|
| Status |
Public on Aug 01, 2015 |
| Title |
HT_42T_H031 rep1 |
| Sample type |
RNA |
| |
|
| Source name |
6 IU/g Vit. D supplemented_tumor
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain background: Sprague Dawley
gender: male
diet: supplemented with 6 IU/g vitamin D3(+6D)
animal model: TAA-induced rat intrahepatic cholangiocarcinoma model
tissue: tumor part
|
| Treatment protocol |
Animals were sacrificed and then tissue were dissected and immersed in liquid nitrogen. The samples were kept at -80C before RNA extraction.
|
| Growth protocol |
Animals were fed with different diet and then TAA was used to induce tumorgenesis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280>1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN>8).
|
| Label |
Cy5
|
| Label protocol |
1 µg of total RNA was reverse-transcribed and amplified using Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dyes (Amersham Pharmacia, Piscataway, NJ, USA).
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| |
|
| Hybridization protocol |
Fluorescent targets were hybridized to the Mouse Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization at 50C, non-specific binding targets were washed away by three different washing steps (Wash I: 42C 5 mins; Wash II: 42C, 5 mins, 25C 5 mins; Wash III: rinse 20 times)
|
| Scan protocol |
The arrays were scanned by GenePix 4200A 01 Autoloader (635nm power 100 PMT 320 ; 532nm power 10, PMT 335) and quantify the fluoresence intensity.
|
| Description |
42T_H031
|
| Data processing |
The signal intensity of each spot was loaded into Rosetta Resolver System® (Rosetta Biosoftware) to process data analysis. The error model of Rosetta Resolver System® could remove both systematic and random errors form the data. We filtered out spots that the flag is less than 0. Spots that passed the criteria were normalized by 50% media scaling normalization method. Normalize intensities: Median scaling performed on data set without flagged and control data. Merge technical replicate data: Average intensity values calculated on technical replicates ['avrg_data.txt' available on Series records].
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).
|
| |
|
| Submission date |
Jul 17, 2013 |
| Last update date |
Aug 01, 2015 |
| Contact name |
Chun-Nan Yeh |
| E-mail(s) |
yehchunnan@gmail.com
|
| Organization name |
Chang Gung Medical Foundation
|
| Department |
General Surgery
|
| Street address |
No.5, Fusing St.
|
| City |
Gueishan Township |
| State/province |
Taoyuan County |
| ZIP/Postal code |
333 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL13694 |
| Series (1) |
| GSE48961 |
The effect of vitamin D supplementation on tumorigenesis in a thioacetamide (TAA)-induced rat intrahepatic cholangiocarcinoma model |
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