NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1821408 Query DataSets for GSM1821408
Status Public on Jan 13, 2016
Title H3K27ac Chimpanzee Brain Putamen PT1
Sample type SRA
 
Source name Chimpanzee female putamen tissue
Organism Pan troglodytes
Characteristics tissue: Putamen
gender: Female
age: 47
Cause of death: Cardiomyopathy, nephritis
postmortem delay: 12 hrs
experiment type: ChIP-Seq
chip antibody: H3K27ac (Abcam, ab4729)
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 Jul 14, 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 GPL16809
Series (1)
GSE67978 Epigenomic annotation of gene regulatory alterations during evolution of the primate brain
Relations
BioSample SAMN03858013
SRA SRX1096844

Supplementary file Size Download File type/resource
GSM1821408_H3K27ac_Chimpanzee_Brain_Putamen_PT1_panTro4.bw 102.8 Mb (ftp)(http) BW
GSM1821408_H3K27ac_Chimpanzee_Brain_Putamen_PT1_panTro4_peaks.narrowPeak.gz 863.4 Kb (ftp)(http) NARROWPEAK
GSM1821408_H3K27ac_Chimpanzee_Brain_Putamen_PT1_panTro4_peaks.txt.gz 966.5 Kb (ftp)(http) TXT
GSM1821408_H3K27ac_Chimpanzee_Brain_Putamen_PT1_panTro4_treat_pileup.bedGraph.gz 117.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap