|
| Status |
Public on May 11, 2024 |
| Title |
gastrocnemius_mdx_CHP_rep5 |
| Sample type |
SRA |
| |
|
| Source name |
Gastrocnemius
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Gastrocnemius
strain: C57BL/10ScSn-Dmdmdx
treatment: CHP
|
| Treatment protocol |
Mdx mice were treated from week 7 to week 22 of age with CHP at a dose of 35 mg/kg or water as control, BL10 mice received water (control), three times per week by oral gavage. 18-month-old male C57BL6/J mice received DW or CHP (35mg/kg/day) orally for 6 months.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For the DMD study, RNA was extracted in Trizol (TriPure, Roche) from frozen ventricles or GM tissue, using the NucleoSpin RNA extraction kit (Macherey-Nagel). From age mice, total RNA was extracted from GM using NucleoZOL reagent (740404.200, Macherey-Nagel).
RNA libraries were prepared for sequencing using standard protocols with polyA enrichment.
Paired-end RNA sequencing was performed using BGISEQ-500 for the DMD study and Illumina NovaSeq for the aging study.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
84
raw_counts_gastrocnemius_dmd.csv
|
| Data processing |
After sequencing, the raw reads were filtered by removing adaptor sequences, contamination and low-quality (RIN <8) reads from the raw reads.
All samples passed quality check by FastQC.
Sequenced reads were mapped to the GRCm38 mm10 primary assembly of the mouse genome using ensembl release 95 gene annotation with STAR aligner version 2.6.0a.
Reads were counted using STAR aligner.
Assembly: mm10
Supplementary files format and content: csv file with raw counts for each gene and sample
|
| |
|
| Submission date |
Aug 28, 2023 |
| Last update date |
May 11, 2024 |
| Contact name |
Keno Strotjohann |
| E-mail(s) |
kenostrotjohann@gmail.com
|
| Organization name |
École Polytechnique Fédérale de Lausanne (EPFL)
|
| Department |
School of Life Sciences, Institute of Bioengineering
|
| Lab |
Laboratory of Integrative Systems Physiology (LISP)
|
| Street address |
Route Cantonale
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE241771 |
Cyclo His-Pro halts skeletal muscle degeneration and cardiomyopathy in murine myopathy models |
|
| Relations |
| BioSample |
SAMN37171480 |
| SRA |
SRX21488095 |
