|
| Status |
Public on Jan 01, 2023 |
| Title |
33 |
| Sample type |
SRA |
| |
|
| Source name |
Cholecalciferol_Standard dose _muscle
|
| Organism |
Sus scrofa domesticus |
| Characteristics |
treatment: Cholecalciferol
dose: Standard dose
Sex: Female
tissue: Muscle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Collected tissues were stored at -80°C. RNA was isolated using Trizol reagent. QuantSeq 3′mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) with 100ng/ul total RNA was used to construct sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Female
|
| Data processing |
Quality control (fastQC)
Filtration of low quality reads (phred quality <20). Minimal length of reads set to 35. Removal of adaptors (Flexbar)
Mapping with default options (Tophat)
Counting reads to Ensembl GTF version 95 intervals (htseq-count) and differential expresion calculated with the use of Deseq2
Assembly: Sus Scrofa 11.1
|
| |
|
| Submission date |
Apr 26, 2022 |
| Last update date |
Jan 01, 2023 |
| Contact name |
Alicja Wierzbicka |
| E-mail(s) |
alicja.wierzbicka@iz.edu.pl
|
| Organization name |
National Research Institute of Animal Produstion
|
| Street address |
ul. Sarego 2
|
| City |
Kraków |
| ZIP/Postal code |
31-047 |
| Country |
Poland |
| |
|
| Platform ID |
GPL32212 |
| Series (1) |
| GSE201510 |
NGS-Muscle of swine supplemented with cholecalciferol and 25(OH)D |
|
| Relations |
| BioSample |
SAMN27777023 |
| SRA |
SRX14997839 |
