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Sample GSM5182748 Query DataSets for GSM5182748
Status Public on Feb 04, 2022
Title Control Rep1
Sample type SRA
 
Source name Skeletal muscle stem cells
Organism Mus musculus
Characteristics tissue: Hindlimb muscles
age: 9-week old
treatment: Oil
Treatment protocol Tamoxifen (150 µl of 20 mg/ml) (Sigma, Cat# T5648) dissolved in corn oil (Sigma, Cat# C8267) were injected intraperitoneally for a total of 5 consecutive days to induce Cre-mediated recombination.
Growth protocol Isolated satellite cells were resuspended in the DMEM/F12 (gibco, Cat# 10565-018) containing 20% FBS, 2% Ultroser G (Pall, Cat# 15950-017), and Antibiotic-Antimycotic. Cells were cultured for 3 days in 8-well chamber slide (Thermo Scientific, Cat# 177445) with 1 mg/ml of Matrigel (Corning, Cat# 354230) at 5000 cells/cm2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from satellite cells with RNeasy Plus Micro Kit (Qiagen, Cat# 74034).
RNA-seq libraries were prepared using Ultra II Directional RNA Library Prep Kit for Illumina (NEB, Cat# E7760L) with NEBNext rRNA Depletion Kit (NEB, Cat# E6310X) according to the manufacturer’s instructions. The libraries were sequenced using NovaSeq 6000 Sequencing System (Illumina) with 150 bp paired end reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The RNA-Seq analysis was performed with RaNA-Seq (Prieto and Barrios, 2019). For transposable elements (TE) analysis, raw reads were trimmed using TrimGalore (version 0.6.6; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to the reference genome (GRCm38, PRI) with annotation (PRI, https://www.gencodegenes.org/mouse/) using STAR (v2.7.6a) (Dobin et al., 2013).
TE families were quantified using featureCounts (v2.0.1) (Liao et al., 2014) with following options (-M -T 1 -s 0 -p) and TE annotation (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/).
The differentially expressed TEs were extracted by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: DE.tsv, Counts_TE.txt, DESeq2_TE.txt
 
Submission date Mar 18, 2021
Last update date Feb 04, 2022
Contact name Hiroshi Sakai
E-mail(s) sakai.hiroshi.wh@ehime-u.ac.jp
Phone +81-89-960-5925
Organization name Ehime University
Department Proteo-Science Center
Lab Division of Integrative Pathophysiology
Street address Shitsukawa
City Toon
State/province Ehime
ZIP/Postal code 791-0295
Country Japan
 
Platform ID GPL24247
Series (2)
GSE169192 Uhrf1 control the proliferation and the differentiation of satellite cells [RNA-Seq]
GSE169193 Uhrf1 control the proliferation and the differentiation of satellite cells
Relations
BioSample SAMN18353086
SRA SRX10380750

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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