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| Status |
Public on Aug 31, 2021 |
| Title |
control_SCs_Dex_rep2 |
| Sample type |
SRA |
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| Source name |
primary satellite cell
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Muscle satellite cell
agent: Dex
genotype: wildtype
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| Treatment protocol |
For Dex treatment, 10uM of dexamethasone (Sigma-Aldrich) was added to the medium.
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| Growth protocol |
Mouse primary SCs were isolated from hindlimb muscles from male MCK Cre:Klf5flox/flox and control (Klf5flox/flox) mice. After excess fat, connective tissue and tendons were removed, hindlimb muscles were minced and digested in 0.2% collagenase type II (Worthington Biochemical Corp., Freehold, NJ) for 1 h at 37℃. Mononuclear cells were stained with PE-Cy7-conjugated anti-CD31, anti-CD45 and anti-Ly6A/E as well as FITC-conjugated anti CD106 antibodies for 30 min on ice and resuspended in PBS containing 2% FBS. SCs were isolated using a FACS Aria III flow cytometer (BD Biosciences). Debris and dead cells were excluded by forward scatter, side scatter and 7-AAD gating. Data were collected using FACS Diva software and FlowJo (BD Biosciences). SCs were cultured in GlutaMax DMEM (Life Technologies, Grand Island, NY) supplemented with 10 ng/ml basic fibroblast growth factor (Cell Signaling Technology, Beverly, MA) and 1% penicillin-streptomycin at 37℃ under 5% CO2. Myogenic differentiation was induced in GlutaMax DMEM supplemented with 5% horse serum and 1% penicillin-streptomycin at 37℃ under 5% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Poly-A mRNA was extracted from total RNA by using an NEBNext Poly(A) mRNA magnetic Isolation module (NEB), after which RNA-seq libraries were prepared using a NEBNext UltraII RNA Library Prep kit for Illumina (NEB) according to the manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
Dex-treated control SCs
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| Data processing |
Reads were aligned to the mm9 mouse genome using STAR.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using Homer.
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| Submission date |
Jan 19, 2021 |
| Last update date |
Aug 31, 2021 |
| Contact name |
Ichiro Manabe |
| E-mail(s) |
manabe-tky@umin.ac.jp
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| Organization name |
Chiba University
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| Street address |
1-8-1 Inohana, Chuo
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| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
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| Platform ID |
GPL18480 |
| Series (2) |
| GSE165071 |
Analysis of effects of KLF5 on dexamethasone-mediated atrophy in mouse satellite cells [RNA] |
| GSE165072 |
KLF5 on dexamethasone-mediated atrophy in mouse satellite cells |
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| Relations |
| BioSample |
SAMN17379527 |
| SRA |
SRX9895134 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5025648_control_SCs_Dex_rep2.ucsc.bedGraph.gz |
61.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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