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| Status |
Public on Jun 23, 2021 |
| Title |
1846: Human - rat multiome mix (RNA component) |
| Sample type |
SRA |
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| Source name |
Skeletal muscle
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| Organisms |
Homo sapiens; Rattus norvegicus |
| Characteristics |
tissue: Skeletal muscle
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| 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 (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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
***Raw data are unavailable due to patient privacy concerns***
nuclear RNA
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| 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)
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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 |
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 |
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| Relations |
| BioSample |
SAMN19836051 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5396683_1846_RNA-hg19.bed.gz |
3.0 Gb |
(ftp)(http) |
BED |
| GSM5396683_1846_RNA-hg19.fwd.bw |
224.7 Mb |
(ftp)(http) |
BW |
| GSM5396683_1846_RNA-hg19.rev.bw |
224.7 Mb |
(ftp)(http) |
BW |
| GSM5396683_1846_RNA-rn6.bed.gz |
2.2 Gb |
(ftp)(http) |
BED |
| GSM5396683_1846_RNA-rn6.fwd.bw |
120.2 Mb |
(ftp)(http) |
BW |
| GSM5396683_1846_RNA-rn6.rev.bw |
125.2 Mb |
(ftp)(http) |
BW |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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