|
| Status |
Public on Oct 30, 2020 |
| Title |
20065FL-01-02-15 |
| Sample type |
SRA |
| |
|
| Source name |
fat
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Zlotnicka White
day: 180
Sex: female
shear force: low fat content
replicant: 8
|
| Growth protocol |
All pigs were female and they were maintained at Pig Test Station under the same feeding and housing conditions and were slaughtered when they reached 100±2 kg.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated by RNA was isolated by the PureLink™ RNA Mini Kit (Ambion, Cambridge, UK) according to the manufacturer’s recommendations. The RIN values were over 7 what was estimated by TapeStation2200 and RNA tapes (Agilent, Palo Alto, USA).
The cDNA libraries were prepared by TruSeq RNA Sample Preparation Kit v2 (Illumina) according to the supplied protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences.
The raw reads were aligned to the Sus scrofa genome (Sscrofa11.1) as a reference, while the whole procedure was followed by alignment parameters from ENCODE3's STAR-RSEM pipeline
The quality control metrics across aligned reads per sample were obtained using RNA-SeQC software
The differential expression estimation was proceed with utilization of DeSeq2 Bioconductor R-project package.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: genes_fat.csv.gz
Supplementary_files_format_and_content: genes_liver.csv.gz
|
| |
|
| Submission date |
Oct 29, 2020 |
| Last update date |
Oct 30, 2020 |
| Contact name |
Kacper Zukowski |
| E-mail(s) |
zukowski.kacper@gmail.com
|
| Organization name |
National Research Institute of Animal Production
|
| Street address |
Krakowska 1 Street
|
| City |
Balice |
| ZIP/Postal code |
32-083 |
| Country |
Poland |
| |
|
| Platform ID |
GPL24486 |
| Series (1) |
| GSE160436 |
Liver and fat transcriptomic changes related to fat content in pigs |
|
| Relations |
| BioSample |
SAMN16595836 |
| SRA |
SRX9401149 |
