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| Status |
Public on Aug 31, 2021 |
| Title |
SCs_Dex_rep1 |
| 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
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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 C57BL6 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 |
genomic DNA |
| Extraction protocol |
Nuclei were extracted from approximately 50,000 cells. After transposase reactions, cellular DNA was immediately purified. The DNA was amplified for 14 cycles using Nextera primer Ad1 and a unique Ad2.n barcoding primer with NEBNext High-Fidelity 2XPCR Master Mix (NEB). The resulting libraries were size selected to 175-225 bp, purified.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
Dex-treated
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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) |
| GSE165070 |
Analysis of accessible chromatin regions in response to dexamethasone mediated-atrophy in mouse satellite cells [ATAC] |
| GSE165072 |
KLF5 on dexamethasone-mediated atrophy in mouse satellite cells |
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| Relations |
| BioSample |
SAMN17379509 |
| SRA |
SRX9895130 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5025643_SCs_Dex_rep1.ucsc.bedGraph.gz |
39.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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