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Sample GSM1974555 Query DataSets for GSM1974555
Status Public on Jan 13, 2016
Title Input Human Brain CaudateNucleus HS1
Sample type SRA
 
Source name Human female caudate nucleus tissue
Organism Homo sapiens
Characteristics tissue: Caudate nucleus
gender: Female
age: 68
Cause of death: Myocardial decompensation with sepsis
postmortem delay: 4.2 hrs
experiment type: Input
chip antibody: none
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 NextSeq 500
 
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 Dec 17, 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 GPL18573
Series (1)
GSE67978 Epigenomic annotation of gene regulatory alterations during evolution of the primate brain
Relations
BioSample SAMN04349533
SRA SRX1490480

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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