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| Status |
Public on Jun 23, 2021 |
| Title |
63_20-hg19: Human snATAC 20k nuclei |
| 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 |
Two pieces of tissue (weighing 85.3 mg and 85.8 mg) were cut from one human skeletal muscle sample and two tissue pieces (weighing 95.9 mg and 92.6 mg) were cut from a second human skeletal muscle sample (quadriceps femoris muscle group). Each of the samples was cut on dry ice using a frozen scalpel to prevent thawing. The samples were pulverized using a CP02 cryoPREP automated dry pulverizer (Covaris 500001). We developed a customized nuclei isolation protocol (https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S2.pdf) derived from the previously published ENCODE protocol (The ENCODE Project Consortium 2012, 2012). All four pulverized tissue pieces were mixed and redistributed to perform four different nuclei isolations. The desired concentration of nuclei was achieved by resuspending the appropriate number of nuclei in 1X diluted nuclei buffer.
The nuclei were submitted to the University of Michigan Advanced Genomics core for processing on the 10x Genomics Chromium platform. Nuclei were loaded at 20K nuclei/well.
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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 |
SAMN19836042 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5396673_63_20-hg19.bed.gz |
6.4 Gb |
(ftp)(http) |
BED |
| GSM5396673_63_20-hg19.broadPeak.gz |
6.3 Mb |
(ftp)(http) |
BROADPEAK |
| GSM5396673_63_20-hg19.bw |
2.4 Gb |
(ftp)(http) |
BW |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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