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Sample GSM2191931 Query DataSets for GSM2191931
Status Public on Jun 22, 2016
Title ChIP-seq from midbrain (ENCLB607GZL)
Sample type SRA
 
Source name Mus musculus strain B6NCrl midbrain tissue mixed sex embryo (12.5 days)
Organism Mus musculus
Characteristics antibody: H3K4me3
tissue_type: midbrain
biomaterial_type: tissue
description: Midbrain from 120 embryonic 12.5 day mice
biosample encode accession: ENCBS309WCU (SAMN05202069)
age: 12.5 day
donor_id: ENCDO956IXV
dev stage: embryonic
Sex: pooled male and female
health state: healthy
lab: Len Pennacchio, LBNL
link: ENCBS309WCU at ENCODE; https://www.encodeproject.org/ENCBS309WCU/
link: Derived from ENCODE donor ENCDO956IXV; https://www.encodeproject.org/ENCDO956IXV/
link: excision protocol; https://www.encodeproject.org/documents/631aa21c-8e48-467e-8cac-d40c875b3913/@@download/attachment/StandardTissueExcisionProtocol_02132017.pdf
Extracted molecule genomic DNA
Extraction protocol general protocol: https://www.encodeproject.org/documents/89795b31-e65a-42ca-9d7b-d75196f6f4b3/@@download/attachment/Ren%20Lab%20ENCODE%20Chromatin%20Immunoprecipitation%20Protocol_V2.pdf
general protocol: https://www.encodeproject.org/documents/4f73fbc3-956e-47ae-aa2d-41a7df552c81/@@download/attachment/Ren_ChIP_Library_Preparation_v060614.pdf
general protocol: https://www.encodeproject.org/documents/3125496b-c833-4414-bf5f-84dd633eb30d/@@download/attachment/Ren_Tissue_Fixation_and_Sonication_v060614.pdf
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Description https://www.encodeproject.org/experiments/ENCSR554TSO/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 ChIP-seq on embryonic 12.5 day mouse midbrain
experiment encode accession: ENCSR554TSO
assay title: ChIP-seq
assembly: mm10
possible controls: ENCSR415FCU
encode release date: 2016-03-30
lab: Bing Ren, UCSD
library encode accession: ENCLB607GZL
size range: 300-500
Data processing See GSM*_README.txt supplementary file linked below
 
Submission date Jun 07, 2016
Last update date May 15, 2019
Contact name ENCODE DCC
E-mail(s) encode-help@lists.stanford.edu
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
 
Platform ID GPL21103
Series (1)
GSE82784 ChIP-seq from midbrain (ENCSR554TSO)
Relations
BioSample SAMN05202069
SRA SRX1833737
Named Annotation GSM2191931_ENCFF658ICC_signal_p-value_mm10.bigWig
Named Annotation GSM2191931_ENCFF946YBS_peaks_mm10.bed.gz
Named Annotation GSM2191931_ENCFF466MOK_fold_change_over_control_mm10.bigWig

Supplementary file Size Download File type/resource
GSM2191931_ENCFF220HPC_peaks_mm10.bigBed 1.7 Mb (ftp)(http) BIGBED
GSM2191931_ENCFF466MOK_fold_change_over_control_mm10.bigWig 655.3 Mb (ftp)(http) BIGWIG
GSM2191931_ENCFF658ICC_signal_p-value_mm10.bigWig 587.1 Mb (ftp)(http) BIGWIG
GSM2191931_ENCFF946YBS_peaks_mm10.bed.gz 548.3 Kb (ftp)(http) BED
GSM2191931_ENCLB607GZL_README.txt.gz 1.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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