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| Status |
Public on Jun 23, 2021 |
| Title |
HSM1.bulk.rep1.hg19: Human bulk ATAC, sample HSM1 rep 1 |
| Sample type |
SRA |
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| Source name |
Skeletal muscle
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Skeletal muscle
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
2 tissue pieces weighing 99.4 mg and 80.7 mg were cut from one human skeletal muscle sample (HSM1) and 2 pieces weighing 67.6 mg and 103.5 mg were cut from a second human skeletal muscle sample (HSM2). Each of the samples was cut on dry ice using frozen scalpel to prevent thawing. The samples were pulverized using a CP02 cryoPREP automated dry pulverizer (Covaris 500001). For bulk ATAC-seq we followed the nuclei isolation protocol outlined in https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S2.pdf, except in the final step the nuclei were resuspended in 250 μL of 1% BSA in PBS.
The nuclei were counted in Countess II FL Automated Cell Counter, and the appropriate volume of the suspension for 50K nuclei was spun down and used for the downstream transposition reaction (a modified version of the ENCODE protocol; https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S3.pdf) (The ENCODE Project Consortium 2012, 2012)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
***Raw data are unavailable due to patient privacy concerns***
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| Data processing |
Adapters were trimmed using cta (v. 0.1.2; https://github.com/ParkerLab/cta)
For single-nucleus experiments, we used a custom python script (available in https://github.com/porchard/snATACseq-NextFlow) for 10x Genomics barcode correction
Reads were mapped using BWA-MEM (-I 200,200,5000 -M; v. 0.7.15-r1140). If the sample contained only human nuclei, we used the hg19 reference genome. If the sample contained human and rat nuclei, we mapped the library twice, once to hg19 and once to rn6
For single-nucleus experiments, we filtered out nuclei corresponding to 10x barcodes with fewer than 1000 alignments in the BAM file
We used Picard MarkDuplicates to mark duplicates, and filtered to high-quality, non-duplicate autosomal read pairs using SAMtools view with flags ‘-f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048 -q 30’
We anonymized the BAM files using anonymizeBAM (--strict; v. 0.4.5)
We generated single-end BED files using bedtools bamtobed
We called peaks and generated bedGraph files using macs2 callpeak -f BED --SPMR --nomodel --shift -100 --extsize 200 -B --broad --keep-dup all
We generated the bigWig file from the bedGraph file using bedGraphToBigWig from the UCSC genome browser
Genome_build: hg19 (human) and rn6 (when rat nuclei were included in the library)
Supplementary_files_format_and_content: ATAC-seq read mapping locations, anonymized (BED files)
Supplementary_files_format_and_content: ATAC-seq signal tracks (bigWig files)
Supplementary_files_format_and_content: ATAC-seq peak calls (broadPeak files)
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| Submission date |
Jun 23, 2021 |
| Last update date |
Jun 23, 2021 |
| Contact name |
Stephen C.J. Parker |
| Organization name |
University of Michigan
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| Street address |
100 Washtenaw Avenue
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE178733 |
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits [snATAC-seq] |
| GSE178735 |
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits |
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| Relations |
| BioSample |
SAMN19836040 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5396675_HSM1.bulk.rep1.hg19.bed.gz |
1.1 Gb |
(ftp)(http) |
BED |
| GSM5396675_HSM1.bulk.rep1.hg19.broadPeak.gz |
4.2 Mb |
(ftp)(http) |
BROADPEAK |
| GSM5396675_HSM1.bulk.rep1.hg19.bw |
825.7 Mb |
(ftp)(http) |
BW |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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