gastroesophageal Junction

value: adult

value: 53 year

value: ENCBS783BYN at ENCODE; https://www.encodeproject.org/ENCBS783BYN/

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


title: sc-shTdg8

value: Single mouse embryonic stem cells, E14


title: ChIP-seq from Loucy (ENCLB998KLX)

description:
https://www.encodeproject.org/experiments/ENCSR186EAD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR186EAD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR648HLP
encode release date: 2016-11-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB998KLX
size range: 200-600

value: Loucy

value: immortalized cell line

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

value: female

value: 38 year

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

value: ENCBS170DPY at ENCODE; https://www.encodeproject.org/ENCBS170DPY/

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

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

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


title: ChIP-seq from adrenal gland (ENCLB670CFC)

description:
https://www.encodeproject.org/experiments/ENCSR177QFY/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR177QFY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828HXJ
encode release date: 2016-10-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB670CFC
size range: 200-600

source_name: Homo sapiens adrenal gland tissue male adult (54 years)

value: adrenal gland

value: tissue

value: EnTEX:Adrenal Gland

value: male

value: 54 year

value: Bradley Bernstein, Broad

value: ENCBS078MQQ at ENCODE; https://www.encodeproject.org/ENCBS078MQQ/

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


title: ChIP-seq from Loucy (ENCLB642DOZ)

description:
https://www.encodeproject.org/experiments/ENCSR186EAD/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR186EAD
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR648HLP
encode release date: 2016-11-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB642DOZ
size range: 200-600
nucleic acid starting quantity: 34.76
nucleic acid starting quantity units: ng

value: Loucy

value: immortalized cell line

value: adult

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


title: sc-shTdg6

value: Single mouse embryonic stem cells, E14

value: shTdg


title: ChIP-seq from A673 (ENCLB017BXD)

description:
https://www.encodeproject.org/experiments/ENCSR196CXJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR196CXJ
assay title: ChIP-seq
encode release date: 2016-05-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB017BXD
size range: 200-600

source_name: Homo sapiens A673 immortalized cell line

value: Control

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

value: unknown

value: female

value: 15 year

value: ENCBS615MBV at ENCODE; https://www.encodeproject.org/ENCBS615MBV/

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

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


title: sc-shTdg2


title: sc-shTdg3


title: sc-shTdg4


title: ChIP-seq from adrenal gland (ENCLB281DGJ)

description:
https://www.encodeproject.org/experiments/ENCSR177QFY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR177QFY
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR828HXJ
encode release date: 2016-10-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB281DGJ
size range: 200-600

value: adrenal gland

value: tissue

value: EnTEX:Adrenal Gland

value: male

value: 54 year

value: Bradley Bernstein, Broad


title: ChIP-seq from bipolar spindle neuron (ENCLB738OMX)

description:
https://www.encodeproject.org/experiments/ENCSR175OYG/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR175OYG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR001KCX
encode release date: 2017-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB738OMX
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: bipolar spindle neuron

value: in vitro differentiated cells

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

value: 53 year

value: adult

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: sc-shTdg17-PBAT-MAB

value: Single mouse embryonic stem cells, E14

value: shTdg


title: ChIP-seq from thyroid gland (ENCLB058OFH)

description:
https://www.encodeproject.org/experiments/ENCSR164POT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR164POT
assay title: ChIP-seq
encode release date: 2016-05-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB058OFH
size range: 200-600

value: Control

value: thyroid gland

value: ENCBS050AKF at ENCODE; https://www.encodeproject.org/ENCBS050AKF/

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


title: ChIP-seq from HCT116 (ENCLB523TSS)

description:
https://www.encodeproject.org/experiments/ENCSR161MXP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR161MXP
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR198WIH
encode release date: 2017-01-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB523TSS
size range: 200-600

source_name: Homo sapiens HCT116 immortalized cell line

value: immortalized cell line

value: cells obtained from ATCC

value: unknown

value: male

value: colorectal carcinoma

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

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

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

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


title: sc-shTdg5


title: sc-shTdg14-PBAT-MAB


title: sc-shTdg10


title: sc-shTdg15-PBAT-MAB


title: ChIP-seq from HCT116 (ENCLB029TSZ)

description:
https://www.encodeproject.org/experiments/ENCSR161MXP/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR161MXP
assay title: ChIP-seq
assembly: hg19, GRCh38
possible controls: ENCSR198WIH
encode release date: 2017-01-23
lab: Bradley Bernstein, Broad
library encode accession: ENCLB029TSZ
size range: 200-600
nucleic acid starting quantity: 74.58
nucleic acid starting quantity units: ng

value: Bradley Bernstein, Broad


title: sc-shTdg13


title: ChIP-seq from gastrocnemius medialis (ENCLB843GIW)

description:
https://www.encodeproject.org/experiments/ENCSR161HZJ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR161HZJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR897RRA
encode release date: 2016-10-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB843GIW
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: 54 year

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


title: ChIP-seq from Karpas-422 (ENCLB408PTN)

description:
https://www.encodeproject.org/experiments/ENCSR159CDJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR159CDJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR367UDO
encode release date: 2014-07-11
lab: Bradley Bernstein, Broad
library encode accession: ENCLB408PTN
size range: 200-600

source_name: Homo sapiens Karpas-422 immortalized cell line

value: Karpas422- Human B cell non-Hodgkin lymphoma

value: 73 year

value: female

value: human B cell non-Hodgkin's lymphoma

value: ENCBS301UOD at ENCODE; https://www.encodeproject.org/ENCBS301UOD/

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: PPN-liMAB-rep2

source_name: Zygotic paternal pronuclei

value: Around 150 zygotic paternal pronuclei

value: Wild type


title: ChIP-seq from bipolar spindle neuron (ENCLB147HOI)

description:
https://www.encodeproject.org/experiments/ENCSR175OYG/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR175OYG
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR001KCX
encode release date: 2017-01-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB147HOI
size range: 200-600

value: bipolar spindle neuron

value: in vitro differentiated cells

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

value: 53 year

value: male

value: Thomas Gingeras, CSHL

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

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


title: sc-shTdg12

value: Single mouse embryonic stem cells, E14

value: shTdg


title: sc-shTdg1


title: ChIP-seq from thoracic aorta (ENCLB000ORB)

description:
https://www.encodeproject.org/experiments/ENCSR158PLZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR158PLZ
assay title: ChIP-seq
encode release date: 2016-08-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB000ORB
size range: 200-600

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

value: Control

value: thoracic aorta

value: tissue

value: EnTEX:Artery- Aorta

value: adult

value: 37 year

value: Bradley Bernstein, Broad

value: ENCBS882JUX at ENCODE; https://www.encodeproject.org/ENCBS882JUX/

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


title: ChIP-seq from gastrocnemius medialis (ENCLB027VNS)

description:
https://www.encodeproject.org/experiments/ENCSR161HZJ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR161HZJ
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR897RRA
encode release date: 2016-10-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB027VNS
size range: 200-600

value: gastrocnemius medialis

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

value: 54 year

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

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


title: PPN-liMAB-rep1

value: Around 150 zygotic paternal pronuclei

value: Wild type


title: ChIP-seq from thoracic aorta (ENCLB308TVO)

description:
https://www.encodeproject.org/experiments/ENCSR158PLZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR158PLZ
assay title: ChIP-seq
encode release date: 2016-08-10
lab: Bradley Bernstein, Broad
library encode accession: ENCLB308TVO
size range: 200-600

value: male

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


title: ChIP-seq from induced pluripotent stem cell (ENCLB098CZE)

description:
https://www.encodeproject.org/experiments/ENCSR154HDX/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR154HDX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2017-01-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB098CZE
size range: 200-600

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

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

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

value: 53 year

value: Thomas Gingeras, CSHL

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

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

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

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


title: PPN-liBS-rep2

value: Around 75 zygotic paternal pronuclei


title: ChIP-seq from smooth muscle cell (ENCLB428ZUX)

description:
https://www.encodeproject.org/experiments/ENCSR143RMH/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR143RMH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB428ZUX
size range: 200-600
nucleic acid starting quantity: 10.375
nucleic acid starting quantity units: ng

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

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

value: embryonic

value: female

value: healthy

value: Richard Myers, HAIB

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

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


title: ChIP-seq from induced pluripotent stem cell (ENCLB916GVQ)

description:
https://www.encodeproject.org/experiments/ENCSR154HDX/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR154HDX
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR773IYZ
encode release date: 2017-01-19
lab: Bradley Bernstein, Broad
library encode accession: ENCLB916GVQ
size range: 200-600

value: induced pluripotent stem cell

value: induced pluripotent stem cell line

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

value: 53 year

value: adult

value: male

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


title: PPN-liBS-rep1

value: Around 75 zygotic paternal pronuclei

value: Wild type


title: ChIP-seq from SK-N-MC (ENCLB914AVX)

description:
https://www.encodeproject.org/experiments/ENCSR152QRE/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq against H3K4me1 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: ENCSR152QRE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR899XXQ
encode release date: 2016-11-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB914AVX
size range: 200-600

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: ENCBS734TWP at ENCODE; https://www.encodeproject.org/ENCBS734TWP/

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


title: ChIP-seq from SK-N-MC (ENCLB568HLM)

description:
https://www.encodeproject.org/experiments/ENCSR152QRE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-seq against H3K4me1 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: ENCSR152QRE
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR899XXQ
encode release date: 2016-11-14
lab: Bradley Bernstein, Broad
library encode accession: ENCLB568HLM
size range: 200-600
nucleic acid starting quantity: 105
nucleic acid starting quantity units: ng

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


title: DnmtTKO-ESC-liMAB-rep1

source_name: Mouse embryonic stem cells

value: Around 100 mouse embryonic stem cells, J1

value: Dnmt TKO


title: ChIP-seq from smooth muscle cell (ENCLB523RNC)

description:
https://www.encodeproject.org/experiments/ENCSR143RMH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR143RMH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB523RNC
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

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: 4cell-3d

source_name: Single 4-cell blastomere

value: Single mouse 4-cell blastomere

value: Wild type


title: ChIP-seq from smooth muscle cell (ENCLB382KRQ)

description:
https://www.encodeproject.org/experiments/ENCSR143RMH/
***************
biological replicate number: 2
technical replicate number: 2
description:
experiment encode accession: ENCSR143RMH
assay title: ChIP-seq
assembly: GRCh38, hg19
possible controls: ENCSR729MRJ
encode release date: 2016-04-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB382KRQ
size range: 200-600
nucleic acid starting quantity: 14.3
nucleic acid starting quantity units: ng

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


title: ChIP-seq from GM12878 (ENCLB552LWE)

description:
https://www.encodeproject.org/experiments/ENCSR142REC/
***************
biological replicate number: 3
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: ENCLB552LWE
size range: 200-600

source_name: Homo sapiens GM12878 immortalized cell line

value: Control

value: immortalized cell line

value: adult

value: unknown

value: Bradley Bernstein, Broad

value: ENCBS900QPF at ENCODE; https://www.encodeproject.org/ENCBS900QPF/

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


title: ChIP-seq from GM12878 (ENCLB399DLQ)

description:
https://www.encodeproject.org/experiments/ENCSR142REC/
***************
biological replicate number: 4
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: ENCLB399DLQ
size range: 200-600

value: female

value: ENCBS127ZRH at ENCODE; https://www.encodeproject.org/ENCBS127ZRH/


title: 4cell-3b


title: 4cell-3c


title: 4cell-3a


title: sc-shTdg16-PBAT-MAB

value: Single mouse embryonic stem cells, E14

value: shTdg


title: ChIP-seq from GM12878 (ENCLB652KAS)

description:
https://www.encodeproject.org/experiments/ENCSR142REC/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR142REC
assay title: ChIP-seq
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB652KAS
size range: 200-600


title: ChIP-seq from GM12878 (ENCLB641LWV)

description:
https://www.encodeproject.org/experiments/ENCSR142REC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR142REC
assay title: ChIP-seq
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB641LWV
size range: 200-600

value: ENCBS330WEW at ENCODE; https://www.encodeproject.org/ENCBS330WEW/


title: ChIP-seq from GM12878 (ENCLB067ZPY)

description:
https://www.encodeproject.org/experiments/ENCSR142REC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR142REC
assay title: ChIP-seq
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB067ZPY
size range: 200-600

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


title: ChIP-seq from GM12878 (ENCLB534MCJ)

description:
https://www.encodeproject.org/experiments/ENCSR142REC/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR142REC
assay title: ChIP-seq
encode release date: 2016-10-27
lab: Bradley Bernstein, Broad
library encode accession: ENCLB534MCJ
size range: 200-600


title: 4cell-1d


title: 4cell-2c-PBAT-MAB


title: ChIP-seq from neural progenitor cell (ENCLB107NYY)

description:
https://www.encodeproject.org/experiments/ENCSR139PIA/
***************
biological replicate number: 2
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: ENCLB107NYY
size range: 200-600

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

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: 4cell-2b-PBAT-MAB

value: Single mouse 4-cell blastomere

value: Wild type


title: 4cell-2a-PBAT-MAB