title: ChIP-seq from midbrain (ENCLB669YTA)

description:
https://www.encodeproject.org/experiments/ENCSR525BTK/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 15.5 day mouse midbrain
experiment encode accession: ENCSR525BTK
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR748XBE
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB669YTA
size range: 300-500

value: midbrain

value: Midbrain from 62 embryonic 15.5 day mice

value: ENCBS381PEJ at ENCODE; https://www.encodeproject.org/ENCBS381PEJ/


title: microRNA-seq from liver (ENCLB083OTU)

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/ENCSR510TFQ/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq  on embryonic 14.5 day mouse liver
experiment encode accession: ENCSR510TFQ
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB083OTU
size range: <30

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus strain B6NCrl liver tissue mixed sex embryo (14.5 days)

value: liver

value: tissue

tag: description

value: single liver from pup 1 pregnant 2 collected 7/17/2014

tag: biosample encode accession

tag: age

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

tag: lab

value: Barbara Wold, Caltech

tag: link

value: ENCBS314UPI at ENCODE; https://www.encodeproject.org/ENCBS314UPI/

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


title: ChIP-seq from neural tube (ENCLB661WQA)

description:
https://www.encodeproject.org/experiments/ENCSR517UZA/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 15.5 day mouse neural tube
experiment encode accession: ENCSR517UZA
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR351BDM
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB661WQA
size range: 300-500

library_source: genomic

molecule: genomic DNA

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

tag: antibody

value: neural tube

value: Neural tube from 62 embryonic 15.5 day mice

tag: health state

value: healthy

value: Len Pennacchio, LBNL

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


title: microRNA-seq from liver (ENCLB236OWO)

description:
https://www.encodeproject.org/experiments/ENCSR510TFQ/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq  on embryonic 14.5 day mouse liver
experiment encode accession: ENCSR510TFQ
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB236OWO
size range: <30

value: single liver from pup 1 pregnant 2 collected 7/15/2014

value: ENCBS237YNZ at ENCODE; https://www.encodeproject.org/ENCBS237YNZ/


title: FLAG/HA-Dicer PAR-CLIP La kd, rep 2

city: Regensburg

first: Gerhard

last: Lehmann

address: Universitaetsstrasse 31

department: Biochemistry 1

country: Germany

institute: University of Regensburg

description:
Small RNA sequencing data.
Dicer-parclip_La-kd_rep2
Processed data file: tRNA_counts.txt
Processed data file: tRNA_DESeq2_analysis.txt

data_processing:
Illumina HiSeq 2000 pipeline: HCS 2.2.38 / RTA 1.18.61/ Recipe Fragment: 1.5.14.0.
5' end as well as 3' end adapters were trimmed from sequenced reads using flexbar (v2.5).
Reads were collapsed so that PCR amplification biases could be eliminated.
The random 4mers at the 5' and 3' ends of the collapsed reads were trimmed.
Resulting reads were mapped against the hg19 genome using bwa mem (v0.7.12-r1039).
A custom script identified aligned reads with at least one RNA T:C transition that were used in part of our analysis.
The overlaps with annotated tRNAs of all reads, or of reads with at least one RNA T:C transition, were counted using the GenomicAlignment Bioconductor package.
Differential expression of tRNAs based on those counts was done using the DESeq2 Bioconductor package.
Genome_build: tRNA: gtRNAdb, hg19, status 2015-11
Genome_build: miRNAs: miRBase21
Supplementary_files_format_and_content: tRNA_counts.txt: Tab-delimited text file; Raw tRNA counts when mapping to hg19 and using reads with RNA T:C transitions.
Supplementary_files_format_and_content: tRNA_DESeq2_analysis.txt: Tab-delimited text file; DESeq2 results for all tRNAs.

organism: Homo sapiens

source_name: HEK293 FLAG/HA-Dicer cells, La knockdown

growth_protocol: HEK293 FLAG/HA-Dicer cells were cultivated in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 mg/mL streptomycin. Cells were grown under standard conditions at 37°C in 5% CO2 atmosphere.

extract_protocol:
PAR-CLIP experiments were performed as described in Rybak-Wolf et al. 2014.
For generation of small RNA libraries, the following 3' adapter [5'-Phos-NNNNTGGAATTCTCGGGTGCCAAGG-Inv(dT)-3'] and 5' adapter (5'- GUUCAGAGUUCUACAGUCCGACGAUCNNNN-3'] were used.

treatment_protocol: Cells were reverse transfected with RNAiMax according to the manufacturer's instructions using 40 nM siRNA. Cells were expanded after 2 days and harvested at day 4 post-transfection. Induction of protein expression with 1 μg/ml doxycycline and labeling with 100 μM 4-thiouridine (4SU) was performed 9-12 h before crosslinking. Cells were treated additionally with 100 µM 4SU 4 h before crosslinking.

tag: cell type

value: HEK293 FLAG/HA-Dicer

tag: knockdown

value: La siRNA, S:r(AGAUUGGAUGCUUGCUGAA)dTdT, AS:r(UUCAGCAAGCAUCCAAUCU)dTdT

tag: affinity purification

value: anti-FLAG immunoprecipitation


title: FLAG/HA-Dicer PAR-CLIP La kd, rep 1

description:
Small RNA sequencing data.
Dicer-parclip_La-kd_rep1
Processed data file: tRNA_counts.txt
Processed data file: tRNA_DESeq2_analysis.txt


title: DDIS rep 8

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

data_processing:
Paired-end 50 bp reads generated on Illumina HiSeq were aligned to the human genome version GRCh37.64 using TopHat v2.0.4 (Trapnell et al., 2009). Read counts were obtained using HTSeq-count v0.5.3p9 (Anders et al., 2014), normalised and tested for differential gene expression using the Bioconductor package DESeq v1.10.1 (Anders and Huber, 2010).
Multiple testing corrections were applied using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed such that FDR < 0.01.
Genome_build: GRCh37.64
Supplementary_files_format_and_content: HTSeq-count gene counts

source_name: IMR90 cells

growth_protocol: Cells were grown in DMEM media with 10% FBS at 37C in a 5% O2 / 5% CO2 atmosphere

extract_protocol:
Total RNA (miRNeasy kit, Qiagen) from the cultures cells was used to prepare libraries using the TruSeq RNA sample preparation kit (Illumina).
as per instructions from the TruSeq RNA sample preparation kit

treatment_protocol: Either 6 days of 100nM 4OHT to induce RIS or 2 days 100uM Etoposide followed by 5 days further culture to induce DDIS

tag: sample group

value: DDIS


title: DNase-seq from heart (ENCLB016PCE)

description:
https://www.encodeproject.org/experiments/ENCSR005WPU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR005WPU
assay title: DNase-seq
assembly: mm10
encode release date: 2016-05-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB016PCE
instrument models: Illumina NextSeq 500,Illumina HiSeq 2500

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

value: heart

value: tissue

value: 0 day

value: postnatal

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS811IJW at ENCODE; https://www.encodeproject.org/ENCBS811IJW/


title: DDIS rep 5


title: DDIS rep 2


title: ChIP-seq from heart (ENCLB758GHH)

description:
https://www.encodeproject.org/experiments/ENCSR501GBJ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 13.5 day mouse heart
experiment encode accession: ENCSR501GBJ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR077QRY
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB758GHH
size range: 300-500

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

value: Heart from embryonic 13.5 day mice

value: embryonic

value: pooled male and female

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

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


title: ChIP-seq from midbrain (ENCLB071BSW)

description:
https://www.encodeproject.org/experiments/ENCSR502WUI/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 11.5 day mouse midbrain
experiment encode accession: ENCSR502WUI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR081UQY
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB071BSW
size range: 300-500

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

value: midbrain

value: Midbrain from 88 embyronic 11.5 day mice

value: healthy

value: Len Pennacchio, LBNL

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


title: DDIS rep 3

value: DDIS


title: ChIP-seq from liver (ENCLB773JSI)

description:
https://www.encodeproject.org/experiments/ENCSR510CGB/
***************
biological replicate number: 1
technical replicate number: 2,1,3
description: H3K36me3 ChIP-seq on embryonic 15.5 day mouse liver
experiment encode accession: ENCSR510CGB
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR274AQL
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB773JSI
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

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

value: liver

value: tissue

value: Liver from 78 embryonic 15.5 day mice

value: ENCBS734ENZ at ENCODE; https://www.encodeproject.org/ENCBS734ENZ/


title: DDIS rep 1


title: RIS rep 8

value: RIS


title: FLAG/HA-Dicer PAR-CLIP control kd, rep 1

description:
Small RNA sequencing data.
Dicer-parclip_UB-kd_rep1
Processed data file: tRNA_counts.txt
Processed data file: tRNA_DESeq2_analysis.txt

source_name: HEK293 FLAG/HA-Dicer cells, control knockdown

value: HEK293 FLAG/HA-Dicer

value: control siRNA, S:r(UUGUCUUGCAUUCGACUAAU)dT, AS:r(UUAGUCGAAUGCAAGACAAU)dT

value: anti-FLAG immunoprecipitation


title: DDIS rep 4


title: ChIP-seq from heart (ENCLB125WNQ)

description:
https://www.encodeproject.org/experiments/ENCSR501GBJ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 13.5 day mouse heart
experiment encode accession: ENCSR501GBJ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR077QRY
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB125WNQ
size range: 300-500

value: heart

value: Heart from embryonic 13.5 day mice

value: embryonic

value: pooled male and female

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


title: ChIP-seq from midbrain (ENCLB454ICM)

description:
https://www.encodeproject.org/experiments/ENCSR502WUI/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 11.5 day mouse midbrain
experiment encode accession: ENCSR502WUI
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR081UQY
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB454ICM
size range: 300-500

value: midbrain

value: Midbrain of 109 embyronic 11.5 day mice

value: healthy

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

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


title: ChIP-seq from kidney (ENCLB845JZD)

description:
https://www.encodeproject.org/experiments/ENCSR499NUH/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K9me3 ChIP-seq on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR499NUH
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR780JSE
encode release date: 2016-03-16
lab: Bing Ren, UCSD
library encode accession: ENCLB845JZD
size range: 300-500

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

value: kidney

value: tissue

value: Kidney from 78 embryonic 15.5 day mice

value: Len Pennacchio, LBNL

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


title: DDIS rep 6

value: DDIS


title: RIS rep 5

value: RIS


title: RIS rep 6


title: RIS rep 7


title: RIS rep 1


title: DDIS rep 7


title: ChIP-seq from kidney (ENCLB660ZLB)

description:
https://www.encodeproject.org/experiments/ENCSR499NUH/
***************
biological replicate number: 2
technical replicate number: 2,1
description: H3K9me3 ChIP-seq on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR499NUH
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR780JSE
encode release date: 2016-03-16
lab: Bing Ren, UCSD
library encode accession: ENCLB660ZLB
size range: 300-500

value: Kidney from 62 embryonic 15.5 day mice

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


title: ChIP-seq from stomach (ENCLB191FUA)

description:
https://www.encodeproject.org/experiments/ENCSR497YBQ/
***************
biological replicate number: 1
technical replicate number: 1
description: Input control ChIP-seq on embryonic 14.5 day mouse stomach
experiment encode accession: ENCSR497YBQ
assay title: ChIP-seq
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB191FUA
size range: 300-500

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

value: Control

value: stomach

value: Stomach pooled from embryonic 14.5 day mice

value: embryonic

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

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


title: microRNA-seq from neural tube (ENCLB486PZP)

description:
https://www.encodeproject.org/experiments/ENCSR498DIP/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq  on embryonic 14.5 day mouse neural tube
experiment encode accession: ENCSR498DIP
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB486PZP
size range: <30

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

value: neural tube

value: single neural tube from pup 1 pregnant 2 collected 7/29/2014

value: pooled male and female

value: Barbara Wold, Caltech

value: ENCBS883PNF at ENCODE; https://www.encodeproject.org/ENCBS883PNF/


title: RIS rep 2


title: Control rep 6


title: Control rep 5


title: Control rep 4


title: RIS rep 4


title: Control rep 3


title: microRNA-seq from neural tube (ENCLB706GWH)

description:
https://www.encodeproject.org/experiments/ENCSR498DIP/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq  on embryonic 14.5 day mouse neural tube
experiment encode accession: ENCSR498DIP
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB706GWH
size range: <30

value: tissue

value: single neural tube from pup 1 pregnant 1 collected 7/29/2014

value: ENCBS431CVS at ENCODE; https://www.encodeproject.org/ENCBS431CVS/

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


title: Control rep 8


title: microRNA-seq from kidney (ENCLB177PNN)

description:
https://www.encodeproject.org/experiments/ENCSR497ERE/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq  on embryonic 14.5 day mouse kidney
experiment encode accession: ENCSR497ERE
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB177PNN
size range: <30

source_name: Mus musculus strain B6NCrl kidney tissue mixed sex embryo (14.5 days)

value: kidney

value: 2 kidneys from pup 1 pregnant 2 collected 7/15/2014

value: ENCBS731ALA at ENCODE; https://www.encodeproject.org/ENCBS731ALA/


title: Control rep 7

value: Control


title: Control rep 2


title: microRNA-seq from kidney (ENCLB869CAV)

description:
https://www.encodeproject.org/experiments/ENCSR497ERE/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq  on embryonic 14.5 day mouse kidney
experiment encode accession: ENCSR497ERE
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-01-06
lab: Ali Mortazavi, UCI
library encode accession: ENCLB869CAV
size range: <30

value: 2 kidneys from pup 1 pregnant 2 collected 7/17/2014

value: ENCBS454WSU at ENCODE; https://www.encodeproject.org/ENCBS454WSU/


title: RIS_rep_5

data_processing:
Single-end 40 bp reads generated on Illumina HiSeq were aligned to the human genome version GRCh37.64 using TopHat v2.0.4 (Trapnell et al., 2009). Read counts were obtained using HTSeq-count v0.5.3p9 (Anders et al., 2014), normalised and tested for differential gene expression using the Bioconductor package DESeq v1.10.1 (Anders and Huber, 2010).
Multiple testing corrections were applied using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed such that FDR < 0.01.
Genome_build: GRCh37.64
Supplementary_files_format_and_content: HTSeq-count gene counts

extract_protocol:
Total RNA (RNEasy Plus kit, Qiagen) from the cultured cells was used to prepare libraries using the TruSeq RNA sample preparation kit (Illumina).
as per instructions from the TruSeq RNA sample preparation kit

treatment_protocol: Control: vehicle-treated, control vector transduced ER:RAS IMR90 cells; RIS: 4OHT-treated, control vector transduced ER:RAS IMR90 cells; NIS: vehicle-treated, N1ICD-FLAG transduced ER:RAS IMR90 cells; RNIS: 4OHT-treated, N1ICD-FLAG transduced ER:RAS IMR90 cells.

tag: n11cd factor

value: No

tag: 4oht factor

value: Yes

tag: vec factor


title: RIS rep 3

value: RIS


title: RIS_rep_3


title: ChIP-seq from forebrain (ENCLB993BQD)

description:
https://www.encodeproject.org/experiments/ENCSR496TBX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 13.5 day mouse forebrain
experiment encode accession: ENCSR496TBX
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR583ZEV
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB993BQD
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: healthy

value: Len Pennacchio, LBNL

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


title: ChIP-seq from forebrain (ENCLB208VLY)

description:
https://www.encodeproject.org/experiments/ENCSR496TBX/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 13.5 day mouse forebrain
experiment encode accession: ENCSR496TBX
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR583ZEV
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB208VLY
size range: 300-500

value: tissue

value: pooled male and female

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


title: RIS_rep_4


title: Control rep 1


title: ChIP-seq from stomach (ENCLB010KMD)

description:
https://www.encodeproject.org/experiments/ENCSR497YBQ/
***************
biological replicate number: 2
technical replicate number: 1
description: Input control ChIP-seq on embryonic 14.5 day mouse stomach
experiment encode accession: ENCSR497YBQ
assay title: ChIP-seq
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB010KMD
size range: 300-500

value: stomach

value: Stomach pooled from embryonic 14.5 day mice

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

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


title: ChIP-seq from lung (ENCLB278KDL)

description:
https://www.encodeproject.org/experiments/ENCSR523IIH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on postnatal 0 day mouse lung
experiment encode accession: ENCSR523IIH
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR241RIG
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB278KDL
size range: 300-500

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

value: lung

value: Lung from 15 postnatal 0 day mice

value: 0 day

value: postnatal

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


title: RIS_rep_2

value: No

value: Yes


title: ChIP-seq from neural tube (ENCLB164SZF)

description:
https://www.encodeproject.org/experiments/ENCSR489HYX/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 11.5 day mouse neural tube
experiment encode accession: ENCSR489HYX
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR138YZB
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB164SZF
size range: 300-500

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

value: neural tube

value: Neural tube from 109 embyronic 11.5 day mice

value: embryonic

value: healthy

value: ENCBS402TUS at ENCODE; https://www.encodeproject.org/ENCBS402TUS/

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


title: Control_rep_4

value: Vec


title: Control_rep_2


title: ChIP-seq from neural tube (ENCLB222ZFY)

description:
https://www.encodeproject.org/experiments/ENCSR489HYX/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 11.5 day mouse neural tube
experiment encode accession: ENCSR489HYX
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR138YZB
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB222ZFY
size range: 300-500

value: tissue

value: Neural tube from 88 embyronic 11.5 day mice

value: pooled male and female

value: Len Pennacchio, LBNL

value: ENCBS183YVD at ENCODE; https://www.encodeproject.org/ENCBS183YVD/


title: RNIS_rep_6


title: RIS_rep_1


title: Control_rep_5


title: Control_rep_6


title: RNIS_rep_5


title: ChIP-seq from heart (ENCLB625KOB)

description:
https://www.encodeproject.org/experiments/ENCSR488OCA/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on postnatal 0 day mouse heart
experiment encode accession: ENCSR488OCA
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR334IOH
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB625KOB
size range: 300-500

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

value: heart

value: Heart from 15 postnatal 0 day mice

value: 0 day

value: ENCBS041AAA at ENCODE; https://www.encodeproject.org/ENCBS041AAA/

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


title: RNIS_rep_4

value: Yes

value: No


title: RNIS_rep_1


title: Control_rep_1


title: NIS_rep_6


title: ChIP-seq from midbrain (ENCLB346YHL)

description:
https://www.encodeproject.org/experiments/ENCSR486MHP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 15.5 day mouse midbrain
experiment encode accession: ENCSR486MHP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR748XBE
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB346YHL
size range: 300-500

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

value: midbrain

value: Midbrain from 62 embryonic 15.5 day mice

value: embryonic

value: ENCBS381PEJ at ENCODE; https://www.encodeproject.org/ENCBS381PEJ/


title: ChIP-seq from heart (ENCLB022EIT)

description:
https://www.encodeproject.org/experiments/ENCSR488OCA/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on postnatal 0 day mouse heart
experiment encode accession: ENCSR488OCA
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR334IOH
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB022EIT
size range: 300-500

value: Heart from pooled postnatal 0 day mice

value: postnatal

value: healthy

value: ENCBS557AAA at ENCODE; https://www.encodeproject.org/ENCBS557AAA/


title: RIS_rep_6


title: NIS_rep_3


title: Control_rep_3

value: Vec


title: NIS_rep_1


title: RNIS_rep_3


title: RNIS_rep_2


title: ChIP-seq from midbrain (ENCLB085YLW)

description:
https://www.encodeproject.org/experiments/ENCSR486MHP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 15.5 day mouse midbrain
experiment encode accession: ENCSR486MHP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR748XBE
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB085YLW
size range: 300-500

value: tissue

value: Midbrain from 78 embryonic 15.5 day mice

value: pooled male and female

value: Len Pennacchio, LBNL

value: ENCBS190ETJ at ENCODE; https://www.encodeproject.org/ENCBS190ETJ/

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


title: ChIP-seq from midbrain (ENCLB760UWM)

description:
https://www.encodeproject.org/experiments/ENCSR487RAU/
***************
biological replicate number: 2
technical replicate number: 2,1
description: H3K36me3 ChIP-seq on embryonic 15.5 day mouse midbrain
experiment encode accession: ENCSR487RAU
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR748XBE
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB760UWM
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500


title: microRNA-seq from kidney (ENCLB067PRU)

description:
https://www.encodeproject.org/experiments/ENCSR484EVA/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq  on postnatal 0 day mouse kidney
experiment encode accession: ENCSR484EVA
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-02-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB067PRU
size range: <30

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

value: kidney

value: 2 kidneys from pup2 pregnant 1

value: 0 day

value: not collected

value: Barbara Wold, Caltech

value: ENCBS540QNA at ENCODE; https://www.encodeproject.org/ENCBS540QNA/


title: ChIP-seq from intestine (ENCLB658VSG)

description:
https://www.encodeproject.org/experiments/ENCSR485GTY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 14.5 day mouse intestine
experiment encode accession: ENCSR485GTY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR645QSY
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB658VSG
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 24 embryonic 14.5 day mice

value: embryonic

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

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


title: ChIP-seq from intestine (ENCLB836KZK)

description:
https://www.encodeproject.org/experiments/ENCSR483KOD/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K36me3 ChIP-seq on postnatal 0 day mouse intestine
experiment encode accession: ENCSR483KOD
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR898PML
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB836KZK
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

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

value: tissue

value: Intestine from pooled postnatal 0 day mice

value: postnatal

value: healthy

value: ENCBS560AAA at ENCODE; https://www.encodeproject.org/ENCBS560AAA/


title: ChIP-seq from stomach (ENCLB010UKF)

description:
https://www.encodeproject.org/experiments/ENCSR483DEV/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR483DEV
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR240XQT
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB010UKF
size range: 300-500

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: pooled male and female

value: Len Pennacchio, LBNL

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

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


title: ChIP-seq from intestine (ENCLB419YQB)

description:
https://www.encodeproject.org/experiments/ENCSR483KOD/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K36me3 ChIP-seq on postnatal 0 day mouse intestine
experiment encode accession: ENCSR483KOD
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR898PML
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB419YQB
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

value: Intestine from 15 postnatal 0 day mice

value: 0 day

value: ENCBS044AAA at ENCODE; https://www.encodeproject.org/ENCBS044AAA/


title: GR-ChIPed-control

city: Beijing

first: Xiao-Dong

last: Su

address: No.5 Yiheyuan Road, Haidian District

department: School of Life Science

country: China

institute: Peking University

description:
ChIPed DNA was treated by bisulfite conversion
Sample 2

data_processing:
library strategy: Bisulfite-ChIP-seq
We have sequenced two times for every sample and merged them into one dataset before data processing, respectively. Bismark was used to align the sequencing data to human genome hg18 and calculate the methylated cytosine sites.
Because the average insert size of all samples are less than 205bp, which indicate that the reads from two ends have overlapped reading in the middle, then a no_overlap process was used to reduce these double reads in the bismark_methylation_extractor step.  PCR redundancy data were removed by samtools rmdup.
The following data screening and statistics were done by programs written by Perl.
For credible, we only selected the data which were sequenced 4 or more than 4 times, and calculated the methylation level for each ChIPed C by methylated reads/total reads.
We screened the half of GRE sequence “AGAACA” from the GR ChIPed data, and E-box sequence “CACGTG” from the BAML1/CLOCK ChIPed data, then we calculated the distance between these sequences to the nearest transcriptional start site(TSS), which is generated from the gene database based on hg18.
Genome_build: hg18
Supplementary_files_format_and_content: Txt files were generated using programs written by Perl. The labels of arrays are Chromosome/Position/Chain/mC/Total/Sequence/Distance to nearset TSS(bp)/Gene name

source_name: HEK-293T Cell

growth_protocol: For GR, GR-pCMV14 and DNMT3A-pLX304 vectors,  for BAML1-CLOCK, BMAL1-pCMV14, CLOCK-pCMV14 and DNMT3A-pLX304 vectors  were co-transfected into HEK-293T cells using the Genscort II transfection reagent (Wisegen) and overexpressed for 24 hours.

extract_protocol:
Then cells were collected after 24 hours incubation followed by the ChIP experiment which was performed as described in previous studies. (Dahl and Collas, 2008)
Libraries were constructed with NEBNext DNA Library Prep Master Mix Set for Illumina (NEB).  After end repair and dA-tailing, methylated adaptors (NEBNext Multiplex Oligos for Illumina) were applied to ligate with DNA followed by bisulfite conversion using EZ DNA Methylation Kit (Zymo research).  Then DNA was recovered using AMPure XP beads (Beckman Coulter) after PCR amplification and sequenced by Hiseq2000 (Illumina).

treatment_protocol: Sample 1 &2: Dexamethasone (Sigma Aldrich) was added to a final concentration of 4nM after 24 hours to make GR transfer into the nucleus.

tag: cell line

tag: genotype/variation

value: GR, DNMT3a overexpression

tag: co-transfected vectors

value: GR-pCMV14 and DNMT3A-pLX304

tag: treated with

value: Dexamethasone (24h)

tag: chip antibody

value: IgG


title: BMAL1-CLOCK-ChIPed

description:
ChIPed DNA was treated by bisulfite conversion
Sample 3

value: BMAL1, CLOCK, DNMT3a overexpression

value: BMAL1-pCMV14, CLOCK-pCMV14 and DNMT3A-pLX304

value: Anti-Flag antibody

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat. #

tag: chip antibody lot #


title: NIS_rep_4

source_name: IMR90 cells

value: Yes

value: No


title: ChIP-seq from intestine (ENCLB992NGV)

description:
https://www.encodeproject.org/experiments/ENCSR485GTY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 14.5 day mouse intestine
experiment encode accession: ENCSR485GTY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR645QSY
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB992NGV
size range: 300-500

tag: antibody

value: intestine

value: tissue

tag: description

value: Intestine from 34 embryonic 14.5 day mice

tag: biosample encode accession

tag: age

tag: dev stage

value: embryonic

tag: Sex

value: pooled male and female

value: healthy

tag: lab

tag: link

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

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


title: NIS_rep_5

tag: sample group

tag: n11cd factor

tag: 4oht factor

tag: vec factor


title: DNase-seq from stomach (ENCLB707AXB)

description:
https://www.encodeproject.org/experiments/ENCSR969OPE/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR969OPE
assay title: DNase-seq
assembly: mm10
encode release date: 2016-05-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB707AXB

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

value: stomach

value: 0 day

value: postnatal

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS514EXL at ENCODE; https://www.encodeproject.org/ENCBS514EXL/

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


title: ChIP-seq from liver (ENCLB212NGD)

description:
https://www.encodeproject.org/experiments/ENCSR479LFP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 15.5 day mouse liver
experiment encode accession: ENCSR479LFP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR274AQL
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB212NGD
size range: 300-500

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

value: liver

value: Liver from 78 embryonic 15.5 day mice

tag: health state

value: Len Pennacchio, LBNL

value: ENCBS734ENZ at ENCODE; https://www.encodeproject.org/ENCBS734ENZ/


title: NIS_rep_2

value: Yes

value: No


title: BMAL1-CLOCK-ChIPed-control

description:
ChIPed DNA was treated by bisulfite conversion
Sample 4

tag: cell line

tag: genotype/variation

value: BMAL1, CLOCK, DNMT3a overexpression

tag: co-transfected vectors

value: BMAL1-pCMV14, CLOCK-pCMV14 and DNMT3A-pLX304

tag: treated with

tag: chip antibody

value: IgG


title: ChIP-seq from embryonic facial prominence (ENCLB410UBV)

description:
https://www.encodeproject.org/experiments/ENCSR481SGM/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 14.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR481SGM
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR329ZEN
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB410UBV
size range: 300-500

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

tag: antibody

value: embryonic facial prominence

value: tissue

tag: description

value: Craniofacial prominence from 34 embryonic 14.5 day mice

value: embryonic

value: pooled male and female

value: healthy

value: ENCBS024AAA at ENCODE; https://www.encodeproject.org/ENCBS024AAA/

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


title: DNase-seq from stomach (ENCLB455MQX)

description:
https://www.encodeproject.org/experiments/ENCSR969OPE/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR969OPE
assay title: DNase-seq
assembly: mm10
encode release date: 2016-05-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB455MQX
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: stomach

tag: biosample encode accession

tag: age

value: 0 day

value: postnatal

value: not collected

value: John Stamatoyannopoulos, UW

value: ENCBS814CAO at ENCODE; https://www.encodeproject.org/ENCBS814CAO/

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


title: GR-ChIPed

description:
ChIPed DNA was treated by bisulfite conversion
Sample 1

value: GR, DNMT3a overexpression

value: GR-pCMV14 and DNMT3A-pLX304

value: Dexamethasone (24h)

value: Anti-Flag antibody

tag: chip antibody vendor

value: Sigma

tag: chip antibody cat. #

tag: chip antibody lot #


title: microRNA-seq from kidney (ENCLB235HXH)

description:
https://www.encodeproject.org/experiments/ENCSR484EVA/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq  on postnatal 0 day mouse kidney
experiment encode accession: ENCSR484EVA
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-02-04
lab: Ali Mortazavi, UCI
library encode accession: ENCLB235HXH
size range: <30

value: kidney

value: tissue

value: 2 kidneys from pup1 pregnant 1

tag: dev stage

tag: Sex

tag: lab

value: Barbara Wold, Caltech

tag: link

value: ENCBS103FKB at ENCODE; https://www.encodeproject.org/ENCBS103FKB/


title: ChIP-seq from stomach (ENCLB859PHK)

description:
https://www.encodeproject.org/experiments/ENCSR483DEV/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 15.5 day mouse stomach
experiment encode accession: ENCSR483DEV
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR240XQT
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB859PHK
size range: 300-500

value: stomach

value: Stomach from 78 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

tag: health state

value: healthy

value: Len Pennacchio, LBNL

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


title: ChIP-seq from heart (ENCLB852TPQ)

description:
https://www.encodeproject.org/experiments/ENCSR467UGM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 16.5 day mouse heart
experiment encode accession: ENCSR467UGM
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR685AMF
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB852TPQ
size range: 300-500

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

value: heart

value: Heart pooled from embyonic 16.5 day mice

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

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


title: DNase-seq from embryonic facial prominence (ENCLB338AZH)

description:
https://www.encodeproject.org/experiments/ENCSR959HKR/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 14.5 day mixed embryonic mouse craniofacial tissue
experiment encode accession: ENCSR959HKR
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB338AZH
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (14.5 days)

value: embryonic facial prominence

value: John Stamatoyannopoulos, UW

value: ENCBS581IAA at ENCODE; https://www.encodeproject.org/ENCBS581IAA/


title: ChIP-seq from embryonic facial prominence (ENCLB137NDC)

description:
https://www.encodeproject.org/experiments/ENCSR481SGM/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 14.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR481SGM
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR329ZEN
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB137NDC
size range: 300-500

value: tissue

value: Craniofacial prominence from 24 embryonic 14.5 day mice

value: ENCBS012AAA at ENCODE; https://www.encodeproject.org/ENCBS012AAA/

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


title: ChIP-seq from hindbrain (ENCLB040RLX)

description:
https://www.encodeproject.org/experiments/ENCSR472YGQ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 ChIP-seq on postnatal 0 day mouse hindbrain
experiment encode accession: ENCSR472YGQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR066SPF
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB040RLX
size range: 300-500

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

value: hindbrain

value: Hindbrain from pooled postnatal 0 day mice

value: 0 day

value: postnatal

value: ENCBS556AAA at ENCODE; https://www.encodeproject.org/ENCBS556AAA/


title: ChIP-seq from hindbrain (ENCLB163FOK)

description:
https://www.encodeproject.org/experiments/ENCSR472YGQ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on postnatal 0 day mouse hindbrain
experiment encode accession: ENCSR472YGQ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR066SPF
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB163FOK
size range: 300-500

value: Hindbrain from 15 postnatal 0 day mice

value: pooled male and female

value: healthy

value: Len Pennacchio, LBNL

value: ENCBS040AAA at ENCODE; https://www.encodeproject.org/ENCBS040AAA/


title: ChIP-seq from heart (ENCLB549GMS)

description:
https://www.encodeproject.org/experiments/ENCSR467UGM/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K36me3 ChIP-seq on embryonic 16.5 day mouse heart
experiment encode accession: ENCSR467UGM
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR685AMF
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB549GMS
size range: 300-500

value: heart

value: Heart from 41 embyonic 16.5 day mice

value: embryonic

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

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


title: DNase-seq from thymus (ENCLB371KCF)

description:
https://www.encodeproject.org/experiments/ENCSR935RRY/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on postnatal mixed mouse thymus
experiment encode accession: ENCSR935RRY
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB371KCF
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

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

value: thymus

value: tissue

value: John Stamatoyannopoulos, UW

value: ENCBS344JQT at ENCODE; https://www.encodeproject.org/ENCBS344JQT/


title: DNase-seq from embryonic facial prominence (ENCLB083JNB)

description:
https://www.encodeproject.org/experiments/ENCSR959HKR/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 14.5 day mixed embryonic mouse craniofacial tissue
experiment encode accession: ENCSR959HKR
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB083JNB

value: embryonic facial prominence

value: ENCBS249FSZ at ENCODE; https://www.encodeproject.org/ENCBS249FSZ/


title: DNase-seq from thymus (ENCLB504VIQ)

description:
https://www.encodeproject.org/experiments/ENCSR935RRY/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on postnatal mixed mouse thymus
experiment encode accession: ENCSR935RRY
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB504VIQ

value: 0 day

value: postnatal

value: ENCBS297AVO at ENCODE; https://www.encodeproject.org/ENCBS297AVO/


title: ChIP-seq from midbrain (ENCLB993NAA)

description:
https://www.encodeproject.org/experiments/ENCSR465TIZ/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K27me3 ChIP-seq on embryonic 16.5 day mouse midbrain
experiment encode accession: ENCSR465TIZ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR817FFF
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB993NAA
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

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

value: midbrain

value: Midbrain from 37 embryonic 16.5 day mice

value: pooled male and female

value: healthy

value: ENCBS463JSE at ENCODE; https://www.encodeproject.org/ENCBS463JSE/


title: ChIP-seq from neural tube (ENCLB277DNU)

description:
https://www.encodeproject.org/experiments/ENCSR466ZQC/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 11.5 day mouse neural tube
experiment encode accession: ENCSR466ZQC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR138YZB
encode release date: 2016-03-17
lab: Bing Ren, UCSD
library encode accession: ENCLB277DNU
size range: 300-500

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

value: neural tube

value: Neural tube from 88 embyronic 11.5 day mice

value: embryonic

value: Len Pennacchio, LBNL

value: ENCBS183YVD at ENCODE; https://www.encodeproject.org/ENCBS183YVD/


title: DNase-seq from limb (ENCLB701OTG)

description:
https://www.encodeproject.org/experiments/ENCSR661HDP/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 11.5 day mixed embryonic mouse limb
experiment encode accession: ENCSR661HDP
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB701OTG
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

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

value: limb

value: tissue

value: John Stamatoyannopoulos, UW

value: ENCBS365WHE at ENCODE; https://www.encodeproject.org/ENCBS365WHE/

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


title: DNase-seq from limb (ENCLB557EUN)

description:
https://www.encodeproject.org/experiments/ENCSR636NXY/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 14.5 day mixed embryonic mouse limb
experiment encode accession: ENCSR636NXY
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB557EUN
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Mus musculus strain B6NCrl limb tissue mixed sex embryo (14.5 days)

value: ENCBS654PZU at ENCODE; https://www.encodeproject.org/ENCBS654PZU/


title: DNase-seq from hindbrain (ENCLB310LJW)

description:
https://www.encodeproject.org/experiments/ENCSR469VGZ/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on postnatal mixed mouse hindbrain
experiment encode accession: ENCSR469VGZ
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB310LJW
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex postnatal (0 days)

value: hindbrain

value: 0 day

value: postnatal

value: ENCBS057ODY at ENCODE; https://www.encodeproject.org/ENCBS057ODY/


title: ChIP-seq from neural tube (ENCLB574FFO)

description:
https://www.encodeproject.org/experiments/ENCSR466ZQC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 11.5 day mouse neural tube
experiment encode accession: ENCSR466ZQC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR138YZB
encode release date: 2016-03-17
lab: Bing Ren, UCSD
library encode accession: ENCLB574FFO
size range: 300-500

value: Neural tube from 109 embyronic 11.5 day mice

value: pooled male and female

value: healthy

value: ENCBS402TUS at ENCODE; https://www.encodeproject.org/ENCBS402TUS/


title: DNase-seq from embryo (ENCLB399ZHJ)

description:
https://www.encodeproject.org/experiments/ENCSR774TQO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR774TQO
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB399ZHJ

source_name: Mus musculus strain B6NCrl embryo tissue mixed sex embryo (11 day)

value: embryo

value: 11 day

value: embryonic

value: ENCBS648FKI at ENCODE; https://www.encodeproject.org/ENCBS648FKI/


title: DNase-seq from forebrain (ENCLB070NQB)

description:
https://www.encodeproject.org/experiments/ENCSR791AJY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR791AJY
assay title: DNase-seq
assembly: mm10
encode release date: 2015-11-05
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB070NQB

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex postnatal (0 days)

value: forebrain

value: tissue

value: ENCBS284MHV at ENCODE; https://www.encodeproject.org/ENCBS284MHV/


title: DNase-seq from embryo (ENCLB225OFJ)

description:
https://www.encodeproject.org/experiments/ENCSR774TQO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR774TQO
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB225OFJ

value: John Stamatoyannopoulos, UW

value: ENCBS623YUL at ENCODE; https://www.encodeproject.org/ENCBS623YUL/

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


title: DNase-seq from limb (ENCLB581HRN)

description:
https://www.encodeproject.org/experiments/ENCSR661HDP/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 11.5 day mixed embryonic mouse limb
experiment encode accession: ENCSR661HDP
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB581HRN

value: limb

value: ENCBS920QKF at ENCODE; https://www.encodeproject.org/ENCBS920QKF/


title: DNase-seq from midbrain (ENCLB400VPZ)

description:
https://www.encodeproject.org/experiments/ENCSR367FCW/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 14.5 day mixed embryonic mouse midbrain
experiment encode accession: ENCSR367FCW
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB400VPZ

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (14.5 days)

value: midbrain

value: ENCBS278POI at ENCODE; https://www.encodeproject.org/ENCBS278POI/


title: ChIP-seq from midbrain (ENCLB584OBI)

description:
https://www.encodeproject.org/experiments/ENCSR465TIZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on embryonic 16.5 day mouse midbrain
experiment encode accession: ENCSR465TIZ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR817FFF
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB584OBI
size range: 300-500

value: Midbrain pooled from embyonic 16.5 day mice

value: pooled male and female

value: Len Pennacchio, LBNL

value: ENCBS684MLE at ENCODE; https://www.encodeproject.org/ENCBS684MLE/


title: ChIP-seq from heart (ENCLB734BAS)

description:
https://www.encodeproject.org/experiments/ENCSR463GJL/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 11.5 day mouse heart
experiment encode accession: ENCSR463GJL
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR317ENO
encode release date: 2016-02-18
lab: Bing Ren, UCSD
library encode accession: ENCLB734BAS
size range: 300-500

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

value: heart

value: Heart from 109 embyronic 11.5 day mice

value: healthy

value: ENCBS225RIF at ENCODE; https://www.encodeproject.org/ENCBS225RIF/


title: DNase-seq from limb (ENCLB588UWH)

description:
https://www.encodeproject.org/experiments/ENCSR636NXY/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 14.5 day mixed embryonic mouse limb
experiment encode accession: ENCSR636NXY
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB588UWH

value: tissue

value: embryonic

value: ENCBS088CNL at ENCODE; https://www.encodeproject.org/ENCBS088CNL/


title: DNase-seq from hindbrain (ENCLB774LAD)

description:
https://www.encodeproject.org/experiments/ENCSR358ESL/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 11.5 day mixed embryonic mouse hindbrain
experiment encode accession: ENCSR358ESL
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB774LAD
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

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

value: hindbrain

value: John Stamatoyannopoulos, UW

value: ENCBS351XQS at ENCODE; https://www.encodeproject.org/ENCBS351XQS/


title: ChIP-seq from forebrain (ENCLB758LEN)

description:
https://www.encodeproject.org/experiments/ENCSR465PLB/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR465PLB
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR398NCK
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB758LEN
size range: 300-500

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: DNase-seq from midbrain (ENCLB790JOB)

description:
https://www.encodeproject.org/experiments/ENCSR767AJS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR767AJS
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB790JOB
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

source_name: Mus musculus strain B6NCrl midbrain tissue mixed sex postnatal (0 days)

value: midbrain

value: pooled male and female

value: ENCBS671UBL at ENCODE; https://www.encodeproject.org/ENCBS671UBL/

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


title: DNase-seq from midbrain (ENCLB527TCS)

description:
https://www.encodeproject.org/experiments/ENCSR767AJS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR767AJS
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB527TCS

value: healthy

value: ENCBS282XKA at ENCODE; https://www.encodeproject.org/ENCBS282XKA/


title: ChIP-seq from intestine (ENCLB984LHC)

description:
https://www.encodeproject.org/experiments/ENCSR672UQX/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K9me3 ChIP-seq on postnatal 0 day mouse intestine
experiment encode accession: ENCSR672UQX
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR898PML
encode release date: 2016-02-18
lab: Bing Ren, UCSD
library encode accession: ENCLB984LHC
size range: 300-500
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

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

value: intestine

value: tissue

value: Intestine from pooled postnatal 0 day mice

value: Len Pennacchio, LBNL

value: ENCBS560AAA at ENCODE; https://www.encodeproject.org/ENCBS560AAA/


title: ChIP-seq from forebrain (ENCLB086HMC)

description:
https://www.encodeproject.org/experiments/ENCSR465PLB/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on postnatal 0 day mouse forebrain
experiment encode accession: ENCSR465PLB
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR398NCK
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB086HMC
size range: 300-500

value: forebrain

value: Forebrain from 15 postnatal 0 day mice

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


title: DNase-seq from lung (ENCLB936JCO)

description:
https://www.encodeproject.org/experiments/ENCSR742DUR/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 14.5 day mixed embryonic mouse lung
experiment encode accession: ENCSR742DUR
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB936JCO
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Mus musculus strain B6NCrl lung tissue mixed sex embryo (14.5 days)

value: lung

value: embryonic

value: John Stamatoyannopoulos, UW

value: ENCBS665FLY at ENCODE; https://www.encodeproject.org/ENCBS665FLY/


title: DNase-seq from forebrain (ENCLB491WIB)

description:
https://www.encodeproject.org/experiments/ENCSR337EDG/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 14.5 day mixed embryonic mouse forebrain
experiment encode accession: ENCSR337EDG
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB491WIB

source_name: Mus musculus strain B6NCrl forebrain tissue mixed sex embryo (14.5 days)

value: pooled male and female

value: ENCBS402PEQ at ENCODE; https://www.encodeproject.org/ENCBS402PEQ/


title: ChIP-seq from forebrain (ENCLB396BWU)

description:
https://www.encodeproject.org/experiments/ENCSR462KTT/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 16.5 day mouse forebrain
experiment encode accession: ENCSR462KTT
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR587JRQ
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB396BWU
size range: 300-500

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

value: Forebrain from 41 embyonic 16.5 day mice

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

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


title: DNase-seq from retina (ENCLB831QLC)

description:
https://www.encodeproject.org/experiments/ENCSR488VEQ/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 14.5 day mixed embryonic mouse retina
experiment encode accession: ENCSR488VEQ
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB831QLC
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Mus musculus strain B6NCrl retina tissue mixed sex embryo (14.5 days)

value: retina

value: healthy

value: ENCBS384MHN at ENCODE; https://www.encodeproject.org/ENCBS384MHN/


title: DNase-seq from midbrain (ENCLB342ZJE)

description:
https://www.encodeproject.org/experiments/ENCSR292QBA/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 11.5 day embryonic mouse midbrain
experiment encode accession: ENCSR292QBA
assay title: DNase-seq
assembly: mm10
encode release date: 2015-10-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB342ZJE
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

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

value: midbrain

value: tissue

value: ENCBS994RMB at ENCODE; https://www.encodeproject.org/ENCBS994RMB/


title: DNase-seq from midbrain (ENCLB777SBO)

description:
https://www.encodeproject.org/experiments/ENCSR367FCW/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 14.5 day mixed embryonic mouse midbrain
experiment encode accession: ENCSR367FCW
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB777SBO

value: ENCBS322XWL at ENCODE; https://www.encodeproject.org/ENCBS322XWL/


title: ChIP-seq from intestine (ENCLB975RYB)

description:
https://www.encodeproject.org/experiments/ENCSR464MQU/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 14.5 day mouse intestine
experiment encode accession: ENCSR464MQU
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR645QSY
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB975RYB
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 24 embryonic 14.5 day mice

value: Len Pennacchio, LBNL

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

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


title: ChIP-seq from limb (ENCLB669WDA)

description:
https://www.encodeproject.org/experiments/ENCSR462BZP/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 13.5 day mouse limb
experiment encode accession: ENCSR462BZP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR465WTL
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB669WDA
size range: 300-500

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

value: limb

value: Limb from embryonic 13.5 day mice

value: embryonic

value: pooled male and female

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


title: DNase-seq from embryo (ENCLB923KFC)

description:
https://www.encodeproject.org/experiments/ENCSR172RHR/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 10.5 day mouse embryo.
experiment encode accession: ENCSR172RHR
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB923KFC

source_name: Mus musculus strain B6NCrl embryo tissue mixed sex embryo (10.5 days)

value: embryo

value: John Stamatoyannopoulos, UW

value: ENCBS262GTO at ENCODE; https://www.encodeproject.org/ENCBS262GTO/

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


title: DNase-seq from forebrain (ENCLB476UNY)

description:
https://www.encodeproject.org/experiments/ENCSR337EDG/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 14.5 day mixed embryonic mouse forebrain
experiment encode accession: ENCSR337EDG
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB476UNY
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

value: forebrain

value: tissue

value: healthy

value: ENCBS804ZEI at ENCODE; https://www.encodeproject.org/ENCBS804ZEI/


title: DNase-seq from liver (ENCLB995ATO)

description:
https://www.encodeproject.org/experiments/ENCSR216UMD/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR216UMD
assay title: DNase-seq
assembly: mm10
encode release date: 2016-05-18
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB995ATO
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

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

value: liver

value: 0 day

value: postnatal

value: not collected

value: ENCBS761QGT at ENCODE; https://www.encodeproject.org/ENCBS761QGT/


title: DNase-seq from embryonic facial prominence (ENCLB311SIU)

description:
https://www.encodeproject.org/experiments/ENCSR196VDE/
***************
biological replicate number: 1
technical replicate number: 1
description: DNase-seq on 11.5 day mixed embryonic mouse craniofacial tissue
experiment encode accession: ENCSR196VDE
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB311SIU
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

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

value: embryonic facial prominence

value: ENCBS004ULJ at ENCODE; https://www.encodeproject.org/ENCBS004ULJ/


title: DNase-seq from embryonic facial prominence (ENCLB578XNO)

description:
https://www.encodeproject.org/experiments/ENCSR196VDE/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 11.5 day mixed embryonic mouse craniofacial tissue
experiment encode accession: ENCSR196VDE
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB578XNO
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000,Illumina NextSeq 500

value: embryonic

value: pooled male and female

value: ENCBS024VHL at ENCODE; https://www.encodeproject.org/ENCBS024VHL/


title: ChIP-seq from forebrain (ENCLB962LEB)

description:
https://www.encodeproject.org/experiments/ENCSR462KTT/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me2 ChIP-seq on embryonic 16.5 day mouse forebrain
experiment encode accession: ENCSR462KTT
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR587JRQ
encode release date: 2014-12-17
lab: Bing Ren, UCSD
library encode accession: ENCLB962LEB
size range: 300-500

value: Forebrain pooled from embyonic 16.5 day mice

value: Len Pennacchio, LBNL

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


title: ChIP-seq from limb (ENCLB261XMP)

description:
https://www.encodeproject.org/experiments/ENCSR462BZP/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K9ac ChIP-seq on embryonic 13.5 day mouse limb
experiment encode accession: ENCSR462BZP
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR465WTL
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB261XMP
size range: 300-500

value: limb

value: Limb from embryonic 13.5 day mice

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

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


title: DNase-seq from hindbrain (ENCLB859MLN)

description:
https://www.encodeproject.org/experiments/ENCSR179PIH/
***************
biological replicate number: 2
technical replicate number: 1
description: DNase-seq on 14.5 day embryonic mouse hindbrain
experiment encode accession: ENCSR179PIH
assay title: DNase-seq
assembly: mm10
encode release date: 2015-09-14
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB859MLN
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Mus musculus strain B6NCrl hindbrain tissue mixed sex embryo (14.5 days)

value: hindbrain

value: tissue

value: healthy

value: John Stamatoyannopoulos, UW

value: ENCBS921IRD at ENCODE; https://www.encodeproject.org/ENCBS921IRD/


title: DNase-seq from lung (ENCLB087FMN)

description:
https://www.encodeproject.org/experiments/ENCSR094XAY/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR094XAY
assay title: DNase-seq
assembly: mm10
encode release date: 2016-05-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB087FMN
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

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

value: lung

value: 0 day

value: postnatal

value: not collected

value: ENCBS690CMB at ENCODE; https://www.encodeproject.org/ENCBS690CMB/


title: microRNA-seq from embryonic facial prominence (ENCLB247PJB)

description:
https://www.encodeproject.org/experiments/ENCSR461SRF/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq on embryonic 15.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR461SRF
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB247PJB
size range: <30

source_name: Mus musculus strain B6NCrl embryonic facial prominence tissue mixed sex embryo (15.5 days)

value: embryonic facial prominence

value: Embryonic facial prominence from 78 embryonic 15.5 day mice

value: embryonic

value: pooled male and female

value: ENCBS543BPM at ENCODE; https://www.encodeproject.org/ENCBS543BPM/


title: DNase-seq from heart (ENCLB845CHQ)

description:
https://www.encodeproject.org/experiments/ENCSR005WPU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR005WPU
assay title: DNase-seq
assembly: mm10
encode release date: 2016-05-11
lab: John Stamatoyannopoulos, UW
library encode accession: ENCLB845CHQ
instrument models: Illumina HiSeq 2500,Illumina NextSeq 500

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

value: heart

value: ENCBS337GRG at ENCODE; https://www.encodeproject.org/ENCBS337GRG/


title: microRNA-seq from embryonic facial prominence (ENCLB583TXK)

description:
https://www.encodeproject.org/experiments/ENCSR461SRF/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq on embryonic 15.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR461SRF
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-03-16
lab: Ali Mortazavi, UCI
library encode accession: ENCLB583TXK
size range: <30

value: Embryonic facial prominence from 62 embryonic 15.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS900XQR at ENCODE; https://www.encodeproject.org/ENCBS900XQR/

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


title: ChIP-seq from hindbrain (ENCLB302ROA)

description:
https://www.encodeproject.org/experiments/ENCSR458PAO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on postnatal 0 day mouse hindbrain
experiment encode accession: ENCSR458PAO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR066SPF
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB302ROA
size range: 300-500

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

value: hindbrain

value: tissue

value: Hindbrain from 15 postnatal 0 day mice

value: healthy

value: ENCBS040AAA at ENCODE; https://www.encodeproject.org/ENCBS040AAA/

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


title: ChIP-seq from embryonic facial prominence (ENCLB853QLZ)

description:
https://www.encodeproject.org/experiments/ENCSR981PSX/
***************
biological replicate number: 1
technical replicate number: 1,2
description: Control ChIP-seq on embryonic 15.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR981PSX
assay title: ChIP-seq
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB853QLZ
size range: 300-500
instrument models: Illumina HiSeq 2500,Illumina HiSeq 4000

value: Control

value: embryonic facial prominence


title: ChIP-seq from neural tube (ENCLB229KNK)

description:
https://www.encodeproject.org/experiments/ENCSR977DCO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 14.5 day mouse neural tube
experiment encode accession: ENCSR977DCO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR254WNU
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB229KNK
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 24 embryonic 14.5 day mice

value: embryonic

value: ENCBS013AAA at ENCODE; https://www.encodeproject.org/ENCBS013AAA/


title: ChIP-seq from stomach (ENCLB696ZOS)

description:
https://www.encodeproject.org/experiments/ENCSR976GSO/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K9me3 ChIP-seq on embryonic 14.5 day mouse stomach
experiment encode accession: ENCSR976GSO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR497YBQ
encode release date: 2016-03-16
lab: Bing Ren, UCSD
library encode accession: ENCLB696ZOS
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: pooled male and female

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


title: ChIP-seq from embryonic facial prominence (ENCLB312KDQ)

description:
https://www.encodeproject.org/experiments/ENCSR457HDY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27me3 ChIP-seq on embryonic 14.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR457HDY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR329ZEN
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB312KDQ
size range: 300-500

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

value: Craniofacial prominence from 24 embryonic 14.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS012AAA at ENCODE; https://www.encodeproject.org/ENCBS012AAA/


title: ChIP-seq from stomach (ENCLB084DDB)

description:
https://www.encodeproject.org/experiments/ENCSR976GSO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 ChIP-seq on embryonic 14.5 day mouse stomach
experiment encode accession: ENCSR976GSO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR497YBQ
encode release date: 2016-03-16
lab: Bing Ren, UCSD
library encode accession: ENCLB084DDB
size range: 300-500

value: tissue

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


title: ChIP-seq from forebrain (ENCLB702KPF)

description:
https://www.encodeproject.org/experiments/ENCSR975QSF/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K4me1 ChIP-seq on embryonic 11.5 day mouse forebrain
experiment encode accession: ENCSR975QSF
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR024JAN
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB702KPF
size range: 300-500

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

value: forebrain

value: Forebrain from 109 embyronic 11.5 day mice

value: healthy

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

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


title: microRNA-seq from liver (ENCLB718QBT)

description:
https://www.encodeproject.org/experiments/ENCSR456CZD/
***************
biological replicate number: 1
technical replicate number: 1
description: miRNA-seq  on postnatal 0 day mouse liver
experiment encode accession: ENCSR456CZD
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB718QBT
size range: <30

value: liver

value: 1 liver from pup1 pregnant 1

value: 0 day

value: postnatal

value: not collected

value: Barbara Wold, Caltech

value: ENCBS196YDO at ENCODE; https://www.encodeproject.org/ENCBS196YDO/


title: microRNA-seq from liver (ENCLB749OCP)

description:
https://www.encodeproject.org/experiments/ENCSR456CZD/
***************
biological replicate number: 2
technical replicate number: 1
description: miRNA-seq  on postnatal 0 day mouse liver
experiment encode accession: ENCSR456CZD
assay title: microRNA-seq
assembly: mm10
encode release date: 2016-02-18
lab: Ali Mortazavi, UCI
library encode accession: ENCLB749OCP
size range: <30

value: 1 liver from pup2 pregnant 1

value: ENCBS270QZU at ENCODE; https://www.encodeproject.org/ENCBS270QZU/


title: ChIP-seq from neural tube (ENCLB540UZO)

description:
https://www.encodeproject.org/experiments/ENCSR977DCO/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 14.5 day mouse neural tube
experiment encode accession: ENCSR977DCO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR254WNU
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB540UZO
size range: 300-500

value: neural tube

value: Neural tube from 34 embryonic 14.5 day mice

value: embryonic

value: pooled male and female

value: Len Pennacchio, LBNL

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

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


title: ChIP-seq from heart (ENCLB044RCD)

description:
https://www.encodeproject.org/experiments/ENCSR965JWF/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K9me3 ChIP-seq on postnatal 0 day mouse heart
experiment encode accession: ENCSR965JWF
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR334IOH
encode release date: 2016-02-17
lab: Bing Ren, UCSD
library encode accession: ENCLB044RCD
size range: 300-500

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

value: heart

value: tissue

value: Heart from 15 postnatal 0 day mice

value: healthy

value: ENCBS041AAA at ENCODE; https://www.encodeproject.org/ENCBS041AAA/


title: ChIP-seq from forebrain (ENCLB570IQR)

description:
https://www.encodeproject.org/experiments/ENCSR975QSF/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K4me1 ChIP-seq on embryonic 11.5 day mouse forebrain
experiment encode accession: ENCSR975QSF
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR024JAN
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB570IQR
size range: 300-500

value: forebrain

value: Forebrain from 88 embyronic 11.5 day mice

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

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


title: WGBS from stomach (ENCLB561VTJ)

description:
https://www.encodeproject.org/experiments/ENCSR953WFU/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 16.5 day mouse stomach
experiment encode accession: ENCSR953WFU
assay title: WGBS
assembly: mm10
encode release date: 2014-12-17
lab: Joe Ecker, Salk
library encode accession: ENCLB561VTJ
size range: 180-500

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

value: Stomach pooled from embyonic 16.5 day mice

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


title: WGBS from stomach (ENCLB306QZQ)

description:
https://www.encodeproject.org/experiments/ENCSR953WFU/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 16.5 day mouse stomach
experiment encode accession: ENCSR953WFU
assay title: WGBS
assembly: mm10
encode release date: 2014-12-17
lab: Joe Ecker, Salk
library encode accession: ENCLB306QZQ
size range: 180-500

value: Stomach from 41 embyonic 16.5 day mice

value: embryonic

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


title: ChIP-seq from embryonic facial prominence (ENCLB347NYY)

description:
https://www.encodeproject.org/experiments/ENCSR981PSX/
***************
biological replicate number: 2
technical replicate number: 1,2,4,3
description: Control ChIP-seq on embryonic 15.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR981PSX
assay title: ChIP-seq
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB347NYY
size range: 300-500
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000,Illumina HiSeq 4000

value: Control

value: embryonic facial prominence

value: Embryonic facial prominence from 62 embryonic 15.5 day mice

value: pooled male and female

value: Len Pennacchio, LBNL

value: ENCBS900XQR at ENCODE; https://www.encodeproject.org/ENCBS900XQR/


title: ChIP-seq from heart (ENCLB481BSS)

description:
https://www.encodeproject.org/experiments/ENCSR965JWF/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K9me3 ChIP-seq on postnatal 0 day mouse heart
experiment encode accession: ENCSR965JWF
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR334IOH
encode release date: 2016-02-17
lab: Bing Ren, UCSD
library encode accession: ENCLB481BSS
size range: 300-500

value: heart

value: tissue

value: Heart from pooled postnatal 0 day mice

value: 0 day

value: postnatal

value: healthy

value: ENCBS557AAA at ENCODE; https://www.encodeproject.org/ENCBS557AAA/

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


title: WGBS from stomach (ENCLB562VGY)

description:
https://www.encodeproject.org/experiments/ENCSR953WFU/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 16.5 day mouse stomach
experiment encode accession: ENCSR953WFU
assay title: WGBS
assembly: mm10
encode release date: 2014-12-17
lab: Joe Ecker, Salk
library encode accession: ENCLB562VGY
size range: 180-500

value: stomach

value: Stomach pooled from embyonic 16.5 day mice

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

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


title: ChIP-seq from heart (ENCLB575OEY)

description:
https://www.encodeproject.org/experiments/ENCSR963OLG/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K27me3 ChIP-seq on embryonic 11.5 day mouse heart
experiment encode accession: ENCSR963OLG
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR317ENO
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB575OEY
size range: 300-500

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

value: Heart from 109 embyronic 11.5 day mice

value: embryonic

value: ENCBS225RIF at ENCODE; https://www.encodeproject.org/ENCBS225RIF/


title: WGBS from midbrain (ENCLB187HBU)

description:
https://www.encodeproject.org/experiments/ENCSR952CMN/
***************
biological replicate number: 2
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 13.5 day mouse midbrain
experiment encode accession: ENCSR952CMN
assay title: WGBS
assembly: mm10
encode release date: 2015-08-18
lab: Joe Ecker, Salk
library encode accession: ENCLB187HBU
size range: 180-500

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

value: midbrain

value: Midbrain from embryonic 13.5 day mice

value: pooled male and female

value: Len Pennacchio, LBNL

value: ENCBS725LVX at ENCODE; https://www.encodeproject.org/ENCBS725LVX/


title: ChIP-seq from kidney (ENCLB076PRN)

description:
https://www.encodeproject.org/experiments/ENCSR455UTX/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K36me3 ChIP-seq on embryonic 15.5 day mouse kidney
experiment encode accession: ENCSR455UTX
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR780JSE
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB076PRN
size range: 300-500
instrument models: Illumina HiSeq 2000,Illumina HiSeq 2500

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

value: kidney

value: tissue

value: Kidney from 78 embryonic 15.5 day mice

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


title: WGBS from midbrain (ENCLB992EWU)

description:
https://www.encodeproject.org/experiments/ENCSR952CMN/
***************
biological replicate number: 1
technical replicate number: 1
description: Whole genome bisulfite-seq on embryonic 13.5 day mouse midbrain
experiment encode accession: ENCSR952CMN
assay title: WGBS
assembly: mm10
encode release date: 2015-08-18
lab: Joe Ecker, Salk
library encode accession: ENCLB992EWU
size range: 180-500

value: healthy

value: ENCBS185VNZ at ENCODE; https://www.encodeproject.org/ENCBS185VNZ/


title: WGBS from midbrain (ENCLB056QQU)

description:
https://www.encodeproject.org/experiments/ENCSR952CMN/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 13.5 day mouse midbrain
experiment encode accession: ENCSR952CMN
assay title: WGBS
assembly: mm10
encode release date: 2015-08-18
lab: Joe Ecker, Salk
library encode accession: ENCLB056QQU
size range: 180-500


title: WGBS from stomach (ENCLB387WVK)

description:
https://www.encodeproject.org/experiments/ENCSR953WFU/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 16.5 day mouse stomach
experiment encode accession: ENCSR953WFU
assay title: WGBS
assembly: mm10
encode release date: 2014-12-17
lab: Joe Ecker, Salk
library encode accession: ENCLB387WVK
size range: 180-500

value: stomach

value: Stomach from 41 embyonic 16.5 day mice

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


title: WGBS from embryonic facial prominence (ENCLB442RHA)

description:
https://www.encodeproject.org/experiments/ENCSR950OMB/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 11.5 day mouse facial prominence
experiment encode accession: ENCSR950OMB
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB442RHA
size range: 180-500

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: WGBS from embryonic facial prominence (ENCLB721LQB)

description:
https://www.encodeproject.org/experiments/ENCSR950OMB/
***************
biological replicate number: 2
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 11.5 day mouse facial prominence
experiment encode accession: ENCSR950OMB
assay title: WGBS
assembly: mm10
encode release date: 2014-06-30
lab: Joe Ecker, Salk
library encode accession: ENCLB721LQB
size range: 180-500

value: Craniofacial prominence from 88 embyronic 11.5 day mice

value: embryonic

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


title: ChIP-seq from lung (ENCLB127BCB)

description:
https://www.encodeproject.org/experiments/ENCSR452WYC/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 14.5 day mouse lung
experiment encode accession: ENCSR452WYC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR280SYC
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB127BCB
size range: 300-500

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

value: lung

value: Lung from 24 embryonic 14.5 day mice

value: pooled male and female

value: Len Pennacchio, LBNL

value: ENCBS006AAA at ENCODE; https://www.encodeproject.org/ENCBS006AAA/

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


title: ChIP-seq from midbrain (ENCLB336UWH)

description:
https://www.encodeproject.org/experiments/ENCSR951UWY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 ChIP-seq on postnatal 0 day mouse midbrain
experiment encode accession: ENCSR951UWY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR889XXJ
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB336UWH
size range: 300-500

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

value: midbrain

value: tissue

value: Midbrain from 15 postnatal 0 day mice

value: 0 day

value: postnatal

value: healthy

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


title: ChIP-seq from midbrain (ENCLB383MSN)

description:
https://www.encodeproject.org/experiments/ENCSR449EUZ/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 15.5 day mouse midbrain
experiment encode accession: ENCSR449EUZ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR748XBE
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB383MSN
size range: 300-500

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

value: Midbrain from 62 embryonic 15.5 day mice

value: ENCBS381PEJ at ENCODE; https://www.encodeproject.org/ENCBS381PEJ/

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


title: ChIP-seq from midbrain (ENCLB581XKD)

description:
https://www.encodeproject.org/experiments/ENCSR449EUZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 ChIP-seq on embryonic 15.5 day mouse midbrain
experiment encode accession: ENCSR449EUZ
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR748XBE
encode release date: 2015-11-03
lab: Bing Ren, UCSD
library encode accession: ENCLB581XKD
size range: 300-500

value: Midbrain from 78 embryonic 15.5 day mice

value: embryonic

value: ENCBS190ETJ at ENCODE; https://www.encodeproject.org/ENCBS190ETJ/


title: ChIP-seq from embryonic facial prominence (ENCLB747CKB)

description:
https://www.encodeproject.org/experiments/ENCSR457HDY/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27me3 ChIP-seq on embryonic 14.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR457HDY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR329ZEN
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB747CKB
size range: 300-500

value: embryonic facial prominence

value: Craniofacial prominence from 34 embryonic 14.5 day mice

value: pooled male and female

value: ENCBS024AAA at ENCODE; https://www.encodeproject.org/ENCBS024AAA/


title: ChIP-seq from hindbrain (ENCLB164FJX)

description:
https://www.encodeproject.org/experiments/ENCSR972MUO/
***************
biological replicate number: 1
technical replicate number: 1,2
description: H3K36me3 ChIP-seq on embryonic 13.5 day mouse hindbrain
experiment encode accession: ENCSR972MUO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR545RUT
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB164FJX
size range: 300-500
instrument models: Illumina HiSeq 2500,Illumina HiSeq 2000

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

value: hindbrain

value: Hindbrain from embryonic 13.5 day mice

value: Len Pennacchio, LBNL

value: ENCBS052EWC at ENCODE; https://www.encodeproject.org/ENCBS052EWC/


title: ChIP-seq from heart (ENCLB075GGK)

description:
https://www.encodeproject.org/experiments/ENCSR963OLG/
***************
biological replicate number: 2
technical replicate number: 1,2
description: H3K27me3 ChIP-seq on embryonic 11.5 day mouse heart
experiment encode accession: ENCSR963OLG
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR317ENO
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB075GGK
size range: 300-500

value: heart

value: tissue

value: Heart from embryonic 11.5 day mice

value: ENCBS046IMM at ENCODE; https://www.encodeproject.org/ENCBS046IMM/


title: ChIP-seq from embryonic facial prominence (ENCLB100XEW)

description:
https://www.encodeproject.org/experiments/ENCSR447BVY/
***************
biological replicate number: 1
technical replicate number: 2,1
description: H3K36me3 ChIP-seq on embryonic 13.5 day mouse embryonic facial prominence
experiment encode accession: ENCSR447BVY
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR742ZUI
encode release date: 2015-06-23
lab: Bing Ren, UCSD
library encode accession: ENCLB100XEW
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 from embryonic 13.5 day mice

value: healthy

value: ENCBS764ZZN at ENCODE; https://www.encodeproject.org/ENCBS764ZZN/


title: ChIP-seq from lung (ENCLB299WEX)

description:
https://www.encodeproject.org/experiments/ENCSR452WYC/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K27ac ChIP-seq on embryonic 14.5 day mouse lung
experiment encode accession: ENCSR452WYC
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR280SYC
encode release date: 2014-06-30
lab: Bing Ren, UCSD
library encode accession: ENCLB299WEX
size range: 300-500

value: lung

value: Lung from 34 embryonic 14.5 day mice

value: embryonic

value: ENCBS018AAA at ENCODE; https://www.encodeproject.org/ENCBS018AAA/

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


title: WGBS from midbrain (ENCLB780ARR)

description:
https://www.encodeproject.org/experiments/ENCSR952CMN/
***************
biological replicate number: 1
technical replicate number: 2
description: Whole genome bisulfite-seq on embryonic 13.5 day mouse midbrain
experiment encode accession: ENCSR952CMN
assay title: WGBS
assembly: mm10
encode release date: 2015-08-18
lab: Joe Ecker, Salk
library encode accession: ENCLB780ARR
size range: 180-500

value: midbrain

value: Midbrain from embryonic 13.5 day mice

value: pooled male and female

value: ENCBS185VNZ at ENCODE; https://www.encodeproject.org/ENCBS185VNZ/

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