|
| Status |
Public on Nov 07, 2008 |
| Title |
Duodenum_swimming_n1 |
| Sample type |
RNA |
| |
|
| Source name |
Duodenum_swim
|
| Organism |
Rattus norvegicus |
| Characteristics |
SEX: Female
STRAIN: Sprague Dawley
AGE: 9 weeks
|
| Biomaterial provider |
National Laboratory Animal Center, Salaya Campus, Mahidol University, Nakhon Pathom, Thailand
|
| Treatment protocol |
Rats were randomly divided into 2 groups, control and swimming groups. Swimming exercise group was assigned to perform endurance swimming for 2 weeks. Swimming rats were initially trained for a week until they could swim non stop 1 hour/day. Swimming frequency was 5 days/week. The age-matched control remained sedentary for 2 weeks in a swimming pool. The water temperature was maintained at 30-32°C. After exercise, rats were dried with a towel and hair dryer.
|
| Growth protocol |
Eight-week-old female Sprague-Dawley rats were housed in the laboratory animal husbandry unit for a week prior to the experiment under 12:12 h dark-light cycle and were fed regular pellets and distilled water ad libitum. The room had a temperature of 20-25°C and humidity of 50-60%. This study has been approved by the Institutional Animal Care and Use Committee (IACUC) of the Faculty of Science, Mahidol University, Thailand.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10-cm duodenal segments of rats were removed and cut longitudinally along the radix mesenterii to expose the mucosa. Intestinal epithelial cells were collected by scraping the mucosal surface with an ice-cold glass slide.
|
| Label |
Biotin
|
| Label protocol |
Total RNA was reverse transcribed to synthesize first and second strand cDNA. After cDNA purification, it was used for in vitro transcription to synthesize biotinylated cRNA according to Illumina TotalPrep RNA Amplification Kit's instruction (Illumina)
|
| |
|
| Hybridization protocol |
Beadchips were hybridized at 58°C for 20 hours. After washing, they were blocked non-specific binding with blocking buffer at room temperature for 10 min. Hybridization was detected by incubating with 2 mL blocking buffer containing streptavidin-Cy3 for 10 min. Hybridization reagents and protocol were used according to IntelliHyb Seal's instruction (Illumina)
|
| Scan protocol |
BeadStation 500GX Genetic Analysis System is used to scan the fluorescent signals at the dual laser excitation of 532 nm and 635 nm, and emission spectrum of 550-600 nm and 650-700 nm. Image registration and data extraction are automatic.
|
| Description |
Each array probes 21,910 genes and contains 22,523 oligonucleotide probes (50-bases gene-specific probe and 29-bases address sequence per probe), which were selected from the National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database release 16.
|
| Data processing |
The Illumina’s Cubic-Spline normalization algorithm was applied to adjust sample signals to minimize the effects of variation arising from non-biological factors. Comparisons between samples from control and CMA rats were done with the t-test differential expression algorithm.
|
| |
|
| Submission date |
Nov 06, 2008 |
| Last update date |
Nov 06, 2008 |
| Contact name |
Narattaphol Charoenphandhu |
| Organization name |
Faculty of Science, Mahidol University
|
| Department |
Department of Physiology
|
| Lab |
Consortium for Calcium and Bone Research
|
| Street address |
Rama 6 Rd, Rachthevee
|
| City |
Bangkok |
| ZIP/Postal code |
10400 |
| Country |
Thailand |
| |
|
| Platform ID |
GPL6101 |
| Series (1) |
| GSE13499 |
Transcriptome responses of duodenal epithelial cells to endurance swimming in female rats. |
|
