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Sample GSM1821392 Query DataSets for GSM1821392
Status Public on Jan 13, 2016
Title H3K4me3 Human Brain WhiteMatter HS1 Rep2
Sample type SRA
Source name Human female white matter tissue
Organism Homo sapiens
Characteristics tissue: White matter
gender: Female
age: 68
Cause of death: Myocardial decompensation with sepsis
postmortem delay: 4.2 hrs
experiment type: ChIP-Seq
chip antibody: H3K4me3 (Millipore 07-473)
Extracted molecule genomic DNA
Extraction protocol Crosslink, Lyse and Immunoprecipitate
Illumina Truseq DNA library protocol
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing Mapping Illumina: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S --phred64-quals -q -l 40/45 -n 1
Mapping SOLiD: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S -l 50 -n 3 -C -Q -f
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g hs --nomodel --extsize 400 --llocal 100000
genome build: hg38, rheMac3, panTro4, mm10
processed data files format and content: txt files contain called peaks
processed data files format and content: narrowPeak files contain called peaks in BED format
processed data files format and content: bedGraph files contain treat pileup
processed data files format and content: bw files contain treat pileup read per million (RPM) normalized in bigWig format
Submission date Jul 14, 2015
Last update date May 15, 2019
Contact name Menno P Creyghton
Organization name Hubrecht Institute
Lab Creyghton
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
Platform ID GPL11154
Series (1)
GSE67978 Epigenomic annotation of gene regulatory alterations during evolution of the primate brain
BioSample SAMN03857997
SRA SRX1096828

Supplementary file Size Download File type/resource 116.7 Mb (ftp)(http) BW
GSM1821392_H3K4me3_Human_Brain_WhiteMatter_HS1_hg38_Rep2_peaks.narrowPeak.gz 776.3 Kb (ftp)(http) NARROWPEAK
GSM1821392_H3K4me3_Human_Brain_WhiteMatter_HS1_hg38_Rep2_peaks.txt.gz 867.6 Kb (ftp)(http) TXT
GSM1821392_H3K4me3_Human_Brain_WhiteMatter_HS1_hg38_Rep2_treat_pileup.bedGraph.gz 131.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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