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| Status |
Public on Dec 20, 2019 |
| Title |
Human_PrefrontalCortex_NeuNpositive_ATAC_2 |
| Sample type |
SRA |
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| Source name |
Human Prefrontal Cortex
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Human 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 |
GPL18573 |
| Series (1) |
| GSE130871 |
Hominin-specific regulatory elements selectively emerged in oligodendrocytes and are disrupted in autism patients |
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| Relations |
| BioSample |
SAMN12818060 |
| SRA |
SRX6887598 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4089135_Human_PrefrontalCortex_NeuNpositive_ATAC_2.bw |
184.7 Mb |
(ftp)(http) |
BW |
| GSM4089135_Human_PrefrontalCortex_NeuNpositive_ATAC_2_peaks.narrowPeak.gz |
365.2 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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