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Sample GSM4089143 Query DataSets for GSM4089143
Status Public on Dec 20, 2019
Title Macaque_PrefrontalCortex_NeuNpositive_ATAC_3
Sample type SRA
 
Source name Macaque Prefrontal Cortex
Organism Macaca mulatta
Characteristics tissue: Macaque Prefrontal Cortex
Extracted molecule genomic DNA
Extraction protocol NEBNext High-Fidelity PCR (NEB)
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing ChIP-seq: Illumina sequencing reads were aligned using bowtie version 1.1.2 ((http://bowtie-bio.sourceforge.net) excluding reads with more than 1 mismatch (seed length of 36 base pairs (bp)) or with multiple alignment. Duplicate reads were discarded using Samtools version 1.3.1. Peak-calling was done using MACS2 version 2.1.1.20160309 (pvalue < 10-5, extsize 300, local lambda 100,000). Reads in peaks were counted using Bedtools version 2.26.
ATAC-seq: Illumina sequencing reads were trimmed to remove Nextera adapters using cutadapt (1.13). Reads were mapped using bowtie version 1.1.2 (http://bowtie-bio.sourceforge.net) excluding reads with more than 1 mismatch (seed length 36 base pairs) or with multiple aligment. Duplicate reads were discarded using Samtools verions 1.3.1. Peak-calling was done using MACS2 version 2.1.1.20160309 (pvalue < 10-5, extsize 300, local lambda 100,000). Reads in peaks were counted using Bedtools version 2.26
Genome_build: Homo sapiens: hg38, Pan troglodytes: panTro5, Macaca mulatta: rheMac8, Callithrix jacchus: calJac3
Supplementary_files_format_and_content: ChIP-seq and ATAC-seq peaks called by MACS2 are in _peaks.narrowPeak; H3K27ac and ATAC bigwig files are in .bw
 
Submission date Sep 23, 2019
Last update date Dec 20, 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 GPL21120
Series (1)
GSE130871 Hominin-specific regulatory elements selectively emerged in oligodendrocytes and are disrupted in autism patients
Relations
BioSample SAMN12818055
SRA SRX6887606

Supplementary file Size Download File type/resource
GSM4089143_Macaque_PrefrontalCortex_NeuNpositive_ATAC_3.bw 171.1 Mb (ftp)(http) BW
GSM4089143_Macaque_PrefrontalCortex_NeuNpositive_ATAC_3_peaks.narrowPeak.gz 2.4 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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