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Sample GSM340149 Query DataSets for GSM340149
Status Public on Nov 07, 2008
Title Duodenum_swimming_n2
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.

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ILMN_1370549 39.96870
ILMN_1369537 63.01955
ILMN_1358051 45.26269
ILMN_1361746 8.96205
ILMN_1352975 -7.75591
ILMN_1368384 485.30490
ILMN_1355285 12.94350
ILMN_1376898 0.52194
ILMN_1368325 88.76498
ILMN_1353563 417.26520
ILMN_1348794 3839.23000
ILMN_1364273 10.93027
ILMN_1369433 3.36254
ILMN_1349007 184.42420
ILMN_1374156 11.71350
ILMN_1360232 -0.77876
ILMN_1355155 1414.80500
ILMN_1362563 11.45704
ILMN_1355815 11.20574
ILMN_1373215 15.02125

Total number of rows: 22523

Table truncated, full table size 490 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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