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| Status |
Public on Mar 07, 2022 |
| Title |
macaque2_dorsalS1_rep1_atac |
| Sample type |
SRA |
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| Source name |
adult male macaque primary somatosensory cortex, dorsal portion (dorsalS1)
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| Organism |
Macaca mulatta |
| Characteristics |
tissue: primary somatosensory cortex, dorsal portion (dorsalS1)
cell type: bulk tissue
Sex: M
age: 4 years
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| Treatment protocol |
Mice processed for liver samples were injected intravenously with an fluorescent AAV related to tissues for a different study. The procedure was minimally invasive and did not affect the health of the animals. No other animals processed in this study received any treatments.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were extracted from fresh tissue with Dounce homogenization in lysis buffer. The nuclei were pelleted by centrifugation and filtered through 70µm and 40µm strainers.
ATAC-seq libraries were constructed with standard amplification and size selection methods. See publication for more details.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
transposase-accessible DNA
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| Data processing |
ATAC-seq alignment: Macaque, rat, and mouse reads were mapped to the Mmul_8.0.1, rn6, and mm10s genomes, respectively, with Bowtie2 using the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) with default parameters except for "atac.multimapping" : 0 (read filtering), "atac.cap_num_peak" : 300000 (peak calling), "atac.smooth_win" : 150 (peak calling), "atac.enable_idr" : true (peak calling), and "atac.idr_thresh" : 0.1 (peak calling).
ATAC-seq filtering: Duplicate reads, mitochondrial reads, and multi-mapping reads were filtered out as a part of the ENCODE ATAC-seq pipeline. The pipeline also created signal tracks using MACS2.
ATAC-seq peak calling: Within the ENCODE ATAC-seq pipeline workflow, peaks were called on each sample individually, on the pool of biological replicates, on pooled pseudo-replicates, and on self pseudo-replicates using MACS2 and reproducible peaks were determined on biological replicates with an IDR threshold of 0.1.
Other: More information on all data processing and conclusions can be found in the publication.
Genome_build: Mmul_8.0.1, rn6, mm10
Supplementary_files_format_and_content: ATAC-seq peaks called in each sample
Supplementary_files_format_and_content: MACS2 pval signal tracks for each sample in bigwig format
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| Submission date |
Oct 29, 2020 |
| Last update date |
Mar 10, 2022 |
| Contact name |
Morgan Wirthlin |
| E-mail(s) |
mwirthlin@cmu.edu
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| Organization name |
Carnegie Mellon University
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| Department |
Computational Biology
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| Lab |
Andreas Pfenning
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| Street address |
4400 Fifth Ave
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| City |
Pittsburgh |
| State/province |
Pennsylvania |
| ZIP/Postal code |
15213 |
| Country |
USA |
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| Platform ID |
GPL27943 |
| Series (1) |
| GSE159815 |
The Regulatory Evolution of the Primate Fine-Motor System |
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| Relations |
| BioSample |
SAMN16591605 |
| SRA |
SRX9397458 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4872675_M2-S1_R1_001.trim.nodup.no_chrM.tn5.pval.signal.bigwig |
639.9 Mb |
(ftp)(http) |
BIGWIG |
| GSM4872675_M2-S1_R1_001.trim.nodup.no_chrM.tn5.pval0.01.300K.bfilt.narrowPeak.gz |
4.3 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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