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| Status |
Public on Jun 06, 2024 |
| Title |
HSA_AICAR__S462 |
| Sample type |
SRA |
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| Source name |
gastrocnemius muscle
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| Organism |
Mus musculus |
| Characteristics |
tissue: gastrocnemius muscle
mouse id: S462
genotype: HSA transgene
treatment: AICAR
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| Treatment protocol |
AICAR (Toronto Research Chemicals; 500 mg/kg) for 7 days
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| Extracted molecule |
total RNA |
| Extraction protocol |
Gastrocnemius muscles were powdered in liquid nitrogen, and 1/3 of the muscle was used for RNA extraction. The powder was lysed in the RLT buffer provided in the RNeasy mini kit (Qiagen) and homogenized with a syringe. Total RNAs were extracted with the RNeasy Mini Kit (Qiagen), with proteinase K and DNAse treatment.
mRNA-sequencing stranded libraries were generated using the TruSeq Illumina kit according to the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Sample 10
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| Data processing |
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm10, with RNA-STAR (version 2.5.2a, Dobin et al., Bioinformatics 2013), with default parameters except for allowing up 10 hits to genome (outFilterMultimapNmax 10), reporting only one location for hits with equal score (outSAMmultNmax 1), and for filtering reads without evidence in spliced junction table (outFilterType "BySJout").
Raw reads and mapping quality was assessed by the qQCreport function from the R/Bioconductor software package QuasR (version 1.16.0, Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in December 2015) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with EntrezID (1. column), 2. (gene length in bp), and raw counts for each sample
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| Submission date |
Mar 06, 2023 |
| Last update date |
Jun 06, 2024 |
| Contact name |
DBM Bioinformatics Core Facility |
| Phone |
+41612073541
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| Organization name |
University of Basel
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| Department |
Departement of Biomedicine
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| Street address |
Hebelstrasse 20
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| City |
Basel |
| State/province |
BS |
| ZIP/Postal code |
4053 |
| Country |
Switzerland |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE226676 |
Splicing changes in gastrocnemius muscle from 3-month-old HSALR mice |
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| Relations |
| BioSample |
SAMN33593283 |
| SRA |
SRX19566836 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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