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| Status |
Public on Jan 17, 2023 |
| Title |
Young MuSC, FAP, MΦ scRNA-Seq 2 |
| Sample type |
SRA |
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| Source name |
Young MuSC, FAP, MΦ scRNA-Seq
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
age: 5 weeks
tissue: skeletal muscle
cell type: satellite cells, macrophages, fibro-adipofenic progenitor cells
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| Extracted molecule |
total RNA |
| Extraction protocol |
Satellite cells (ITGA7+, CD31-, CD11b-, CD45-, Sca1-), fibro-adipogenic progneitor cells (Sca1+, ITGA7-, CD31-, CD11b-, CD45-), and macrophages (F4/80+, CD11b+, CD45+, CD31-) were isolated by Fluorescence-Activated Cell Sorting (FACS) to receive an estimated total of 2500 cells.
Libraries were created using Chromium Single Cell 3' Reagent Kits (v3 Chemistry).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Young2_MuscleStemCell_2-626294_S5
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| Data processing |
Alevin (a tool integrated with the Salmon software) was used to create per-cell level gene-count matrix.
Genome_build: mm10
Supplementary_files_format_and_content: *quants_mat.gz: compressed count matrices; *quants_mat_cols.txt: column Header (Gene-ids) of the matrix; *quants_mat_rows.txt: Row Index (CB-ids) of the matrix; *quants_tier_mat.gz : Tier categorization of the matrix.
Project’s Website (reproducible notebooks): https://csglab.github.io/transcriptional_reprogramming_muscle_cells/
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| Submission date |
Apr 09, 2021 |
| Last update date |
Jan 17, 2023 |
| Contact name |
Vahab Soleimani |
| E-mail(s) |
[email protected]
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| Organization name |
McGill University
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| Department |
Human Genetics
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| Street address |
3640 rue University
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| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3A 0C7 |
| Country |
Canada |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE171794 |
Single-cell RNA-Sequencing of young and aged satellite cells, macrophages and fibro-adipogenic progenitor cells |
| GSE171998 |
Transcriptional reprogramming of skeletal muscle stem cells by the niche environment |
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| Relations |
| BioSample |
SAMN18684628 |
| SRA |
SRX10564558 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5234343_Young2_MuscleStemCell_2-626294_S5_quants.mat.gz |
18.6 Mb |
(ftp)(http) |
MAT |
| GSM5234343_Young2_MuscleStemCell_2-626294_S5_quants_mat_cols.txt.gz |
313.3 Kb |
(ftp)(http) |
TXT |
| GSM5234343_Young2_MuscleStemCell_2-626294_S5_quants_mat_rows.txt.gz |
20.9 Kb |
(ftp)(http) |
TXT |
| GSM5234343_Young2_MuscleStemCell_2-626294_S5_quants_tier.mat.gz |
16.1 Mb |
(ftp)(http) |
MAT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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