|
| Status |
Public on Aug 11, 2022 |
| Title |
4hpi, RNA Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
4 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: 4hpi
|
| 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 |
SAMN23281085 |
| SRA |
SRX13164863 |
