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Sample GSM5396683 Query DataSets for GSM5396683
Status Public on Jun 23, 2021
Title 1846: Human - rat multiome mix (RNA component)
Sample type SRA
Source name Skeletal muscle
Organisms Homo sapiens; Rattus norvegicus
Characteristics tissue: Skeletal muscle
Extracted molecule total RNA
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 ( and on the previously developed protocol ( to isolate nuclei ( 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 RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description ***Raw data are unavailable due to patient privacy concerns***
nuclear RNA
Data processing snRNA-seq data was processed using starSOLO (STAR v. 2.7.3a; options --soloUMIfiltering MultiGeneUMI --soloCBmatchWLtype 1MM_multi_pseudocounts --soloCellFilter None). For human-only libraries we used the GENCODE v. 19 annotation (with hg19). For human-rat mix libraries we processed the data twice, once for human and once for rat, and used the NCBI Rattus norvegicus Annotation Release 106 with rat genome rn6.
We filtered the mapped BAM file using samtools view -h -b -q 255 -F 4 -F 256 -F 2048
We anonymized the BAM files using anonymizeBAM (--strict; v. 0.4.5)
We generated single-end BED files using bedtools bamtobed
RNA-seq coverage files were generated from the anonymized BAM file using pybedtools (Dale et al., 2011) (a python wrapper around BEDTools; BedTool().genome_coverage() function, with arguments bg=True, split=True, and strand and scale set appropriately to produce both reverse and forward strand bedGraph files scaled to 1 million reads), followed by conversion of bedGraph files to bigWig files using bedGraphToBigWig (v. 4)
Genome_build: hg19 (human) and rn6 (when rat nuclei were included in the library)
Supplementary_files_format_and_content: RNA-seq read mapping locations, anonymized (BED files)
Supplementary_files_format_and_content: RNA-seq signal tracks for forward and reverse strands (bigWig 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)
GSE178734 Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits [snRNA-seq]
GSE178735 Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
BioSample SAMN19836051

Supplementary file Size Download File type/resource
GSM5396683_1846_RNA-hg19.bed.gz 3.0 Gb (ftp)(http) BED 224.7 Mb (ftp)(http) BW 224.7 Mb (ftp)(http) BW
GSM5396683_1846_RNA-rn6.bed.gz 2.2 Gb (ftp)(http) BED 120.2 Mb (ftp)(http) BW 125.2 Mb (ftp)(http) BW
Raw data not provided for this record
Processed data provided as supplementary file

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