|
| Status |
Public on Nov 12, 2018 |
| Title |
s_16 high feed conversion ratio |
| Sample type |
SRA |
| |
|
| Source name |
pituitary
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: pituitary
group: high feed conversion ratio
age: 3 months
strain: Pulawska breed
gender: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was isolated using by TriReagent (Ambion, Life Technologies). The fat samples were collected immediately after slaughter and stored in tubes with RNAlater (Ambion). The fat samples were homogenized with the use of zirconium oxide beads (diameter 0.5 mm) in BulletBlender homogenizer (Next Advance Inc., USA).The concentration and quality of RNA were estimated on TapeStation 2200 (Agilent Technologies, Warsaw, Poland) using RNA Screen Tape (Agilent Technologies). The RNA samples with RIN (RNA integrity number) above 8.0 were used to further analyses.
The cDNA libraries were prepared from 300ng of total RNA by using TruSeq RNA Kit v2 kit (Cat#FC-122-1001) according to protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| 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: raw.genes.pituitary.csv.gz: raw gene counts
Supplementary_files_format_and_content: res.genes.pituitary.csv.gz: DESeq2 results for differential expressed gene analysis
|
| |
|
| Submission date |
Nov 08, 2018 |
| Last update date |
Nov 12, 2018 |
| 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 |
GPL21186 |
| Series (1) |
| GSE122343 |
Pituitary transcriptomic changes dependent on feed conversion in pigs |
|
| Relations |
| BioSample |
SAMN10397254 |
| SRA |
SRX4997266 |
