|
| Status |
Public on Jun 29, 2022 |
| Title |
AT22-EPS |
| Sample type |
SRA |
| |
|
| Source name |
Skeletal muscle
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Skeletal muscle
cell type: Primary skeletal muscle cells
treatment: electrical pulse stimulation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cultured transduced cells was extracted using QIAGEN RNeasy Mini Kit according to the manufacturer’s instructions
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw data (raw reads) of FASTQ format were firstly processed through fastp.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software v2.5
FeatureCounts was used to count the read numbers mapped of each gene and RPKM was then calculated
Differential expression analysis between control and EPS treated cells was performed using DESeq2 R package v2_1.6.3
Assembly: hg38, GRCh38
Supplementary files format and content: excel file include FPKM values for each sample
|
| |
|
| Submission date |
Apr 06, 2022 |
| Last update date |
Jun 29, 2022 |
| Contact name |
G. Hege Thoresen |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Oslo
|
| Department |
Section for Pharmacology and Pharmaceutical Biosciences
|
| Street address |
Sem Sælands vei 3
|
| City |
Oslo |
| ZIP/Postal code |
0371 |
| Country |
Norway |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE200335 |
Gene expression profiles of electrically pulse-stimulated human myotubes |
|
| Relations |
| BioSample |
SAMN27387512 |
| SRA |
SRX14766600 |
