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| Status |
Public on Jan 24, 2022 |
| Title |
005 Coronary artery bulk ATAC |
| Sample type |
SRA |
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| Source name |
Coronary artery
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Coronary artery (LAD)
age: 57
Sex: female
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| Treatment protocol |
Human hearts were obtained from heart transplant recipients or rejected donor hearts. Hearts were all placed in cardioplegic solution prior to dissection of the left anterior descending (LAD), left circumflex (LCX), and right coronary arteries (RCA). All coronary artery samples were flash frozen in liquid nitrogen in the same manner
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen coronary artery segments were broken down into small pieces using mortar and pestle under dry ice and liquid nitrogen. Nuclei were isolated using iodixanol/sucrose gradients following the Omni-ATAC protocol (Corces et al. Nature Methods 2017). 50,000 nuclei were washed in cold ATAC Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) + 0.1% Tween-20 and centrifuged for 10 minutes at 500 g at 4°C. 50,000 nuclei were then resuspended in 50 µl of transposition mix (25 µl 2X TD buffer, 2.5 µl of Tn5 transposase (Illumina), 16.5 µl PBS, 0.01% digitonon, 0.1% Tween-20). Samples were subsequently transposed for 30 minutes at 37°C with shaking (1000 rpm).
Transposed DNA was first purified using the Zymo DNA Clean and Concentrator-5 Kit. Libraries were subsequently constructed and amplified according to Supplementary Protocol 1 in the Omni-ATAC protocol (Corces et al. Nature Methods 2017). Each library underwent 5 cycles of pre-amplification and then additional amplification cycles (determined by qPCR of pre-amplified mixtures)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
005_ATACseq_50k
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| Data processing |
Bulk ATAC-seq sample processing was all conducted using the PEPATAC pipeline (version 0.8.6). This includes alignment, duplicate removal, mitochondrial read removal, and peak-calling
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak (peaks from each individual sample)
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| Submission date |
Nov 08, 2021 |
| Last update date |
Jan 25, 2022 |
| Contact name |
Clint L Miller |
| Organization name |
University of Virginia
|
| Department |
Center for Public Health Genomics
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| Street address |
PO Box 800717
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| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22908 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE188422 |
Chromatin accessibility profiling of human coronary arteries identifes disease regulatory variants |
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| Relations |
| BioSample |
SAMN22985811 |
| SRA |
SRX13058930 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5681679_UVA005_CA_ATAC_peaks_rmBlacklist.narrowPeak.gz |
613.2 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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