|
| Status |
Public on Apr 28, 2020 |
| Title |
ECO-FCE Ileum 436 |
| Sample type |
RNA |
| |
|
| Source name |
Ileum
|
| Organism |
Sus scrofa |
| Characteristics |
feed efficiency: high
gender: female
sow: 1417
cell type: ileal mucosa
|
| Treatment protocol |
Animals differing in feed efficiency traits
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Qiazol reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was column-purified using the RNeasy Kit (Qiagen, Hilden, Germany).
|
| Label |
biotin
|
| Label protocol |
Each RNA sample was transcribed to DNA using the Ambion WT Expression Kit (Ambion, Austin, TX, USA). DNA preparations were fragmented and labelled with the WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).
|
| |
|
| Hybridization protocol |
Labelled DNA was hybridized for 16 hr at 42°C on Snowball Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols
|
| Data processing |
Snowball arrays (Freeman et al. in BMC Biol 2012, 10:90), see the ArrayExpress database, accession no. A-AFFY-189
Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and R environment.
|
| |
|
| Submission date |
Dec 20, 2019 |
| Last update date |
Apr 28, 2020 |
| Contact name |
Henry Reyer |
| Organization name |
Leibniz Institute for Farm Animal Biology (FBN)
|
| Street address |
Wilhelm-Stahl-Allee 2
|
| City |
Dummerstorf |
| ZIP/Postal code |
18196 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16569 |
| Series (2) |
| GSE142434 |
Ileal transcriptome profiles of pigs divergent in feed efficiency |
| GSE142438 |
Caecal and Ileal transcriptome profiles of pigs divergent in feed efficiency |
|
