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| Status |
Public on Sep 29, 2021 |
| Title |
Old_D1_D |
| Sample type |
SRA |
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| Source name |
Tibialis anterior muscle
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J
age: 20 months
Sex: F
tissue: Tibialis anterior muscle
injury: Notexin injury (Day 1)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single-cell RNA-sequencing libraries were prepared using a Chromium Single Cell 3' Reagent Kit (10X Genomics, v3 kit) following the directions of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Libraries were sequenced on Illumina NextSeq 500 using paired-end 26 + 8 + 58 (according to 10X Chromium Single Cell 3' protocol)
Sequences were aligned to mm10 using cellranger v3.1.0 pipeline
Ambient RNA content was removed using SoupX v1.4.5
Gene expression data was processed with Seurat v3.1.5
Initial data filtering (minimum cells to express an included gene = 3, minium genes to be expressed in an included cell = 500)
Filtering by percent mitochondiral genes in included cells (maximum 30%), number of UMIs in included cells (minimum 1000)
Log-normalization of expression data
Cell annotations in metadata derived from shared nearest neighbor clustering
Genome_build: mm10
Supplementary_files_format_and_content: zipped, market exchange format (MEF) for raw, filtered, and scrubbed (SoupX) transcript count matrices; .csv files of single-cell metadata information
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| Submission date |
Nov 25, 2020 |
| Last update date |
Nov 16, 2021 |
| Contact name |
Lauren D Walter |
| E-mail(s) |
[email protected]
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| Organization name |
Cornell University
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| Department |
Biomedical Engineering
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| Lab |
Cosgrove Laboratory
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| Street address |
161 Weill Hall
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE162172 |
Single-cell transcriptomic sampling of regenerating aged mouse hindlimb muscle |
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| Relations |
| BioSample |
SAMN16913848 |
| SRA |
SRX9583836 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4944188_Old_D1_D_filtered_feature_bc_matrix.zip |
42.4 Mb |
(ftp)(http) |
ZIP |
| GSM4944188_Old_D1_D_meta.csv.gz |
436.0 Kb |
(ftp)(http) |
CSV |
| GSM4944188_Old_D1_D_raw_feature_bc_matrix.zip |
77.0 Mb |
(ftp)(http) |
ZIP |
| GSM4944188_Old_D1_D_soupx.zip |
127.2 Mb |
(ftp)(http) |
ZIP |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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