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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 12, 2022 |
| Title |
Transcriptome sequencing analysis of satellite cells by RNA-seq |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Regulation of chromatin accessibility is critical for cell fate decisions. Chromatin architecture responds to extrinsic environments rapidly. The traditional adult stem cell isolation approach requires tissue dissociation, and adult stem cells respond to the stimulation and adapt a different chromatin conformation. Here, we characterized the DNA regulatory landscape and transcriptomic profile of muscle stem cell quiescence exit and self-renewal by time-course profiling of the in situ fixed SCs upon injury-induced activation and during aging. Detailed analysis of the chromatin accessibility profiles leads to the identification of enhancer elements for SC quiescence. Constant activation of the enhancer elements promotes stemness and prevents SCs from differentiation, whereas loss of them causes cell-cycle arrest and essentially leads to defects in SC activation. Interestingly, we also showed that aged SCs display a more open chromatin environment than young SCs. Our compre hensive characterization of the chromatin accessibility and transcriptomic landscapes during SC quiescence exit and self-renewal broadens our understanding of this process and identifies functional distal regulatory elements for SC function.
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| Overall design |
To understand the transcriptomic changes of satellite cells during quiescence exit and regeneration, we performed time-course RNA-seq of satellite cells injured for different time points from mouse hindlimb using PFA perfusion-based sorting scheme.
The polyA+ RNA from fix-sort satellite cells were sequenced using DNBSEQ-G400 sequencer (BGI)
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| Contributor(s) |
Dong A, So W, Zeng W, Liu J, Cheung TH |
| Citation(s) |
36093058 |
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| Submission date |
Nov 18, 2021 |
| Last update date |
Nov 11, 2022 |
| Contact name |
Tom Cheung |
| Organization name |
Hong Kong University of Science and Technology
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| Department |
Division of Life Science
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| Street address |
Clear Water Bay, Kowloon
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| City |
Hong Kong |
| ZIP/Postal code |
N/A |
| Country |
Hong Kong |
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| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL28457 |
DNBSEQ-G400 (Mus musculus) |
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| Samples (30)
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| GSM5694268 |
0.5hpi, RNA Rep2 |
| GSM5694269 |
1hpi, RNA Rep1 |
| GSM5694270 |
1hpi, RNA Rep2 |
| GSM5694271 |
2hpi, RNA Rep1 |
| GSM5694272 |
2hpi, RNA Rep2 |
| GSM5694273 |
4hpi, RNA Rep1 |
| GSM5694274 |
4hpi, RNA Rep2 |
| GSM5694275 |
8hpi, RNA Rep1 |
| GSM5694276 |
8hpi, RNA Rep2 |
| GSM5694277 |
16hpi, RNA Rep1 |
| GSM5694278 |
16hpi, RNA Rep2 |
| GSM5694279 |
32hpi, RNA Rep1 |
| GSM5694280 |
32hpi, RNA Rep2 |
| GSM5694281 |
60hpi, RNA Rep1 |
| GSM5694282 |
60hpi, RNA Rep2 |
| GSM5694283 |
7dpi, RNA Rep1 |
| GSM5694284 |
7dpi, RNA Rep2 |
| GSM5694285 |
14dpi, RNA Rep1 |
| GSM5694286 |
14dpi, RNA Rep2 |
| GSM5694287 |
28dpi, RNA Rep1 |
| GSM5694288 |
28dpi, RNA Rep2 |
| GSM5694289 |
oQSC, RNA Rep1 |
| GSM5694290 |
oQSC, RNA Rep2 |
| GSM5694291 |
oFISC, RNA Rep1 |
| GSM5694292 |
oFISC, RNA Rep2 |
| GSM5694293 |
oASC, RNA Rep1 |
| GSM5694294 |
oASC, RNA Rep2 |
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| This SubSeries is part of SuperSeries: |
| GSE189074 |
Comprehensive Analysis of Chromatin Accessibility Changes during Muscle Stem Cell Quiescence Exit and Self-renewal |
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| Relations |
| BioProject |
PRJNA781463 |
| SRA |
SRP346716 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE189073_activation.csv.gz |
1.3 Mb |
(ftp)(http) |
CSV |
| GSE189073_aging.csv.gz |
851.0 Kb |
(ftp)(http) |
CSV |
| GSE189073_regeneration.csv.gz |
684.2 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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