|
| Status |
Public on Sep 12, 2021 |
| Title |
16-CC-VAR |
| Sample type |
SRA |
| |
|
| Source name |
muscle semimembranosus
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Duroc
diet: commercial diet without vitamin A supplement
scd_rs80912566_genotype: TT
|
| Treatment protocol |
Pigs fed two diets (with and without vitamin A supplements)
|
| Growth protocol |
Pigs reared in standard commercial conditions of growth and fattening.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Direct-zolTM RNA Miniprep Plus Kit (Zymo Research, BioSystems, CA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
barrow, 210 days old, raised in commercial farms
|
| Data processing |
Quality of the raw sequencing data was assessed with the fastp tool
Filtered sequences were aligned to the Sus scrofa reference genome (Sscrofa 11.1) with the STAR 2.5.4b tool
Mapping statuses were analysed with qualimap and plotted by MultiQC v1.0
After the alignment, reads were counted with the Feature Counts v1.24.1 software
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Text table with read counts for each gene and sample
|
| |
|
| Submission date |
Sep 10, 2021 |
| Last update date |
Sep 12, 2021 |
| Contact name |
Roger Ros-Freixedes |
| Organization name |
Universitat de Lleida
|
| Street address |
Av Rovira Roure, 191
|
| City |
Lleida |
| ZIP/Postal code |
25198 |
| Country |
Spain |
| |
|
| Platform ID |
GPL26351 |
| Series (1) |
| GSE183909 |
Transcriptome shifts triggered by vitamin A and SCD genotype interaction in Duroc pigs |
|
| Relations |
| BioSample |
SAMN21385844 |
| SRA |
SRX12132508 |
