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Sample GSM1660051 Query DataSets for GSM1660051
Status Public on Jan 13, 2016
Title H3K27ac Human Brain PrefrontalCortex HS3
Sample type SRA
 
Source name Human female prefrontal cortex tissue
Organism Homo sapiens
Characteristics tissue: Gyrus rectus
gender: Female
age: 59
Cause of death: Uremic coma, brain tumor
postmortem delay: 7.0 hrs
experiment type: ChIP-Seq
chip antibody: H3K27ac (Abcam, ab4729)
Treatment protocol NA
Growth protocol NA
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 Apr 16, 2015
Last update date May 15, 2019
Contact name Menno P Creyghton
E-mail(s) m.creyghton@hubrecht.eu
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
Relations
BioSample SAMN03487950
SRA SRX998300

Supplementary file Size Download File type/resource
GSM1660051_H3K27ac_Human_Brain_PrefrontalCortex_HS3_hg38.bw 216.6 Mb (ftp)(http) BW
GSM1660051_H3K27ac_Human_Brain_PrefrontalCortex_HS3_hg38_peaks.narrowPeak.gz 1.5 Mb (ftp)(http) NARROWPEAK
GSM1660051_H3K27ac_Human_Brain_PrefrontalCortex_HS3_hg38_peaks.txt.gz 1.6 Mb (ftp)(http) TXT
GSM1660051_H3K27ac_Human_Brain_PrefrontalCortex_HS3_hg38_treat_pileup.bedGraph.gz 263.9 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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