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Sample GSM1660018 Query DataSets for GSM1660018
Status Public on Jan 13, 2016
Title H3K27ac Rhesus Brain Putamen RM3
Sample type SRA
 
Source name Rhesus macaque female putamen tissue
Organism Macaca mulatta
Characteristics tissue: Putamen
gender: Female
age: 10
Cause of death: Euthanasia
postmortem delay: 12 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 GPL14954
Series (1)
GSE67978 Epigenomic annotation of gene regulatory alterations during evolution of the primate brain
Relations
BioSample SAMN03487976
SRA SRX998267

Supplementary file Size Download File type/resource
GSM1660018_H3K27ac_Rhesus_Brain_Putamen_RM3_rheMac3.bw 277.8 Mb (ftp)(http) BW
GSM1660018_H3K27ac_Rhesus_Brain_Putamen_RM3_rheMac3_peaks.narrowPeak.gz 1.5 Mb (ftp)(http) NARROWPEAK
GSM1660018_H3K27ac_Rhesus_Brain_Putamen_RM3_rheMac3_peaks.txt.gz 1.7 Mb (ftp)(http) TXT
GSM1660018_H3K27ac_Rhesus_Brain_Putamen_RM3_rheMac3_treat_pileup.bedgraph.gz 329.9 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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