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Status |
Public on Dec 20, 2019 |
Title |
Chimpanzee_PrefrontalCortex_NeuNnegative_ATAC_5 |
Sample type |
SRA |
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Source name |
Chimpanzee Prefrontal Cortex
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Organism |
Pan troglodytes |
Characteristics |
tissue: Chimpanzee Prefrontal Cortex
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Extracted molecule |
genomic DNA |
Extraction protocol |
NEBNext High-Fidelity PCR (NEB)
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
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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
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Submission date |
Sep 23, 2019 |
Last update date |
Dec 20, 2019 |
Contact name |
Menno P Creyghton |
E-mail(s) |
m.creyghton@hubrecht.eu
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Organization name |
Hubrecht Institute
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Lab |
Creyghton
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Street address |
Uppsalalaan 8
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City |
Utrecht |
ZIP/Postal code |
3584 CT |
Country |
Netherlands |
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Platform ID |
GPL21121 |
Series (1) |
GSE130871 |
Hominin-specific regulatory elements selectively emerged in oligodendrocytes and are disrupted in autism patients |
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Relations |
BioSample |
SAMN12818054 |
SRA |
SRX6887601 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4089138_Chimpanzee_PrefrontalCortex_NeuNnegative_ATAC_5.bw |
197.2 Mb |
(ftp)(http) |
BW |
GSM4089138_Chimpanzee_PrefrontalCortex_NeuNnegative_ATAC_5_peaks.narrowPeak.gz |
925.8 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |
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