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Sample GSM1660016 Query DataSets for GSM1660016
Status Public on Jan 13, 2016
Title H3K27ac Rhesus Brain Putamen RM1
Sample type SRA
Source name Rhesus macaque female putamen tissue
Organism Macaca mulatta
Characteristics tissue: Putamen
gender: Female
age: 5
Cause of death: Euthanasia
postmortem delay: 0.5 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
Organization name Hubrecht Institute
Lab Creyghton
Street address Uppsalalaan 8
City Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
Platform ID GPL14954
Series (1)
GSE67978 Epigenomic annotation of gene regulatory alterations during evolution of the primate brain
BioSample SAMN03487974
SRA SRX998265

Supplementary file Size Download File type/resource 121.7 Mb (ftp)(http) BW
GSM1660016_H3K27ac_Rhesus_Brain_Putamen_RM1_rheMac3_peaks.narrowPeak.gz 974.7 Kb (ftp)(http) NARROWPEAK
GSM1660016_H3K27ac_Rhesus_Brain_Putamen_RM1_rheMac3_peaks.txt.gz 1.1 Mb (ftp)(http) TXT
GSM1660016_H3K27ac_Rhesus_Brain_Putamen_RM1_rheMac3_treat_pileup.bedgraph.gz 140.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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