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Sample GSM1660053 Query DataSets for GSM1660053
Status Public on Jan 13, 2016
Title H3K4me3 Rhesus Brain WhiteMatter RM1
Sample type SRA
 
Source name Rhesus macaque female white matter tissue
Organism Macaca mulatta
Characteristics tissue: White matter
gender: Female
age: 5
Cause of death: Euthanasia
postmortem delay: 0.5 hrs
experiment type: ChIP-Seq
chip antibody: H3K4me3 (Millipore 07-473)
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 SAMN03487952
SRA SRX998302

Supplementary file Size Download File type/resource
GSM1660053_H3K4me3_Rhesus_Brain_WhiteMatter_RM1_rheMac3.bw 127.8 Mb (ftp)(http) BW
GSM1660053_H3K4me3_Rhesus_Brain_WhiteMatter_RM1_rheMac3_peaks.narrowPeak.gz 839.0 Kb (ftp)(http) NARROWPEAK
GSM1660053_H3K4me3_Rhesus_Brain_WhiteMatter_RM1_rheMac3_peaks.txt.gz 940.0 Kb (ftp)(http) TXT
GSM1660053_H3K4me3_Rhesus_Brain_WhiteMatter_RM1_rheMac3_treat_pileup.bedgraph.gz 149.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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