|
| Status |
Public on Jan 30, 2013 |
| Title |
Porcine colon_without fiber_160d_9 |
| Sample type |
RNA |
| |
|
| Source name |
Colon_without fiber_160d
|
| Organism |
Sus scrofa |
| Characteristics |
diet: control
tissue: Colon
|
| Treatment protocol |
All pigs were randomly allocated into 2 groups receiving control and fibrous diet with inclusion of pea fiber from weaning age until d 160 post-weaning.
|
| Growth protocol |
The weaned pigs were individually fed in pig experimental pens (0.6×0.8m) and then transferred to growing-finishing pig pen (2.0×3.0m) when pig body weight was app. 20 kg. The pigs were fed in the atmosphere-controlled environment (22～24℃).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen colonic tissues using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
Agilent (Palo Alto, CA, USA) G2519F porcine gene expression microarray slides containing more than 40,000 probes were used. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer’s instructions, followed by RNAeasy column purification (Qiagen, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. Microarrays were hybridized at 65℃ for 17 h and washed with a Gene Expression Washing Buffer Kit (Agilent).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Data processing |
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
|
| |
|
| Submission date |
Jan 30, 2013 |
| Last update date |
Jan 30, 2013 |
| Contact name |
Lianqiang Che |
| E-mail(s) |
[email protected]
|
| Organization name |
Sichuan Agricultural University
|
| Street address |
Huiming Road 211,Wenjiang
|
| City |
Chengdu |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL16571 |
| Series (1) |
| GSE43917 |
Long term intake of pea fiber affects the colonic barrier, bacterial and transcriptional profile using pig as model |
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