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Sample GSM5025651 Query DataSets for GSM5025651
Status Public on Aug 31, 2021
Title KLF5KO_SCs_Dex_rep1
Sample type SRA
 
Source name primary satellite cell
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: Muscle satellite cell
agent: Dex
genotype: Klf5KO
Treatment protocol For Dex treatment, 10uM of dexamethasone (Sigma-Aldrich) was added to the medium.
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.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description Dex-treated Klf5KO SCs
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.
 
Submission date Jan 19, 2021
Last update date Aug 31, 2021
Contact name Ichiro Manabe
E-mail(s) manabe-tky@umin.ac.jp
Organization name Chiba University
Street address 1-8-1 Inohana, Chuo
City Chiba
ZIP/Postal code 260-8670
Country Japan
 
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
Relations
BioSample SAMN17379524
SRA SRX9895137

Supplementary file Size Download File type/resource
GSM5025651_KLF5KO_SCs_Dex_rep1.ucsc.bedGraph.gz 80.7 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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