NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5694276 Query DataSets for GSM5694276
Status Public on Aug 11, 2022
Title 8hpi, RNA Rep2
Sample type SRA
 
Source name 8 hours post-injured satellite cells followed by in situ fixation
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: Skeletal muscle
cell type: Muscle stem cells
treatment: BaCl2 injury
time: 8hpi
Treatment protocol Mouse hind limb was injured by BaCl2 injection. Mice were perfused with PFA before satellite cell isolation.
Growth protocol N/A
Extracted molecule polyA RNA
Extraction protocol RNA was isolated using miRNeasy FFPE Kit (Qiagen).
cDNA was generated following the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) protocol and processed for library generation using Tn5-mediated library generation. Sequencing was carried out in 2 × 100 cycle paired-end mode on a DNBSEQ-G400 sequencer (BGI).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model DNBSEQ-G400
 
Description activation.csv
Data processing To improve mappability of reads, low quality bases were trimmed using Trimmomatic v0.36 (Bolger et al., 2014) with parameters ‘SLIDINGWINDOW:10:20 MINLEN:30’.
Trimmed reads were mapped to mm10 using HISAT2 v2.1.0 (Kim et al., 2015) with default parameters. Unmapped reads and read alignments with a mapping quality below 10 were removed using samtools v1.3 (Li et al., 2009) with parameters ‘-F 516 -q 10 -b’.
After read mapping, StringTie v1.3.3 (Pertea et al., 2015) was used with the default parameters and the Gencode vM19 gene annotation GTF file to estimate the expression of annotated transcripts.
Ballgown v2.2.0 (Frazee et al., 2015) was used to calculate gene expression FPKM values and output the gene expression table.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated value table of genes with their corresponding FPKM values as output by Ballgown
 
Submission date Nov 18, 2021
Last update date Aug 11, 2022
Contact name Tom Cheung
Organization name Hong Kong University of Science and Technology
Department Division of Life Science
Street address Clear Water Bay, Kowloon
City Hong Kong
ZIP/Postal code N/A
Country Hong Kong
 
Platform ID GPL28457
Series (2)
GSE189073 Transcriptome sequencing analysis of satellite cells by RNA-seq
GSE189074 Comprehensive Analysis of Chromatin Accessibility Changes during Muscle Stem Cell Quiescence Exit and Self-renewal
Relations
BioSample SAMN23281087
SRA SRX13164865

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap