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Sample GSM1660041 Query DataSets for GSM1660041
Status Public on Jan 13, 2016
Title H3K27ac Human Brain Putamen HS2
Sample type SRA
Source name Human female putamen tissue
Organism Homo sapiens
Characteristics tissue: Putamen
gender: Female
age: 90
Cause of death: Sepsis
postmortem delay: 15.3 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 AB 5500xl Genetic Analyzer
Description GSM1119207
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
Organization name Hubrecht Institute
Lab Creyghton
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
Platform ID GPL16288
Series (1)
GSE67978 Epigenomic annotation of gene regulatory alterations during evolution of the primate brain
Reanalysis of GSM1119207
BioSample SAMN03487940
SRA SRX998290

Supplementary file Size Download File type/resource 160.0 Mb (ftp)(http) BW
GSM1660041_H3K27ac_Human_Brain_Putamen_HS2_hg38_peaks.narrowPeak.gz 991.4 Kb (ftp)(http) NARROWPEAK
GSM1660041_H3K27ac_Human_Brain_Putamen_HS2_hg38_peaks.txt.gz 1.1 Mb (ftp)(http) TXT
GSM1660041_H3K27ac_Human_Brain_Putamen_HS2_hg38_treat_pileup.bedgraph.gz 189.9 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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