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Sample GSM5396672 Query DataSets for GSM5396672
Status Public on Jun 23, 2021
Title 1846: Human - rat multiome mix (ATAC component)
Sample type SRA
 
Source name Skeletal muscle
Organisms Homo sapiens; Rattus norvegicus
Characteristics tissue: Skeletal muscle
Extracted molecule genomic DNA
Extraction protocol Tissue from human (74mg of pulverized human skeletal muscle) and rat (79mg of pulverized gastrocnemius samples) were used in the multiome experiment. The pulverized tissues were mixed together prior to isolation. For this experiment, we developed a customized protocol based on those recommended by 10x Genomics (https://www.10xgenomics.com/resources/demonstrated-protocols/) and on the previously developed protocol (https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S2.pdf) to isolate nuclei (https://github.com/porchard/muscle-protocols/blob/master/Supplemental_Protocol_S4.pdf). 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. 16.1K nuclei were loaded into a single well.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description ***Raw data are unavailable due to patient privacy concerns***
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)
 
Submission date Jun 23, 2021
Last update date Jun 23, 2021
Contact name Stephen C.J. Parker
Organization name University of Michigan
Street address 100 Washtenaw Avenue
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL27452
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
Relations
BioSample SAMN19836043

Supplementary file Size Download File type/resource
GSM5396672_1846_ATAC-hg19.bed.gz 3.6 Gb (ftp)(http) BED
GSM5396672_1846_ATAC-hg19.broadPeak.gz 4.1 Mb (ftp)(http) BROADPEAK
GSM5396672_1846_ATAC-hg19.bw 1.5 Gb (ftp)(http) BW
GSM5396672_1846_ATAC-rn6.bed.gz 2.2 Gb (ftp)(http) BED
GSM5396672_1846_ATAC-rn6.broadPeak.gz 3.4 Mb (ftp)(http) BROADPEAK
GSM5396672_1846_ATAC-rn6.bw 1.0 Gb (ftp)(http) BW
Raw data not provided for this record
Processed data provided as supplementary file

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