|
| Status |
Public on Apr 19, 2023 |
| Title |
O5c |
| Sample type |
SRA |
| |
|
| Source name |
Extensor digitorum longus muscle
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
gender: male
age: 22 months
treatment: control
cell type: muscle cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from myofibers with Qiagen Rneasy Plus Micro Kit
Reverse transcription was performed with 10ng of total RNA with Clontech SMART-SEQ v4 Ultra Low Input RNA Kit for Sequencing. Sequencing libraries were generated with Nugen Ovation Ultralow System v2.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were adapter- and quality-trimmed with trim_galore (quality cutoff 20, adaptor stringency 1, final length filter 50).
Trimmed reads were mapped to mm10 mouse genome with STAR (mismatch cutoff 4% of read length, no non-canonical junction alignments).
Exonic reads uniquely mapped were summarized over genes with the featureCounts module of the Subread package.
Raw counts were analyzed with DESeq2.
Genome_build: mm10
|
| |
|
| Submission date |
Jan 07, 2022 |
| Last update date |
Apr 19, 2023 |
| Contact name |
Ling Liu |
| E-mail(s) |
lingliu@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
300 Pasteur Drive
|
| City |
Palo Alto |
| ZIP/Postal code |
94306 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE193261 |
Exercise reprograms the inflammatory landscape of multiple stem cell compartments during mammalian aging I |
| GSE196364 |
Exercise reprograms the inflammatory landscape of multiple stem cell compartments during mammalian aging |
|
| Relations |
| BioSample |
SAMN24727968 |
| SRA |
SRX13662932 |
