|
| Status |
Public on May 30, 2013 |
| Title |
Striatum_GHD-1 (reps 1 and 2) |
| Sample type |
RNA |
| |
|
| Source name |
GHD striatum
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Striatum
age: 12 months
gender: Male
strain: FVB
genotype/variation: HD transgenic
|
| Treatment protocol |
The HD transgenic mouse line carried GFP gene fused with exon 1 of the human HTT gene with 84 CAG trinucleotide repeats, and transgene was driven by a human ubiquitin promoter. The HD transgenic mouse line overexpressing miR-196a were obtained by breeding HD transgenic mice with miR-196a mice, which carry percusior miR-196a driven by a human ubiquitin promoter.
|
| Growth protocol |
Mice were matained at National Cheng Kung University, Tainan, Taiwan(ROC) with approvement of the Institutional Animal Care and Use Committees. Under constant environment (22°C; 12-h light/dark cycle), the mice were fed with tap water and standard laboratory chow ad libitum.
|
| 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 50 ℃, non-specific binding targets were washed away by three different washing steps (WashⅠ 42 ℃ 5 mins；Wash Ⅱ 42 ℃, 5 mins, 25 ℃ 5 mins; Wash Ⅲ rinse 20 times)
|
| Scan protocol |
The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 500 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.
|
| Description |
This mice showed weak motor functions of HD.
G1_1
G1_2
|
| 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.
Calculate average ratios of the hybridization replicates and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).
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| |
|
| Submission date |
May 30, 2013 |
| Last update date |
May 30, 2013 |
| Contact name |
Shang-Hsun Yang |
| Organization name |
National Cheng-Kung University
|
| Department |
Department of Physiology, College of Medicine; Institute of Basic Medical Sciences
|
| Lab |
-- None selected --
|
| Street address |
70101
|
| City |
Tainan |
| ZIP/Postal code |
70101 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL13692 |
| Series (1) |
| GSE47500 |
Expression of miR-196a in Huntington's disease transgenic (HD) mice |
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