|
| Status |
Public on Dec 08, 2016 |
| Title |
Wholebood_HP_1_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Wholebood_HP_1_rep1
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: whole blood
disease state: chronic kidney disease
|
| Treatment protocol |
A 2.5 mL sample of whole blood from PD patient was drawn directly to a PAXGene Blood miRNA Kit .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA including miRNA was isolated using the PAXgene Blood miRNA Kit (Qiagen) following the manufacturer's recommendations.
|
| Label |
Hy3
|
| Label protocol |
The first step included a Calf Intestinal Alkaline Phosphatase for removal of 5’-phosphates from terminal of the microRNAs. In the second step, a fluorescent label was attached enzymatically to the 3’-end of the microRNAs in the total RNA sample.
|
| |
|
| Hybridization protocol |
1.5 ug of Hy3-labelled cRNA (specific activity >10.0 pmol Hy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 15 hours at 56°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 2 minute at 56°C with Wash Buffer 1 (20x salt buffer 60 ml, 10% detergent solution 12 ml, nuclease-free water 528 ml), 2 minute at room temperature Wash buffer 2 (20x salt buffer 20 ml, nuclease-free water 285 ml), and 2 minute at room temperatureWash buffer C (20x salt buffer 2 ml, nuclease-free water 198 ml), then dried immediately.
|
| Scan protocol |
Slides were scanned immediately after drying on the Agilent G2565CA DNA Microarray Scanner using one color scan setting.
|
| Description |
miRNA expression in patients with high PTH
|
| Data processing |
The scanned images were analyzed with Agilent Feature Extraction software version 10.7.3.1 using default parameters to obtain background subtracted and spatially detrended processed signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Quantile normalized expression values were obtained with GeneSpring software PX 13.1.
|
| |
|
| Submission date |
Dec 07, 2016 |
| Last update date |
Dec 08, 2016 |
| Contact name |
In-Wha Kim |
| E-mail(s) |
[email protected]
|
| Organization name |
Seoul National University
|
| Department |
College of Pharmacy and Research Institute of Pharmaceutical Sciences
|
| Street address |
1 Gwanak-ro, Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17728 |
| Series (1) |
| GSE90991 |
miRNA profiles associated with adynamic bone disease |
|
