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| Status |
Public on Feb 04, 2022 |
| Title |
Control Rep3 |
| Sample type |
SRA |
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| Source name |
Skeletal muscle stem cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: Hindlimb muscles
age: 9-week old
treatment: Oil
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| 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.
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| 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
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| Phone |
+81-89-960-5925
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| Organization name |
Ehime University
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| Department |
Proteo-Science Center
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| Lab |
Division of Integrative Pathophysiology
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| Street address |
Shitsukawa
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| City |
Toon |
| State/province |
Ehime |
| ZIP/Postal code |
791-0295 |
| Country |
Japan |
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| 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 |
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| Relations |
| BioSample |
SAMN18353084 |
| SRA |
SRX10380752 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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