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Sample GSM1937190

Query DataSets for GSM1937190

Status

Public on Jan 13, 2016

Title

Input Chimpanzee Brain CaudateNucleus PT3

Sample type

SRA

Source name

Chimpanzee female prefrontal cortex tissue

Organism

Pan troglodytes

Characteristics

tissue: Prefrontal cortex
gender: Female
age: 45
Cause of death: Cardiomyopathy, endocardiosis
postmortem delay: 8-12 hrs
experiment type: Input
chip antibody: none

Treatment protocol

Growth protocol

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

Nov 11, 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