title: ChIP-seq from forebrain (ENCLB380JQT)

description:
https://www.encodeproject.org/experiments/ENCSR094TTT/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR094TTT
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR398NCK
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB380JQT
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap forebrain tissue mixed sex postnatal (0 days)

value: Forebrain from 15 postnatal 0 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS038AAA at ENCODE; https://www.encodeproject.org/ENCBS038AAA/


title: ChIP-seq from intestine (ENCLB888CCO)

status: Public on Jun 22 2016

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/ENCSR051CUH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 15.5 day mouse intestine
experiment encode accession: ENCSR051CUH
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR872UEE
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB888CCO
size range: 300-500

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: Mus musculus strain B6NCrl intestine tissue mixed sex embryo (15.5 days)

tag: antibody

value: intestine

value: tissue

tag: description

value: Intestine from 78 embryonic 15.5 day mice

tag: biosample encode accession

tag: age

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

tag: health state

tag: lab

tag: link

value: ENCBS401LLS at ENCODE; https://www.encodeproject.org/ENCBS401LLS/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from forebrain (ENCLB375TZU)

description:
https://www.encodeproject.org/experiments/ENCSR094TTT/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR094TTT
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR398NCK
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB375TZU
size range: 300-500

value: forebrain

value: Forebrain of pooled postnatal 0 day mice

value: 0 day

value: postnatal

value: ENCBS554AAA at ENCODE; https://www.encodeproject.org/ENCBS554AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: WGBS from limb (ENCLB087TET)

description:
https://www.encodeproject.org/experiments/ENCSR099RYD/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 14.5 day mouse limb
experiment encode accession: ENCSR099RYD
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB087TET
size range: 180-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap limb tissue mixed sex embryo (14.5 days)

extract_protocol:
general protocol: https://www.encodeproject.org/documents/665c8f16-3724-4ab7-aa29-688f396bcd4f/@@download/attachment/Ecker_Protocol_Summary.png
general protocol: https://www.encodeproject.org/documents/862389c9-38b6-4e76-8b84-d82fb9a4c6cf/@@download/attachment/Ecker_Replication_Summary.png
extraction method: Qiagen DNeasy Blood and Tissue Kit
general protocol: https://www.encodeproject.org/documents/9d5f346e-88d3-45e2-b28a-2b26f537490f/@@download/attachment/Ecker_Methyl_protocol_v030114.pdf

value: limb

value: Limb from 34 embryonic 14.5 day mice

value: ENCBS023AAA at ENCODE; https://www.encodeproject.org/ENCBS023AAA/


title: ChIP-seq from forebrain (ENCLB379NXP)

description:
https://www.encodeproject.org/experiments/ENCSR093DWU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR093DWU
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR398NCK
encode release date: 2016-02-17
lab: Bing Ren, UCSD
library encode accession: ENCLB379NXP
size range: 300-500

value: healthy

value: Len Pennacchio, LBNL


title: ChIP-seq from stomach (ENCLB393ARS)

description:
https://www.encodeproject.org/experiments/ENCSR048IZJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-seq on postnatal 0 day mouse stomach
experiment encode accession: ENCSR048IZJ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR050VUZ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB393ARS
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap stomach tissue mixed sex postnatal (0 days)

value: stomach

value: tissue

value: Stomach from 15 postnatal 0 day mice

value: ENCBS045AAA at ENCODE; https://www.encodeproject.org/ENCBS045AAA/


title: ChIP-seq from forebrain (ENCLB983EYB)

description:
https://www.encodeproject.org/experiments/ENCSR093DWU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR093DWU
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR398NCK
encode release date: 2016-02-17
lab: Bing Ren, UCSD
library encode accession: ENCLB983EYB
size range: 300-500

value: Forebrain from 15 postnatal 0 day mice

value: pooled male and female

value: ENCBS038AAA at ENCODE; https://www.encodeproject.org/ENCBS038AAA/


title: WGBS from midbrain (ENCLB010VMX)

description:
https://www.encodeproject.org/experiments/ENCSR091VFX/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 11.5 day mouse midbrain
experiment encode accession: ENCSR091VFX
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB010VMX
size range: 180-500

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (11.5 days)

value: midbrain

value: Midbrain of 109 embyronic 11.5 day mice

value: embryonic

value: ENCBS228OBS at ENCODE; https://www.encodeproject.org/ENCBS228OBS/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from neural tube (ENCLB551UZQ)

description:
https://www.encodeproject.org/experiments/ENCSR093BYV/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 14.5 day mouse neural tube
experiment encode accession: ENCSR093BYV
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR254WNU
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB551UZQ
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap neural tube tissue mixed sex embryo (14.5 days)

value: neural tube

value: Neural tube from 34 embryonic 14.5 day mice

value: ENCBS025AAA at ENCODE; https://www.encodeproject.org/ENCBS025AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from stomach (ENCLB543QPY)

description:
https://www.encodeproject.org/experiments/ENCSR048IZJ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-seq on postnatal 0 day mouse stomach
experiment encode accession: ENCSR048IZJ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR050VUZ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB543QPY
size range: 300-500

value: Stomach from pooled postnatal 0 day mice

value: 0 day

value: postnatal

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS561AAA at ENCODE; https://www.encodeproject.org/ENCBS561AAA/


title: WGBS from midbrain (ENCLB140TDY)

description:
https://www.encodeproject.org/experiments/ENCSR091VFX/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 11.5 day mouse midbrain
experiment encode accession: ENCSR091VFX
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB140TDY
size range: 180-500

value: tissue

value: Midbrain from 88 embyronic 11.5 day mice

value: pooled male and female

value: ENCBS802FTI at ENCODE; https://www.encodeproject.org/ENCBS802FTI/


title: microRNA-seq from thymus (ENCLB507ENX)

description:
https://www.encodeproject.org/experiments/ENCSR047EJT/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq  on postnatal 0 day mouse thymus
experiment encode accession: ENCSR047EJT
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB507ENX
size range: <30

library_source: transcriptomic

molecule: total RNA

source_name: Mus musculus strain B6NCrl thymus tissue postnatal (0 days)

value: thymus

value: two thymus lobes from pup3 pregnant 1

value: not collected

value: Barbara Wold, Caltech

value: ENCBS898VIJ at ENCODE; https://www.encodeproject.org/ENCBS898VIJ/


title: ChIP-seq from liver (ENCLB772XLW)

description:
https://www.encodeproject.org/experiments/ENCSR095FDG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 16.5 day mouse liver
experiment encode accession: ENCSR095FDG
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR082JEN
encode release date: 2016-02-17
lab: Bing Ren, UCSD
library encode accession: ENCLB772XLW
size range: 300-500

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (16.5 days)

value: liver

value: Liver from 41 embyonic 16.5 day mice

value: embryonic

value: ENCBS279BWR at ENCODE; https://www.encodeproject.org/ENCBS279BWR/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: WGBS from intestine (ENCLB092PAI)

description:
https://www.encodeproject.org/experiments/ENCSR089FFK/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 14.5 day mouse intestine
experiment encode accession: ENCSR089FFK
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB092PAI
size range: 180-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap intestine tissue mixed sex embryo (14.5 days)

value: intestine

value: Intestine from 24 embryonic 14.5 day mice

value: healthy

value: ENCBS008AAA at ENCODE; https://www.encodeproject.org/ENCBS008AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: WGBS from midbrain (ENCLB964REL)

description:
https://www.encodeproject.org/experiments/ENCSR091VFX/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 11.5 day mouse midbrain
experiment encode accession: ENCSR091VFX
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB964REL
size range: 180-500

value: midbrain

value: tissue

value: Midbrain of 109 embyronic 11.5 day mice

value: pooled male and female

value: Len Pennacchio, LBNL

value: ENCBS228OBS at ENCODE; https://www.encodeproject.org/ENCBS228OBS/


title: ChIP-seq from hindbrain (ENCLB176YEN)

description:
https://www.encodeproject.org/experiments/ENCSR046SWI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on embryonic 16.5 day mouse hindbrain.NOTE- Files associated with this experiment are undergoing additional review and analysis
experiment encode accession: ENCSR046SWI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR752KDM
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB176YEN
size range: 300-500

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (16.5 days)

value: hindbrain

value: Hindbrain pooled from embyonic 16.5 day mice

value: ENCBS436LSH at ENCODE; https://www.encodeproject.org/ENCBS436LSH/


title: WGBS from intestine (ENCLB065JTE)

description:
https://www.encodeproject.org/experiments/ENCSR089FFK/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 14.5 day mouse intestine
experiment encode accession: ENCSR089FFK
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB065JTE
size range: 180-500

value: embryonic


title: WGBS from intestine (ENCLB212OKC)

description:
https://www.encodeproject.org/experiments/ENCSR089FFK/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 14.5 day mouse intestine
experiment encode accession: ENCSR089FFK
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB212OKC
size range: 180-500

value: Intestine from 34 embryonic 14.5 day mice

value: ENCBS020AAA at ENCODE; https://www.encodeproject.org/ENCBS020AAA/


title: microRNA-seq from thymus (ENCLB724KXY)

description:
https://www.encodeproject.org/experiments/ENCSR047EJT/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq  on postnatal 0 day mouse thymus
experiment encode accession: ENCSR047EJT
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-02-02
lab: Ali Mortazavi, UCI
library encode accession: ENCLB724KXY
size range: <30

value: thymus

value: two thymus lobes from pup2 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS079WTJ at ENCODE; https://www.encodeproject.org/ENCBS079WTJ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from neural tube (ENCLB847VQL)

description:
https://www.encodeproject.org/experiments/ENCSR044SNE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 15.5 day mouse neural tube
experiment encode accession: ENCSR044SNE
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR351BDM
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB847VQL
size range: 300-500

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (15.5 days)

value: neural tube

value: tissue

value: Neural tube from 78 embryonic 15.5 day mice

value: pooled male and female

value: healthy

value: ENCBS944KEZ at ENCODE; https://www.encodeproject.org/ENCBS944KEZ/


title: ChIP-seq from forebrain (ENCLB274BQC)

description:
https://www.encodeproject.org/experiments/ENCSR044SUW/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 13.5 day mouse forebrain
experiment encode accession: ENCSR044SUW
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR583ZEV
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB274BQC
size range: 300-500

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (13.5 days)

value: forebrain

value: Forebrain from embryonic 13.5 day mice

value: embryonic

value: Len Pennacchio, LBNL

value: ENCBS273RVL at ENCODE; https://www.encodeproject.org/ENCBS273RVL/


title: ChIP-seq from liver (ENCLB778NAT)

description:
https://www.encodeproject.org/experiments/ENCSR045NOD/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 13.5 day mouse liver
experiment encode accession: ENCSR045NOD
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR220PXJ
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB778NAT
size range: 300-500

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (13.5 days)

value: liver

value: Liver from embryonic 13.5 day mice

value: ENCBS146FGW at ENCODE; https://www.encodeproject.org/ENCBS146FGW/


title: ChIP-seq from midbrain (ENCLB934XBW)

description:
https://www.encodeproject.org/experiments/ENCSR088UKA/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 11.5 day mouse midbrain
experiment encode accession: ENCSR088UKA
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR081UQY
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB934XBW
size range: 300-500

value: midbrain

value: Midbrain from 88 embyronic 11.5 day mice

value: ENCBS802FTI at ENCODE; https://www.encodeproject.org/ENCBS802FTI/


title: ChIP-seq from forebrain (ENCLB303GQD)

description:
https://www.encodeproject.org/experiments/ENCSR044SUW/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 13.5 day mouse forebrain
experiment encode accession: ENCSR044SUW
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR583ZEV
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB303GQD
size range: 300-500

value: ENCBS793ZRY at ENCODE; https://www.encodeproject.org/ENCBS793ZRY/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from neural tube (ENCLB002GIK)

description:
https://www.encodeproject.org/experiments/ENCSR044SNE/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 15.5 day mouse neural tube
experiment encode accession: ENCSR044SNE
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR351BDM
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB002GIK
size range: 300-500

value: neural tube

value: tissue

value: Neural tube from 62 embryonic 15.5 day mice

value: ENCBS206NRE at ENCODE; https://www.encodeproject.org/ENCBS206NRE/


title: ChIP-seq from neural tube (ENCLB960XUI)

description:
https://www.encodeproject.org/experiments/ENCSR087PLZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 13.5 day mouse neural tube
experiment encode accession: ENCSR087PLZ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR295GGT
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB960XUI
size range: 300-500

source_name: Mus musculus strain B6NCrl neural tube tissue mixed sex embryo (13.5 days)

value: Neural tube from embryonic 13.5 day mice

value: pooled male and female

value: healthy

value: ENCBS956BQY at ENCODE; https://www.encodeproject.org/ENCBS956BQY/


title: ChIP-seq from forebrain (ENCLB140CLN)

description:
https://www.encodeproject.org/experiments/ENCSR087JEN/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K36me3 ChIP-seq on embryonic 13.5 day mouse forebrain
experiment encode accession: ENCSR087JEN
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR583ZEV
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB140CLN
size range: 300-500
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

value: forebrain

value: Forebrain from embryonic 13.5 day mice

value: embryonic

value: Len Pennacchio, LBNL

value: ENCBS273RVL at ENCODE; https://www.encodeproject.org/ENCBS273RVL/


title: ChIP-seq from midbrain (ENCLB821ENB)

description:
https://www.encodeproject.org/experiments/ENCSR037HLB/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 14.5 day mouse midbrain
experiment encode accession: ENCSR037HLB
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR413VHH
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB821ENB
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap midbrain tissue mixed sex embryo (14.5 days)

value: midbrain

value: Midbrain from 34 embryonic 14.5 day mice

value: ENCBS015AAA at ENCODE; https://www.encodeproject.org/ENCBS015AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: WGBS from midbrain (ENCLB724WWR)

description:
https://www.encodeproject.org/experiments/ENCSR091VFX/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 11.5 day mouse midbrain
experiment encode accession: ENCSR091VFX
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB724WWR
size range: 180-500

value: Midbrain from 88 embyronic 11.5 day mice

value: ENCBS802FTI at ENCODE; https://www.encodeproject.org/ENCBS802FTI/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from forebrain (ENCLB815WTN)

description:
https://www.encodeproject.org/experiments/ENCSR041KEJ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 13.5 day mouse forebrain
experiment encode accession: ENCSR041KEJ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR583ZEV
encode release date: 2016-03-16
lab: Bing Ren, UCSD
library encode accession: ENCLB815WTN
size range: 300-500

value: tissue

value: ENCBS793ZRY at ENCODE; https://www.encodeproject.org/ENCBS793ZRY/


title: ChIP-seq from limb (ENCLB584XCJ)

description:
https://www.encodeproject.org/experiments/ENCSR085EYQ/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K27me3 ChIP-seq on embryonic 11.5 day mouse limb
experiment encode accession: ENCSR085EYQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR949ZLW
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB584XCJ
size range: 300-500

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (11.5 days)

value: limb

value: Limb from 88 embyronic 11.5 day mice

value: pooled male and female

value: ENCBS681XPR at ENCODE; https://www.encodeproject.org/ENCBS681XPR/


title: ChIP-seq from kidney (ENCLB538KYM)

description:
https://www.encodeproject.org/experiments/ENCSR036YKL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR036YKL
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR780JSE
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB538KYM
size range: 300-500

source_name: Mus musculus strain B6NCrl kidney tissue mixed sex embryo (15.5 days)

value: kidney

value: Kidney from 78 embryonic 15.5 day mice

value: healthy

value: ENCBS899UOK at ENCODE; https://www.encodeproject.org/ENCBS899UOK/


title: ChIP-seq from midbrain (ENCLB005BWP)

description:
https://www.encodeproject.org/experiments/ENCSR037HLB/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 14.5 day mouse midbrain
experiment encode accession: ENCSR037HLB
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR413VHH
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB005BWP
size range: 300-500

value: midbrain

value: Midbrain from 24 embryonic 14.5 day mice

value: embryonic

value: Len Pennacchio, LBNL

value: ENCBS003AAA at ENCODE; https://www.encodeproject.org/ENCBS003AAA/


title: ChIP-seq from limb (ENCLB619PTY)

description:
https://www.encodeproject.org/experiments/ENCSR085EYQ/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K27me3 ChIP-seq on embryonic 11.5 day mouse limb
experiment encode accession: ENCSR085EYQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR949ZLW
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB619PTY
size range: 300-500

value: Limb from 109 embyronic 11.5 day mice

value: ENCBS066IEL at ENCODE; https://www.encodeproject.org/ENCBS066IEL/


title: daf-2(e1370); math-33(tm3561) 15ºC

city: Freiburg

first: Thomas

last: Heimbucher

state: Baden Württemberg

address: Schaenzlestrasse 1

department: Biologie III

country: Germany

institute: Thomas Heimbucher

description:
ADTH09
daf-2(ts); math-33(lf)  15ºC (FPKM)

data_processing:
The paired-end reads were aligned to C elegans genome WS220/ce10  by using STAR aligner (https://github.com/alexdobin/STAR).
The expression of C elegans genes was quantified by using HOMER (http://homer.salk.edu).
The differential gene expression analysis was performed by using edgeR (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html).
Genome_build: WS220/ce10
Supplementary_files_format_and_content: FPKM expression values of C elegans WS220/ce10 genes, as computed by HOMER (http://homer.salk.edu)

organism: Caenorhabditis elegans

growth_protocol: Nematodes were grown as semi-synchronized populations at 15ºC.

extract_protocol:
Total RNA was isolated from approximately 3,000 worms using an RNeasy Kit (Qiagen) with in-column DNase digestion. The RNA quality was verified to have an RNA integrity number (RIN) greater than 8.0 through using a Bioanalyzer (Agilent).
Stranded mRNA-seq (mRNA sequencing) libraries were prepared from poly(A) RNA after oligo(dT) selection.
Paired-end mRNA-seq

treatment_protocol: Nematodes were shifted to 25ºC at the L3/L4 stage for 22 hr or kept at 15ºC.

tag: developmental stage

value: L4; preadults

tag: genotype/variation

tag: condition

value: kept on 15ºC (permissive temperature)

tag: tissue

value: whole nematode


title: ChIP-seq from liver (ENCLB936IWE)

description:
https://www.encodeproject.org/experiments/ENCSR045NOD/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 13.5 day mouse liver
experiment encode accession: ENCSR045NOD
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR220PXJ
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB936IWE
size range: 300-500

value: liver

value: tissue

value: Liver from embryonic 13.5 day mice

value: ENCBS373XWZ at ENCODE; https://www.encodeproject.org/ENCBS373XWZ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: daf-2(e1370) 25ºC

description:
ADTH08
daf-2(ts) 25ºC (FPKM)

value: shifed to 25ºC (restrictive temperature)


title: ChIP-seq from neural tube (ENCLB045XUT)

description:
https://www.encodeproject.org/experiments/ENCSR087PLZ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 13.5 day mouse neural tube
experiment encode accession: ENCSR087PLZ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR295GGT
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB045XUT
size range: 300-500

value: neural tube

value: Neural tube from embryonic 13.5 day mice

value: pooled male and female

value: healthy

value: ENCBS549OYR at ENCODE; https://www.encodeproject.org/ENCBS549OYR/


title: ChIP-seq from liver (ENCLB249EDV)

description:
https://www.encodeproject.org/experiments/ENCSR082JEN/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on embryonic 16.5 day mouse liver
experiment encode accession: ENCSR082JEN
assay title: ChIP-seq
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB249EDV
size range: 300-500

value: Control

value: Liver pooled from embyonic 16.5 day mice

value: embryonic

value: Len Pennacchio, LBNL

value: ENCBS236CDJ at ENCODE; https://www.encodeproject.org/ENCBS236CDJ/


title: WGBS from intestine (ENCLB146WKN)

description:
https://www.encodeproject.org/experiments/ENCSR089FFK/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 14.5 day mouse intestine
experiment encode accession: ENCSR089FFK
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB146WKN
size range: 180-500

value: intestine

value: Intestine from 34 embryonic 14.5 day mice

value: ENCBS020AAA at ENCODE; https://www.encodeproject.org/ENCBS020AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: math-33(tm3561) 25ºC

description:
ADTH06
math-33(lf)  25ºC (FPKM)

value: L4; preadults

value: whole nematode


title: daf-2(e1370); math-33(tm3561) 25ºC

description:
ADTH10
daf-2(ts); math-33(lf)  25ºC   (FPKM)

value: shifed to 25ºC (restrictive temperature)


title: ChIP-seq from liver (ENCLB579ZUF)

description:
https://www.encodeproject.org/experiments/ENCSR082JEN/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control ChIP-seq on embryonic 16.5 day mouse liver
experiment encode accession: ENCSR082JEN
assay title: ChIP-seq
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB579ZUF
size range: 300-500

value: liver

value: tissue

value: Liver from 41 embyonic 16.5 day mice

value: ENCBS279BWR at ENCODE; https://www.encodeproject.org/ENCBS279BWR/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: daf-2(e1370)  15ºC

description:
ADTH07
daf-2(ts) 15ºC (FPKM)

value: kept on 15ºC (permissive temperature)


title: ChIP-seq from kidney (ENCLB214XVO)

description:
https://www.encodeproject.org/experiments/ENCSR036YKL/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR036YKL
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR780JSE
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB214XVO
size range: 300-500

value: kidney

value: Kidney from 62 embryonic 15.5 day mice

value: pooled male and female

value: healthy

value: ENCBS924ZKF at ENCODE; https://www.encodeproject.org/ENCBS924ZKF/


title: ChIP-seq from limb (ENCLB522RGG)

description:
https://www.encodeproject.org/experiments/ENCSR028ZHS/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K9me3 ChIP-seq on embryonic 15.5 day mouse limb
experiment encode accession: ENCSR028ZHS
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR070OXL
encode release date: 2016-03-17
lab: Bing Ren, UCSD
library encode accession: ENCLB522RGG
size range: 300-500

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (15.5 days)

value: limb

value: Limb from 78 embryonic 15.5 day mice

value: embryonic

value: Len Pennacchio, LBNL

value: ENCBS735QNY at ENCODE; https://www.encodeproject.org/ENCBS735QNY/


title: N2 (wild type) 25ºC

description:
ADTH04
N2      25ºC (FPKM)

source_name: N2 (wild type)

value: L4; preadults

value: N2 (wild type)

value: shifed to 25ºC (restrictive temperature)

value: whole nematode


title: ChIP-seq from limb (ENCLB035EKK)

description:
https://www.encodeproject.org/experiments/ENCSR028ZHS/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 15.5 day mouse limb
experiment encode accession: ENCSR028ZHS
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR070OXL
encode release date: 2016-03-17
lab: Bing Ren, UCSD
library encode accession: ENCLB035EKK
size range: 300-500

value: tissue

value: Limb from 62 embryonic 15.5 day mice

value: ENCBS696JKV at ENCODE; https://www.encodeproject.org/ENCBS696JKV/


title: N2 (wild type) 15ºC

description:
ADTH03
N2      15ºC (FPKM)

value: kept on 15ºC (permissive temperature)


title: ChIP-seq from midbrain (ENCLB154TCF)

description:
https://www.encodeproject.org/experiments/ENCSR028VCU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-seq on postnatal 0 day mouse midbrain
experiment encode accession: ENCSR028VCU
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR889XXJ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB154TCF
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap midbrain tissue mixed sex postnatal (0 days)

value: midbrain

value: Midbrain from pooled postnatal 0 day mice

value: 0 day

value: postnatal

value: ENCBS555AAA at ENCODE; https://www.encodeproject.org/ENCBS555AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from heart (ENCLB709ZRH)

description:
https://www.encodeproject.org/experiments/ENCSR080GQM/
***************
biological replicate number: 1
technical replicate number: 1,3,2
description: H3K4me1 ChIP-seq on embryonic 14.5 day mouse heart
experiment encode accession: ENCSR080GQM
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR840PFW
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB709ZRH
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap heart tissue mixed sex embryo (14.5 days)

value: heart

value: Heart from pooled embryonic 14.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: ENCBS563AAA at ENCODE; https://www.encodeproject.org/ENCBS563AAA/


title: daf-16(mu86); daf-2(e1370) 25ºC

description:
ADTH02
daf-16(0); daf-2(ts) 25ºC (FPKM)

value: L4; preadults

value: shifed to 25ºC (restrictive temperature)

value: whole nematode


title: daf-16(mu86); daf-2(e1370) 15ºC

description:
ADTH01
daf-16(0); daf-2(ts) 15ºC (FPKM)


title: ChIP-seq from lung (ENCLB882ZRJ)

description:
https://www.encodeproject.org/experiments/ENCSR025AOC/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K27me3 ChIP-seq on postnatal 0 day mouse lung
experiment encode accession: ENCSR025AOC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR241RIG
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB882ZRJ
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap lung tissue mixed sex postnatal (0 days)

value: lung

value: tissue

value: Lung from 15 postnatal 0 day mice

value: Len Pennacchio, LBNL

value: ENCBS042AAA at ENCODE; https://www.encodeproject.org/ENCBS042AAA/


title: ChIP-seq from heart (ENCLB166YBB)

description:
https://www.encodeproject.org/experiments/ENCSR080GQM/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 14.5 day mouse heart
experiment encode accession: ENCSR080GQM
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR840PFW
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB166YBB
size range: 300-500

value: ENCBS566AAA at ENCODE; https://www.encodeproject.org/ENCBS566AAA/


title: ChIP-seq from midbrain (ENCLB441GHB)

description:
https://www.encodeproject.org/experiments/ENCSR765UOU/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 12.5 day mouse midbrain
experiment encode accession: ENCSR765UOU
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR415FCU
encode release date: 2016-05-06
lab: Bing Ren, UCSD
library encode accession: ENCLB441GHB
size range: 300-500

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (12.5 days)

value: midbrain

value: Midbrain from 88 embryonic 12.5 day mice

value: ENCBS280TPA at ENCODE; https://www.encodeproject.org/ENCBS280TPA/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: IMR90_Roche_1ug

city: new york

first: Thadeous

middle: James

last: Kacmarczyk

state: ny

address: 1300 York Ave

department: Medicine/Hematology-Oncology

institute: Weill Cornell Medicine

data_processing:
Basecalling performed by CASAVA version 1.8.2
filtered for pass filter reads by unix tool grep with a command:  zcat sample_R1.fastq.gz | grep --no-group-separator -A 3 '^@.* [^:]*:N:[^:]*:' > sample_R1_PF.fastq
adapter trimming performed by Flexbar v2.4 with command:  flexbar -r sample_R1_PF.fastq -p sample_R2_PF.fastq -t sample_trimmed -a peadapters.fa -f i1.5 -ao 6 -m 21 -at 2 -ae RIGHT -n 10 -u 2 -j -am 3 -ai -3 -ag -20
align to human genome hg19 performed by Bismark v0.5.4, Bowtie v0.12.7 with command:  bismark -q -un -X 400 -l 100 --phred33-quals --directional hg19 -1 sample_trimmed_1.fastq -2 sample_trimmed_2.fastq
methylation extraction by custom PERL script
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files include for each CpG:  chromosome, base, strand, coverage, frequency C, and frequency T

organism: Homo sapiens

source_name: IMR90, Roche, 1ug starting material

extract_protocol:
Genomic DNA was extracted from the cell lines using standard phenol:chloroform extraction followed by ethanol precipitation.
Roche NimbleGen SeqCap Epi CpGiant libraries were made using 1ug and 0.25ug of starting material, according to the company’s specifications. DNA was sonicated using a Covaris S220 sonicator to obtain products of 180-220bp. DNA was then end-repaired, A-tailed and ligated with methylated indexed-adapters to create pre-capture DNA libraries. The pre-capture libraries were bisulfite converted at 54°C for 1 hour using the Zymo EZ DNA Lightening kit. The bisulfite treated pre-capture libraries were PCR amplified with HiFi HotSart polymerase. The amplified, bisulfite converted sample libraries were then hybridized to the probe pool of fully-, partially- and un-methylated cytosines from both strands of DNA oligos at 42° C for 72 hrs. Hybridized products were purified by capture with Capture Beads and PCR amplified for 15 cycles to create the final libraries.

tag: cell line

value: lung fibroblast

tag: protocol

value: Roche NimbleGen SeqCap Epi CpGiant


title: R_WGBS_EpiG_IMR90_100_12_I12

source_name: IMR90, WGBS

extract_protocol:
Genomic DNA was extracted from the cell lines using standard phenol:chloroform extraction followed by ethanol precipitation.
Whole Genome Bisulfite Sequencing libraries were prepared as:  100 ng of DNA were bisulfite converted using EZ DNA Methylation-Gold Kit and the single stranded DNA obtained processed for library construction using the EpiGnome Methyl-Seq kit as per manufacturer protocol. The DNA was made double stranded by the use of 5’tagged random hexamers and subsequently 3’ tagged with terminal tagging oligo. The di-tagged DNA was enriched using 10 cycles of PCR, with PCR indexed-primers compatible with Illumina sequencing.

value: WGBS


title: math-33(tm3561) 15ºC

description:
ADTH05
math-33(lf)  15ºC (FPKM)

value: kept on 15ºC (permissive temperature)


title: ChIP-seq from forebrain (ENCLB081GHO)

description:
https://www.encodeproject.org/experiments/ENCSR022KDE/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 15.5 day mouse forebrain
experiment encode accession: ENCSR022KDE
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR880HDV
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB081GHO
size range: 300-500

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (15.5 days)

value: forebrain

value: Forebrain from 62 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: ENCBS841GER at ENCODE; https://www.encodeproject.org/ENCBS841GER/


title: ChIP-seq from midbrain (ENCLB571UDK)

description:
https://www.encodeproject.org/experiments/ENCSR081UQY/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on embryonic 11.5 day mouse midbrain
experiment encode accession: ENCSR081UQY
assay title: ChIP-seq
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB571UDK
size range: 300-500

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (11.5 days)

value: Control

value: tissue

value: Midbrain of 109 embyronic 11.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS228OBS at ENCODE; https://www.encodeproject.org/ENCBS228OBS/


title: ChIP-seq from liver (ENCLB896RQH)

description:
https://www.encodeproject.org/experiments/ENCSR075SNV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 14.5 day mouse liver
experiment encode accession: ENCSR075SNV
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR742WLX
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB896RQH
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap liver tissue mixed sex embryo (14.5 days)

value: liver

value: Liver from embryonic 14.5 day mice

value: ENCBS194VTP at ENCODE; https://www.encodeproject.org/ENCBS194VTP/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from stomach (ENCLB635AQB)

description:
https://www.encodeproject.org/experiments/ENCSR023VJO/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 14.5 day mouse stomach
experiment encode accession: ENCSR023VJO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR497YBQ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB635AQB
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap stomach tissue mixed sex embryo (14.5 days)

value: stomach

value: Stomach pooled from embryonic 14.5 day mice

value: ENCBS568AAA at ENCODE; https://www.encodeproject.org/ENCBS568AAA/


title: IMR90-_2

source_name: IMR90, Agilent SureSelect Methyl-seq

extract_protocol:
Genomic DNA was extracted from the cell lines using standard phenol:chloroform extraction followed by ethanol precipitation.
Agilent SureSelect Methyl-Seq libraries were made according to the company’s specifications using 3ug and 1ug of DNA. DNA was sonicated using a Covaris S220 sonicator to obtain products of 150-200bp. DNA was then end-repaired, A-tailed and ligated with methylated adapters to create pre-capture DNA libraries. DNA libraries were then hybridized to the RNA SureSelect Human methyl-seq capture library at 65°C for 16 hrs. Hybridized products were purified by capture with Strepdavin beads and then subjected to bisulfite conversion (64°C for 2.5hr) using the Zymo EZ DNA Gold kit. The bisulfite treated libraries were PCR amplified for 8 cycles with Agilent Taq to get the required amount of DNA library and then indexed by another 6 cycles of PCR amplification to create the final libraries.

value: lung fibroblast

value: Agilent SureSelect Methyl-seq


title: ChIP-seq from stomach (ENCLB572UUJ)

description:
https://www.encodeproject.org/experiments/ENCSR023VJO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 14.5 day mouse stomach
experiment encode accession: ENCSR023VJO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR497YBQ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB572UUJ
size range: 300-500

value: embryonic

value: pooled male and female

value: ENCBS564AAA at ENCODE; https://www.encodeproject.org/ENCBS564AAA/


title: IMR90_1


title: ChIP-seq from limb (ENCLB453VLG)

description:
https://www.encodeproject.org/experiments/ENCSR070OXL/
***************
biological replicate number: 2
technical replicate number: 1,3,2
description: Control ChIP-seq on embryonic 15.5 day mouse limb
experiment encode accession: ENCSR070OXL
assay title: ChIP-seq
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB453VLG
size range: 300-500
instrument models: Illumina HiSeq 2500,Illumina HiSeq 4000

value: Control

value: limb

value: Limb from 62 embryonic 15.5 day mice

value: healthy

value: ENCBS696JKV at ENCODE; https://www.encodeproject.org/ENCBS696JKV/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: IMR90_Roche_0_25ug

source_name: IMR90, Roche, 0.25ug starting material

value: Roche NimbleGen SeqCap Epi CpGiant


title: ChIP-seq from forebrain (ENCLB497RBP)

description:
https://www.encodeproject.org/experiments/ENCSR070MOK/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K27me3 ChIP-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR070MOK
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR398NCK
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB497RBP
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap forebrain tissue mixed sex postnatal (0 days)

value: forebrain

value: tissue

value: Forebrain of pooled postnatal 0 day mice

value: 0 day

value: postnatal

value: Len Pennacchio, LBNL

value: ENCBS554AAA at ENCODE; https://www.encodeproject.org/ENCBS554AAA/


title: ChIP-seq from forebrain (ENCLB511QWW)

description:
https://www.encodeproject.org/experiments/ENCSR022KDE/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 15.5 day mouse forebrain
experiment encode accession: ENCSR022KDE
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR880HDV
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB511QWW
size range: 300-500

value: Forebrain from 78 embryonic 15.5 day mice

value: embryonic

value: ENCBS811RMD at ENCODE; https://www.encodeproject.org/ENCBS811RMD/


title: ChIP-seq from limb (ENCLB508IDN)

description:
https://www.encodeproject.org/experiments/ENCSR022DED/
***************
biological replicate number: 2
technical replicate number: 2,1
description: H3K9me3 ChIP-seq on embryonic 13.5 day mouse limb
experiment encode accession: ENCSR022DED
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR465WTL
encode release date: 2016-02-18
lab: Bing Ren, UCSD
library encode accession: ENCLB508IDN
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (13.5 days)

value: Limb from embryonic 13.5 day mice

value: pooled male and female

value: ENCBS896ZED at ENCODE; https://www.encodeproject.org/ENCBS896ZED/


title: ChIP-seq from embryonic facial prominence (ENCLB079BXD)

description:
https://www.encodeproject.org/experiments/ENCSR027DMG/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 11.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR027DMG
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR068AQC
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB079BXD
size range: 300-500

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (11.5 days)

value: embryonic facial prominence

value: Craniofacial prominence from 88 embyronic 11.5 day mice

value: healthy

value: ENCBS468NAL at ENCODE; https://www.encodeproject.org/ENCBS468NAL/


title: ChIP-seq from midbrain (ENCLB821WAE)

description:
https://www.encodeproject.org/experiments/ENCSR081UQY/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control ChIP-seq on embryonic 11.5 day mouse midbrain
experiment encode accession: ENCSR081UQY
assay title: ChIP-seq
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB821WAE
size range: 300-500

value: Control

value: midbrain

value: Midbrain from 88 embyronic 11.5 day mice

value: ENCBS802FTI at ENCODE; https://www.encodeproject.org/ENCBS802FTI/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from forebrain (ENCLB767CAT)

description:
https://www.encodeproject.org/experiments/ENCSR070MOK/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K27me3 ChIP-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR070MOK
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR398NCK
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB767CAT
size range: 300-500

value: forebrain

value: tissue

value: Forebrain from 15 postnatal 0 day mice

value: 0 day

value: postnatal

value: Len Pennacchio, LBNL

value: ENCBS038AAA at ENCODE; https://www.encodeproject.org/ENCBS038AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from liver (ENCLB571XHL)

description:
https://www.encodeproject.org/experiments/ENCSR075SNV/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K27ac ChIP-seq on embryonic 14.5 day mouse liver
experiment encode accession: ENCSR075SNV
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR742WLX
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB571XHL
size range: 300-500
instrument models: Illumina HiSeq 2500,Illumina HiSeq 4000

value: liver

value: Liver from embryonic 14.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS096GAJ at ENCODE; https://www.encodeproject.org/ENCBS096GAJ/


title: ChIP-seq from limb (ENCLB251GPU)

description:
https://www.encodeproject.org/experiments/ENCSR021ALF/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 14.5 day mouse limb
experiment encode accession: ENCSR021ALF
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR232EOO
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB251GPU
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap limb tissue mixed sex embryo (14.5 days)

value: limb

value: Limb from 34 embryonic 14.5 day mice

value: healthy

value: ENCBS023AAA at ENCODE; https://www.encodeproject.org/ENCBS023AAA/


title: IMR_90

source_name: IMR90, ERRBS

extract_protocol:
Genomic DNA was extracted from the cell lines using standard phenol:chloroform extraction followed by ethanol precipitation.
ERRBS libraries were prepared by digesting 75 ng of DNA with restriction enzyme MspI, followed by post end-repair, A-tailing, and adapter ligation with Illumina TruSeq adapters. The region corresponding to 84-334bp was size-selected as two fractions, and each fraction was subjected to overnight bisulfite conversion (55 cycles of 95 °C for 30 sec, 50 °C for 15 min) using EZ DNA methylation kit (Cat # D5002, Zymo Research, Irvine CA). Purified bisulfite converted DNA was PCR amplified (using TruSeq primers, Illumina Inc. San Diego, CA) for 18 cycles of denaturing, annealing and extension/elongation steps using Roche FastStart (cat # 03 553 361 001):  94 °C for 20 secs, 65 °C for 30 secs, 72 °C for 1 min, followed by 72 °C for 3 min. The resulting libraries were normalized to 2nM and pooled at the same molar ratio.

value: lung fibroblast

value: ERRBS


title: IMR90_A_TruSeq

source_name: IMR90, TruSeq,ERRBS


title: ChIP-seq from lung (ENCLB572JFC)

description:
https://www.encodeproject.org/experiments/ENCSR025AOC/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on postnatal 0 day mouse lung
experiment encode accession: ENCSR025AOC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR241RIG
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB572JFC
size range: 300-500

value: lung

value: tissue

value: Lung from pooled postnatal 0 day mice

value: ENCBS558AAA at ENCODE; https://www.encodeproject.org/ENCBS558AAA/


title: ChIP-seq from limb (ENCLB350ITA)

description:
https://www.encodeproject.org/experiments/ENCSR021ALF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 14.5 day mouse limb
experiment encode accession: ENCSR021ALF
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR232EOO
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB350ITA
size range: 300-500

value: Limb from 24 embryonic 14.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS011AAA at ENCODE; https://www.encodeproject.org/ENCBS011AAA/


title: ChIP-seq from embryonic facial prominence (ENCLB816JAD)

description:
https://www.encodeproject.org/experiments/ENCSR068AQC/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on embryonic 11.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR068AQC
assay title: ChIP-seq
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB816JAD
size range: 300-500

value: Control

value: embryonic facial prominence

value: Craniofacial prominence from 109 embyronic 11.5 day mice

value: ENCBS141GPQ at ENCODE; https://www.encodeproject.org/ENCBS141GPQ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from stomach (ENCLB126YVD)

description:
https://www.encodeproject.org/experiments/ENCSR076MXH/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 14.5 day mouse stomach
experiment encode accession: ENCSR076MXH
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR497YBQ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB126YVD
size range: 300-500

value: stomach

value: Stomach pooled from embryonic 14.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS568AAA at ENCODE; https://www.encodeproject.org/ENCBS568AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from heart (ENCLB829RHE)

description:
https://www.encodeproject.org/experiments/ENCSR069XHI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 13.5 day mouse heart
experiment encode accession: ENCSR069XHI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR077QRY
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB829RHE
size range: 300-500

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (13.5 days)

value: heart

value: tissue

value: Heart from embryonic 13.5 day mice

value: healthy

value: ENCBS490ZWZ at ENCODE; https://www.encodeproject.org/ENCBS490ZWZ/


title: ChIP-seq from embryonic facial prominence (ENCLB372USC)

description:
https://www.encodeproject.org/experiments/ENCSR068AQC/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control ChIP-seq on embryonic 11.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR068AQC
assay title: ChIP-seq
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB372USC
size range: 300-500

value: Craniofacial prominence from 88 embyronic 11.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS468NAL at ENCODE; https://www.encodeproject.org/ENCBS468NAL/


title: ChIP-seq from intestine (ENCLB876EER)

description:
https://www.encodeproject.org/experiments/ENCSR014YAY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on embryonic 14.5 day mouse intestine
experiment encode accession: ENCSR014YAY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR645QSY
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB876EER
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap intestine tissue mixed sex embryo (14.5 days)

value: intestine

value: Intestine from 34 embryonic 14.5 day mice

value: ENCBS020AAA at ENCODE; https://www.encodeproject.org/ENCBS020AAA/


title: ChIP-seq from intestine (ENCLB594ZGO)

description:
https://www.encodeproject.org/experiments/ENCSR014YAY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on embryonic 14.5 day mouse intestine
experiment encode accession: ENCSR014YAY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR645QSY
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB594ZGO
size range: 300-500

value: Intestine from 24 embryonic 14.5 day mice

value: ENCBS008AAA at ENCODE; https://www.encodeproject.org/ENCBS008AAA/


title: ChIP-seq from heart (ENCLB550BKH)

description:
https://www.encodeproject.org/experiments/ENCSR069XHI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 13.5 day mouse heart
experiment encode accession: ENCSR069XHI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR077QRY
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB550BKH
size range: 300-500

value: embryonic

value: ENCBS814PLT at ENCODE; https://www.encodeproject.org/ENCBS814PLT/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from forebrain (ENCLB278YWT)

description:
https://www.encodeproject.org/experiments/ENCSR014TEJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 16.5 day mouse forebrain
experiment encode accession: ENCSR014TEJ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR587JRQ
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB278YWT
size range: 300-500

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (16.5 days)

value: forebrain

value: Forebrain pooled from embyonic 16.5 day mice

value: pooled male and female

value: ENCBS156DHU at ENCODE; https://www.encodeproject.org/ENCBS156DHU/


title: ChIP-seq from forebrain (ENCLB764NOF)

description:
https://www.encodeproject.org/experiments/ENCSR067ZDE/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 11.5 day mouse forebrain
experiment encode accession: ENCSR067ZDE
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR024JAN
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB764NOF
size range: 300-500

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (11.5 days)

value: tissue

value: Forebrain from 88 embyronic 11.5 day mice

value: healthy

value: ENCBS720JOH at ENCODE; https://www.encodeproject.org/ENCBS720JOH/


title: ChIP-seq from forebrain (ENCLB694HYE)

description:
https://www.encodeproject.org/experiments/ENCSR014TEJ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 16.5 day mouse forebrain
experiment encode accession: ENCSR014TEJ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR587JRQ
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB694HYE
size range: 300-500

value: Forebrain from 41 embyonic 16.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS512LKA at ENCODE; https://www.encodeproject.org/ENCBS512LKA/


title: WT_leaves_RNAseq

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
Data was processed as described in Stroud et al., Plos Genetics 2012. Briefly, mRNA-Seq reads were mapped with Bowtie (Langmead, et al. 2009 Genome Biol.) to TAIR8 chr1..5, allowing up to 2 mismatches and retaining only uniquely-mapping reads. To generate wig files, the genome was tiled into 10 bp bins, and the number of reads per million mapping reads per kilobase falling within the bin was calculated.
Genome_build: TAIR8
Supplementary_files_format_and_content: wig

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: WT_leaves_3 week old leaves

extract_protocol:
RNA-seq libraries. RNA-seq experiments were performed in two biological replicates for each genotype. 0.1g of tissue was ground in Trizol (Invitrogen).  Total RNA were treated with DNaseI (Roche), and cleaned up with phenol-chlorophorm and precipitated with ethanol.
Libraries were generated and sequenced following manufacturer instructions (Illumina).

tag: ecotype

value: WT

value: 3 weeks old

value: leaves


title: ChIP-seq from stomach (ENCLB034MUN)

description:
https://www.encodeproject.org/experiments/ENCSR012BVY/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on embryonic 16.5 day mouse stomach
experiment encode accession: ENCSR012BVY
assay title: ChIP-seq
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB034MUN
size range: 300-500

source_name: Mus musculus strain B6NCrl stomach tissue mixed sex embryo (16.5 days)

value: Control

value: stomach

value: Stomach pooled from embyonic 16.5 day mice

value: embryonic

value: ENCBS243DCE at ENCODE; https://www.encodeproject.org/ENCBS243DCE/


title: met1_leaves_RNAseq

source_name: met1_leaves_3 week old leaves


title: ChIP-seq from forebrain (ENCLB240KIF)

description:
https://www.encodeproject.org/experiments/ENCSR066LZB/
***************
biological replicate number: 2
technical replicate number: 1,2,3
description: H3K36me3 ChIP-seq on embryonic 11.5 day mouse forebrain
experiment encode accession: ENCSR066LZB
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR024JAN
encode release date: 2014-07-07
lab: Bing Ren, UCSD
library encode accession: ENCLB240KIF
size range: 300-500

value: forebrain

value: pooled male and female

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from forebrain (ENCLB467POO)

description:
https://www.encodeproject.org/experiments/ENCSR067ZDE/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K4me2 ChIP-seq on embryonic 11.5 day mouse forebrain
experiment encode accession: ENCSR067ZDE
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR024JAN
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB467POO
size range: 300-500

value: tissue

value: Forebrain from 109 embyronic 11.5 day mice

value: ENCBS745VOM at ENCODE; https://www.encodeproject.org/ENCBS745VOM/


title: ChIP-seq from embryonic facial prominence (ENCLB094XNR)

description:
https://www.encodeproject.org/experiments/ENCSR008WOQ/
***************
biological replicate number: 2
technical replicate number: 2,1
description: H3K27me3 ChIP-seq on embryonic 13.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR008WOQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR742ZUI
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB094XNR
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (13.5 days)

value: embryonic facial prominence

value: Embryonic facial prominence from embryonic 13.5 day mice

value: healthy

value: ENCBS847MIW at ENCODE; https://www.encodeproject.org/ENCBS847MIW/


title: ChIP-seq from midbrain (ENCLB064ABA)

description:
https://www.encodeproject.org/experiments/ENCSR065LAB/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K9me3 ChIP-seq on postnatal 0 day mouse midbrain
experiment encode accession: ENCSR065LAB
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR889XXJ
encode release date: 2016-02-17
lab: Bing Ren, UCSD
library encode accession: ENCLB064ABA
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap midbrain tissue mixed sex postnatal (0 days)

value: midbrain

value: Midbrain from pooled postnatal 0 day mice

value: 0 day

value: postnatal

value: Len Pennacchio, LBNL

value: ENCBS555AAA at ENCODE; https://www.encodeproject.org/ENCBS555AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: ChIP-seq from midbrain (ENCLB082GTF)

description:
https://www.encodeproject.org/experiments/ENCSR065LAB/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K9me3 ChIP-seq on postnatal 0 day mouse midbrain
experiment encode accession: ENCSR065LAB
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR889XXJ
encode release date: 2016-02-17
lab: Bing Ren, UCSD
library encode accession: ENCLB082GTF
size range: 300-500

value: Midbrain from 15 postnatal 0 day mice

value: ENCBS039AAA at ENCODE; https://www.encodeproject.org/ENCBS039AAA/


title: microRNA-seq from kidney (ENCLB135RMN)

description:
https://www.encodeproject.org/experiments/ENCSR008EQG/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR008EQG
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB135RMN
size range: <30

source_name: Mus musculus strain B6NCrl kidney tissue mixed sex embryo (15.5 days)

value: kidney

value: Kidney from 78 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS899UOK at ENCODE; https://www.encodeproject.org/ENCBS899UOK/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ChIP-seq from stomach (ENCLB989JCV)

description:
https://www.encodeproject.org/experiments/ENCSR012BVY/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control ChIP-seq on embryonic 16.5 day mouse stomach
experiment encode accession: ENCSR012BVY
assay title: ChIP-seq
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB989JCV
size range: 300-500

value: Control

value: stomach

value: tissue

value: Stomach from 41 embyonic 16.5 day mice

value: healthy

value: ENCBS793TEW at ENCODE; https://www.encodeproject.org/ENCBS793TEW/


title: ChIP-seq from liver (ENCLB799GIK)

description:
https://www.encodeproject.org/experiments/ENCSR058DOA/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 11.5 day mouse liver
experiment encode accession: ENCSR058DOA
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR573MJR
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB799GIK
size range: 300-500

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (11.5 days)

value: liver

value: Liver from pooled embryonic 11.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS522YOW at ENCODE; https://www.encodeproject.org/ENCBS522YOW/


title: microRNA-seq from kidney (ENCLB396JTP)

description:
https://www.encodeproject.org/experiments/ENCSR008EQG/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR008EQG
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB396JTP
size range: <30

value: Kidney from 62 embryonic 15.5 day mice

value: ENCBS924ZKF at ENCODE; https://www.encodeproject.org/ENCBS924ZKF/


title: ESTAIG1.120.1

first: Samuel

last: Hokin

state: California

address: 260 Panama St

department: Plant Biology

institute: Carnegie Institution for Science

description:
OtA3210
Col ESTAIG1

data_processing:
Alignment to genome, TopHat v2.0.10, --no-novel-juncs
Transcript abundances, Cufflinks
Merge transcript abundances, Cuffmerge
Determine differential expression, Cufflinks
Genome_build: TAIR10
Supplementary_files_format_and_content: Normalized FPKM abundance measurements generated by Cufflinks are reported in Barton-ESTAIG1.series_matrix.txt.

source_name: ESTAIG1 seedling, 120 mins, rep 1

growth_protocol: Seeds were surface sterilized in bleach and rinsed multiple times in sterile water. Following two days of stratification at 4 degrees in the dark,50 seeds each were transferred to 250 ml ehrlenmeyer flasks containing 50 mls of sterile MS medium and capped loosely with aluminum foil. Flasks were swirled gently on a platform shaker placed under a bank of cool white fluorescent lamps.

extract_protocol:
Frozen tissue was ground to a fine powder in liquid nitrogen and mRNA was extracted using Quiagen's RNEasy kit.
oligo dT primed cDNA was used as the basis for a library made using standard Illumina protocols.

treatment_protocol: After seven days of growth, estrogen was added to a final concentration of five microMolar to each flask. Plants were quickfrozen in liquid nitrogen 0, 60 and 120 minutes after addition of estrogen.

value: Columbia

tag: treatment

value: estrogen

tag: time

value: 120 mins

value: seedling


title: HepG2 control detection of p53 binding sites

city: Singapore

last: Thurnherr

address: 11 Hospital Drive

country: Singapore

institute: NCCS

data_processing:
Alignment to human genome through BWA
SAM to BAM conversion using samtools
Peak-calling using MACS (version 2.0.9)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: peaks.bed

source_name: Human liver carcinoma cell line

growth_protocol: HepG2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% foetal calf serum.

extract_protocol:
Lysates were clarified from sonicated nuclei and p53-DNA complexes were isolated with p53 antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: The cells were transduced with HBx-expressing or control adenovirus, treated with UVC (254nm) irradiation 48 h post-transduction and harvested 24 h after UV irradiation

tag: transduction

tag: antibody

value: p53 FL-393 antibody

tag: antibody vendor

value: Santa Cruz Biotechnology

tag: antibody catalog number


title: HepG2 treated detection of p53 binding sites

value: HBV HBx protein expressing


title: WGBS from heart (ENCLB173AEF)

description:
https://www.encodeproject.org/experiments/ENCSR050EXR/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 16.5 day mouse heart
experiment encode accession: ENCSR050EXR
assay title: WGBS
assembly: mm10
encode release date: 2014-12-17
lab: Joe Ecker, Salk
library encode accession: ENCLB173AEF
size range: 180-500

source_name: Mus musculus strain B6NCrl heart tissue mixed sex embryo (16.5 days)

value: heart

value: tissue

tag: description

value: Heart pooled from embyonic 16.5 day mice

tag: biosample encode accession

tag: age

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

value: ENCBS955JPC at ENCODE; https://www.encodeproject.org/ENCBS955JPC/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: ESTAIG1.60.2

description:
OtA3020
Col ESTAIG1

source_name: ESTAIG1 seedling, 60 mins, rep 2

tag: genotype/variation

value: 60 mins


title: ESTAIG1.60.3

description:
OtA3021
Col ESTAIG1

source_name: ESTAIG1 seedling, 60 mins, rep 3


title: WGBS from heart (ENCLB103AJJ)

description:
https://www.encodeproject.org/experiments/ENCSR050EXR/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 16.5 day mouse heart
experiment encode accession: ENCSR050EXR
assay title: WGBS
assembly: mm10
encode release date: 2014-12-17
lab: Joe Ecker, Salk
library encode accession: ENCLB103AJJ
size range: 180-500

value: Heart from 41 embyonic 16.5 day mice

tag: health state

value: healthy

tag: lab

value: Len Pennacchio, LBNL

tag: link

value: ENCBS217XWR at ENCODE; https://www.encodeproject.org/ENCBS217XWR/


title: ESTAIG1.120.2

description:
OtA3211
Col ESTAIG1

source_name: ESTAIG1 seedling, 120 mins, rep 2

value: Columbia

value: estrogen

value: 120 mins

tag: tissue


title: ESTAIG1.60.1

description:
OtA3019
Col ESTAIG1

source_name: ESTAIG1 seedling, 60 mins, rep 1

tag: ecotype

value: seedling


title: ESTAIG1.0.3

description:
OtA3209
Col ESTAIG1

source_name: ESTAIG1 seedling, 0 mins, rep 3

tag: treatment

value: 0 mins


title: WGBS from heart (ENCLB452VHJ)

description:
https://www.encodeproject.org/experiments/ENCSR050EXR/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 16.5 day mouse heart
experiment encode accession: ENCSR050EXR
assay title: WGBS
assembly: mm10
encode release date: 2014-12-17
lab: Joe Ecker, Salk
library encode accession: ENCLB452VHJ
size range: 180-500

value: heart


title: WGBS from heart (ENCLB538BQR)

description:
https://www.encodeproject.org/experiments/ENCSR050EXR/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 16.5 day mouse heart
experiment encode accession: ENCSR050EXR
assay title: WGBS
assembly: mm10
encode release date: 2014-12-17
lab: Joe Ecker, Salk
library encode accession: ENCLB538BQR
size range: 180-500

value: tissue


title: ESTAIG1.0.2

description:
OtA3017
Col ESTAIG1

source_name: ESTAIG1 seedling, 0 mins, rep 2

tag: time


title: ChIP-seq from liver (ENCLB428LOQ)

description:
https://www.encodeproject.org/experiments/ENCSR058DOA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 11.5 day mouse liver
experiment encode accession: ENCSR058DOA
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR573MJR
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB428LOQ
size range: 300-500

value: liver

value: Liver from 109 embyronic 11.5 day mice

value: ENCBS746POP at ENCODE; https://www.encodeproject.org/ENCBS746POP/


title: ESTAIG1.0.1

description:
OtA3016
Col ESTAIG1

source_name: ESTAIG1 seedling, 0 mins, rep 1


title: ChIP-seq from hindbrain (ENCLB755CYO)

description:
https://www.encodeproject.org/experiments/ENCSR046SWI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on embryonic 16.5 day mouse hindbrain.NOTE- Files associated with this experiment are undergoing additional review and analysis
experiment encode accession: ENCSR046SWI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR752KDM
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB755CYO
size range: 300-500

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (16.5 days)

value: hindbrain

value: Hindbrain from 37 embryonic 16.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS281ZLI at ENCODE; https://www.encodeproject.org/ENCBS281ZLI/


title: ChIP-seq from heart (ENCLB849ECE)

description:
https://www.encodeproject.org/experiments/ENCSR052CDF/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 14.5 day mouse heart
experiment encode accession: ENCSR052CDF
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR840PFW
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB849ECE
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap heart tissue mixed sex embryo (14.5 days)

value: Heart from pooled embryonic 14.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS563AAA at ENCODE; https://www.encodeproject.org/ENCBS563AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: WT.120.3

description:
OtA3015
Col wild-type

source_name: Wild-type seedling, 120 mins, rep 3

value: Columbia

value: wild-type

value: estrogen

value: 120 mins

value: seedling


title: WT.120.2

description:
OtA3014
Col wild-type

source_name: Wild-type seedling, 120 mins, rep 2


title: WT.120.1

description:
OtA3013
Col wild-type

source_name: Wild-type seedling, 120 mins, rep 1


title: WT.60.2

description:
OtA3208
Col wild-type

source_name: Wild-type seedling, 60 mins, rep 2

value: 60 mins


title: WGBS from hindbrain (ENCLB550WID)

description:
https://www.encodeproject.org/experiments/ENCSR037RNN/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 16.5 day mouse hindbrain
experiment encode accession: ENCSR037RNN
assay title: WGBS
assembly: mm10
encode release date: 2014-12-17
lab: Joe Ecker, Salk
library encode accession: ENCLB550WID
size range: 180-500

value: tissue

value: Hindbrain pooled from embyonic 16.5 day mice

value: ENCBS436LSH at ENCODE; https://www.encodeproject.org/ENCBS436LSH/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: WGBS from hindbrain (ENCLB020XTL)

description:
https://www.encodeproject.org/experiments/ENCSR037RNN/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 16.5 day mouse hindbrain
experiment encode accession: ENCSR037RNN
assay title: WGBS
assembly: mm10
encode release date: 2014-12-17
lab: Joe Ecker, Salk
library encode accession: ENCLB020XTL
size range: 180-500

value: hindbrain

value: Hindbrain from 37 embryonic 16.5 day mice

value: embryonic

value: pooled male and female


title: WT.60.3

description:
OtA3012
Col wild-type

source_name: Wild-type seedling, 60 mins, rep 3


title: WGBS from hindbrain (ENCLB706XHR)

description:
https://www.encodeproject.org/experiments/ENCSR037RNN/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 16.5 day mouse hindbrain
experiment encode accession: ENCSR037RNN
assay title: WGBS
assembly: mm10
encode release date: 2014-12-17
lab: Joe Ecker, Salk
library encode accession: ENCLB706XHR
size range: 180-500

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS281ZLI at ENCODE; https://www.encodeproject.org/ENCBS281ZLI/


title: ChIP-seq from liver (ENCLB088SDS)

description:
https://www.encodeproject.org/experiments/ENCSR037HCS/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K36me3 ChIP-seq on embryonic 13.5 day mouse liver
experiment encode accession: ENCSR037HCS
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR220PXJ
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB088SDS
size range: 300-500
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (13.5 days)

value: liver

value: Liver from embryonic 13.5 day mice

value: ENCBS373XWZ at ENCODE; https://www.encodeproject.org/ENCBS373XWZ/


title: ChIP-seq from liver (ENCLB688EBG)

description:
https://www.encodeproject.org/experiments/ENCSR037HCS/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K36me3 ChIP-seq on embryonic 13.5 day mouse liver
experiment encode accession: ENCSR037HCS
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR220PXJ
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB688EBG
size range: 300-500
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

value: ENCBS146FGW at ENCODE; https://www.encodeproject.org/ENCBS146FGW/


title: WT.0.1

description:
OtA3007
Col wild-type

source_name: Wild-type seedling, 0 mins, rep 1

value: Columbia

value: wild-type

value: estrogen

value: 0 mins

value: seedling


title: ChIP-seq from forebrain (ENCLB277YNG)

description:
https://www.encodeproject.org/experiments/ENCSR041KEJ/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K9me3 ChIP-seq on embryonic 13.5 day mouse forebrain
experiment encode accession: ENCSR041KEJ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR583ZEV
encode release date: 2016-03-16
lab: Bing Ren, UCSD
library encode accession: ENCLB277YNG
size range: 300-500
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (13.5 days)

value: forebrain

value: tissue

value: Forebrain from embryonic 13.5 day mice

value: ENCBS273RVL at ENCODE; https://www.encodeproject.org/ENCBS273RVL/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: WT.0.3

description:
OtA3009
Col wild-type

source_name: Wild-type seedling, 0 mins, rep 3


title: WT.60.1

description:
OtA3207
Col wild-type

source_name: Wild-type seedling, 60 mins, rep 1

value: 60 mins


title: WGBS from liver (ENCLB643ASA)

description:
https://www.encodeproject.org/experiments/ENCSR033PGF/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 11.5 day mouse liver
experiment encode accession: ENCSR033PGF
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB643ASA
size range: 180-500

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (11.5 days)

value: Liver from pooled embryonic 11.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS522YOW at ENCODE; https://www.encodeproject.org/ENCBS522YOW/


title: WGBS from hindbrain (ENCLB912RQB)

description:
https://www.encodeproject.org/experiments/ENCSR037RNN/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 16.5 day mouse hindbrain
experiment encode accession: ENCSR037RNN
assay title: WGBS
assembly: mm10
encode release date: 2014-12-17
lab: Joe Ecker, Salk
library encode accession: ENCLB912RQB
size range: 180-500

value: hindbrain

value: Hindbrain pooled from embyonic 16.5 day mice

value: ENCBS436LSH at ENCODE; https://www.encodeproject.org/ENCBS436LSH/


title: WGBS from lung (ENCLB656EHL)

description:
https://www.encodeproject.org/experiments/ENCSR027ICI/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 15.5 day mouse lung
experiment encode accession: ENCSR027ICI
assay title: WGBS
assembly: mm10
encode release date: 2015-06-23
lab: Joe Ecker, Salk
library encode accession: ENCLB656EHL
size range: 180-500

source_name: Mus musculus strain B6NCrl lung tissue mixed sex embryo (15.5 days)

value: lung

value: Lung from 78 embryonic 15.5 day mice

value: ENCBS467HSM at ENCODE; https://www.encodeproject.org/ENCBS467HSM/


title: WGBS from lung (ENCLB729DSZ)

description:
https://www.encodeproject.org/experiments/ENCSR027ICI/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 15.5 day mouse lung
experiment encode accession: ENCSR027ICI
assay title: WGBS
assembly: mm10
encode release date: 2015-06-23
lab: Joe Ecker, Salk
library encode accession: ENCLB729DSZ
size range: 180-500

value: tissue


title: WGBS from liver (ENCLB288RSV)

description:
https://www.encodeproject.org/experiments/ENCSR033PGF/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 11.5 day mouse liver
experiment encode accession: ENCSR033PGF
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB288RSV
size range: 180-500

value: liver

value: Liver from 109 embyronic 11.5 day mice

value: ENCBS746POP at ENCODE; https://www.encodeproject.org/ENCBS746POP/


title: Culture neuron -RNAi electroporation 48h

city: Shanghai

first: Pingping

last: Zhao

address: No. 320, YueYang Road, Shanghai, China

country: China

institute: Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Base-calling performed by using Illumina software
Removing 3’ adaptor sequence, empty reads, low quality Tags, Tags with a copy number of 1 and those Tags are too long or too short.
Sequenced reads were mapped to rn4 whole genome
Genome_build: rn4
Supplementary_files_format_and_content: text file containing gene expression

organism: Rattus norvegicus

source_name: neurons electroporated with RNAi plasmid

growth_protocol: Somatosensory cortexs of E16 rats' brain were dissected and dissociated into single cells. Medium contained Neurobasal medium, 10% FBS and 2% B27. Neurons were cultured for 48 hours

extract_protocol:
RNA was extracted with Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Dissociated cells were electroporated with control plasmid or RNAi plasmid

tag: strain

value: Sprague-Dawley

tag: Stage

value: brain


title: ChIP-seq from midbrain (ENCLB956WFC)

description:
https://www.encodeproject.org/experiments/ENCSR028VCU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-seq on postnatal 0 day mouse midbrain
experiment encode accession: ENCSR028VCU
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR889XXJ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB956WFC
size range: 300-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap midbrain tissue mixed sex postnatal (0 days)

tag: antibody

value: midbrain

value: Midbrain from 15 postnatal 0 day mice

value: 0 day

value: postnatal

value: ENCBS039AAA at ENCODE; https://www.encodeproject.org/ENCBS039AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: WGBS from lung (ENCLB035AXR)

description:
https://www.encodeproject.org/experiments/ENCSR027ICI/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 15.5 day mouse lung
experiment encode accession: ENCSR027ICI
assay title: WGBS
assembly: mm10
encode release date: 2015-06-23
lab: Joe Ecker, Salk
library encode accession: ENCLB035AXR
size range: 180-500

value: Lung from 62 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS217WPC at ENCODE; https://www.encodeproject.org/ENCBS217WPC/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: WGBS from liver (ENCLB735DHH)

description:
https://www.encodeproject.org/experiments/ENCSR033PGF/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 11.5 day mouse liver
experiment encode accession: ENCSR033PGF
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB735DHH
size range: 180-500

value: liver

value: tissue

value: Liver from 109 embyronic 11.5 day mice


title: ChIP-seq from embryonic facial prominence (ENCLB562WAM)

description:
https://www.encodeproject.org/experiments/ENCSR027DMG/
***************
biological replicate number: 1
technical replicate number: 1,2,3
description: H3K36me3 ChIP-seq on embryonic 11.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR027DMG
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR068AQC
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB562WAM
size range: 300-500

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (11.5 days)

value: embryonic facial prominence

value: Craniofacial prominence from 109 embyronic 11.5 day mice

value: ENCBS141GPQ at ENCODE; https://www.encodeproject.org/ENCBS141GPQ/


title: ChIP-seq from forebrain (ENCLB816SMB)

description:
https://www.encodeproject.org/experiments/ENCSR024JAN/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control ChIP-seq on embryonic 11.5 day mouse forebrain
experiment encode accession: ENCSR024JAN
assay title: ChIP-seq
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB816SMB
size range: 300-500

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (11.5 days)

value: Control

value: forebrain

value: Forebrain from 88 embyronic 11.5 day mice

value: ENCBS720JOH at ENCODE; https://www.encodeproject.org/ENCBS720JOH/


title: WGBS from lung (ENCLB340WGY)

description:
https://www.encodeproject.org/experiments/ENCSR027ICI/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 15.5 day mouse lung
experiment encode accession: ENCSR027ICI
assay title: WGBS
assembly: mm10
encode release date: 2015-06-23
lab: Joe Ecker, Salk
library encode accession: ENCLB340WGY
size range: 180-500

value: lung

value: Lung from 62 embryonic 15.5 day mice


title: ChIP-seq from forebrain (ENCLB413AUI)

description:
https://www.encodeproject.org/experiments/ENCSR024JAN/
***************
biological replicate number: 1
technical replicate number: 1,2
description: Input control ChIP-seq on embryonic 11.5 day mouse forebrain
experiment encode accession: ENCSR024JAN
assay title: ChIP-seq
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB413AUI
size range: 300-500

value: Forebrain from 109 embyronic 11.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS745VOM at ENCODE; https://www.encodeproject.org/ENCBS745VOM/


title: WT.0.2

description:
OtA3008
Col wild-type

source_name: Wild-type seedling, 0 mins, rep 2

value: Columbia

value: wild-type

value: estrogen

value: 0 mins

value: seedling


title: ChIP-seq from limb (ENCLB824YRO)

description:
https://www.encodeproject.org/experiments/ENCSR022DED/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K9me3 ChIP-seq on embryonic 13.5 day mouse limb
experiment encode accession: ENCSR022DED
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR465WTL
encode release date: 2016-02-18
lab: Bing Ren, UCSD
library encode accession: ENCLB824YRO
size range: 300-500
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (13.5 days)

value: limb

value: tissue

value: Limb from embryonic 13.5 day mice

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS176PGP at ENCODE; https://www.encodeproject.org/ENCBS176PGP/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: WGBS from forebrain (ENCLB399EBP)

description:
https://www.encodeproject.org/experiments/ENCSR020GGM/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR020GGM
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB399EBP
size range: 180-500

source_name: Mus musculus strain B6NTac;B6NCrl/Lap forebrain tissue mixed sex postnatal (0 days)

value: forebrain

value: Forebrain of pooled postnatal 0 day mice

value: 0 day

value: postnatal

value: ENCBS554AAA at ENCODE; https://www.encodeproject.org/ENCBS554AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: WGBS from forebrain (ENCLB462LRY)

description:
https://www.encodeproject.org/experiments/ENCSR020GGM/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR020GGM
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB462LRY
size range: 180-500

value: Forebrain from 15 postnatal 0 day mice

value: pooled male and female

value: ENCBS038AAA at ENCODE; https://www.encodeproject.org/ENCBS038AAA/


title: WGBS from forebrain (ENCLB414SVL)

description:
https://www.encodeproject.org/experiments/ENCSR020GGM/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR020GGM
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB414SVL
size range: 180-500


title: WGBS from forebrain (ENCLB967VBA)

description:
https://www.encodeproject.org/experiments/ENCSR019HJV/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 15.5 day mouse forebrain
experiment encode accession: ENCSR019HJV
assay title: WGBS
assembly: mm10
encode release date: 2015-06-23
lab: Joe Ecker, Salk
library encode accession: ENCLB967VBA
size range: 180-500

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (15.5 days)

value: Forebrain from 62 embryonic 15.5 day mice

value: embryonic

value: ENCBS841GER at ENCODE; https://www.encodeproject.org/ENCBS841GER/


title: WGBS from forebrain (ENCLB982VJQ)

description:
https://www.encodeproject.org/experiments/ENCSR019HJV/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 15.5 day mouse forebrain
experiment encode accession: ENCSR019HJV
assay title: WGBS
assembly: mm10
encode release date: 2015-06-23
lab: Joe Ecker, Salk
library encode accession: ENCLB982VJQ
size range: 180-500

value: tissue

value: Forebrain from 78 embryonic 15.5 day mice

value: ENCBS811RMD at ENCODE; https://www.encodeproject.org/ENCBS811RMD/


title: WGBS from forebrain (ENCLB813RGF)

description:
https://www.encodeproject.org/experiments/ENCSR019HJV/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 15.5 day mouse forebrain
experiment encode accession: ENCSR019HJV
assay title: WGBS
assembly: mm10
encode release date: 2015-06-23
lab: Joe Ecker, Salk
library encode accession: ENCLB813RGF
size range: 180-500

value: healthy

value: Len Pennacchio, LBNL


title: WGBS from stomach (ENCLB491WCK)

description:
https://www.encodeproject.org/experiments/ENCSR013VIR/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR013VIR
assay title: WGBS
assembly: mm10
encode release date: 2015-06-23
lab: Joe Ecker, Salk
library encode accession: ENCLB491WCK
size range: 180-500

source_name: Mus musculus strain B6NCrl stomach tissue mixed sex embryo (15.5 days)

value: stomach

value: Stomach from 62 embryonic 15.5 day mice

value: ENCBS355TAQ at ENCODE; https://www.encodeproject.org/ENCBS355TAQ/

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/


title: Culture neuron -control electroporation 48h

source_name: neurons electroporated with control plasmid

value: Sprague-Dawley

value: brain


title: WGBS from stomach (ENCLB519FIR)

description:
https://www.encodeproject.org/experiments/ENCSR013VIR/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR013VIR
assay title: WGBS
assembly: mm10
encode release date: 2015-06-23
lab: Joe Ecker, Salk
library encode accession: ENCLB519FIR
size range: 180-500

value: Stomach from 78 embryonic 15.5 day mice

value: ENCBS915SZN at ENCODE; https://www.encodeproject.org/ENCBS915SZN/


title: WGBS from stomach (ENCLB396CPQ)

description:
https://www.encodeproject.org/experiments/ENCSR013VIR/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR013VIR
assay title: WGBS
assembly: mm10
encode release date: 2015-06-23
lab: Joe Ecker, Salk
library encode accession: ENCLB396CPQ
size range: 180-500

value: pooled male and female


title: WGBS from forebrain (ENCLB047XKP)

description:
https://www.encodeproject.org/experiments/ENCSR020GGM/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR020GGM
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB047XKP
size range: 180-500

value: forebrain

value: Forebrain from 15 postnatal 0 day mice

value: 0 day

value: postnatal

value: ENCBS038AAA at ENCODE; https://www.encodeproject.org/ENCBS038AAA/

value: Derived from ENCODE donor ENCDO469XMJ; https://www.encodeproject.org/ENCDO469XMJ/


title: WGBS from forebrain (ENCLB739QRE)

description:
https://www.encodeproject.org/experiments/ENCSR019HJV/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 15.5 day mouse forebrain
experiment encode accession: ENCSR019HJV
assay title: WGBS
assembly: mm10
encode release date: 2015-06-23
lab: Joe Ecker, Salk
library encode accession: ENCLB739QRE
size range: 180-500

value: tissue

value: Forebrain from 62 embryonic 15.5 day mice

value: embryonic

value: healthy

value: ENCBS841GER at ENCODE; https://www.encodeproject.org/ENCBS841GER/


title: WGBS from stomach (ENCLB568ODR)

description:
https://www.encodeproject.org/experiments/ENCSR013VIR/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR013VIR
assay title: WGBS
assembly: mm10
encode release date: 2015-06-23
lab: Joe Ecker, Salk
library encode accession: ENCLB568ODR
size range: 180-500

value: stomach

value: Len Pennacchio, LBNL

value: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/