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| Status |
Public on Oct 11, 2020 |
| Title |
WT tibialis anterior 24 months 10X snRNA-seq |
| Sample type |
SRA |
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| Source name |
Tibialis anterior muscle
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Whole skeletal muscle
genotype: Wild-type
time point: 24 months
sequencing parameters: 434 million reads
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| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei were isolated from skeletal muscle immediately following euthanasia. Muscle was homogenized and then filtered, and nuclei were purified from the homogenate by staining with Hoechst dye and then FACS sorting for DAPI+ nuclei.
Isolated nuclei were loaded into the 10X Chromium system (targeting ~12,000-13,000 loading count) using the Single Cell 3’ Reagent Kit v3, and libraries were constructed according to the manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw sequencing data of all samples were processed using the cellRanger workflow (version 3.1.0), using a combined intron-exon reference produced as described using the vendor-provided “Generating a Cell Ranger compatible "pre-mRNA" Reference Package” guidelines (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references). In brief, the “pre-mRNA” reference was derived using the default exon-level GTF file provided by 10x Genomics ( http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-mm10-3.0.0.tar.gz). Using the below awk command, this exon-level GTF file into “pre-MRNA” GTF containing intron transcript definitions). Next, the below mkref command was run to produce the final “pre-MRNA” GTF and genome fasta file ($ cellranger mkref --genome=Mmpre --fasta=genome.fa --genes=genes.premrna.gtf). For each dataset, we corrected for ambient background RNA by filtering with the R package SoupX (version 0.3.0), using the inferNonExpressedGenes() function to determine which genes had the highest probability of being ambient mRNA, and the strainCells() function in order to transform count matrices.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5
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| Submission date |
Mar 17, 2020 |
| Last update date |
Oct 12, 2020 |
| Contact name |
Nathan Salomonis |
| E-mail(s) |
nathan.salomonis@cchmc.org
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| Organization name |
Cincinnati Children's Hospital
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| Department |
Biomedical Informatics
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| Lab |
Nathan Salomonis
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| Street address |
3333 Burnet Avenue
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| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE147127 |
Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers |
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| Relations |
| BioSample |
SAMN14392086 |
| SRA |
SRX7939762 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4418991_10X_Millay_Aging_20190326_3v3mm_soupx.h5 |
132.6 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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