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Sample GSM1660062 Query DataSets for GSM1660062
Status Public on Jan 13, 2016
Title H3K27ac Mouse Brain Cerebellum MM1
Sample type SRA
 
Source name Mouse female cerebellum tissue
Organism Mus musculus
Characteristics tissue: Cerebellum
gender: Female
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
 
Description GSM1119262
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 GPL13112
Series (1)
GSE67978 Epigenomic annotation of gene regulatory alterations during evolution of the primate brain
Relations
Reanalysis of GSM1119262
BioSample SAMN03487961
SRA SRX998311

Supplementary file Size Download File type/resource
GSM1660062_H3K27ac_Mouse_Brain_Cerebellum_MM1_mm10.bw 182.2 Mb (ftp)(http) BW
GSM1660062_H3K27ac_Mouse_Brain_Cerebellum_MM1_mm10_peaks.narrowPeak.gz 1018.0 Kb (ftp)(http) NARROWPEAK
GSM1660062_H3K27ac_Mouse_Brain_Cerebellum_MM1_peaks.txt.gz 1.1 Mb (ftp)(http) TXT
GSM1660062_H3K27ac_Mouse_Brain_Cerebellum_MM1_treat_pileup.bedgraph.gz 215.6 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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