|
| Status |
Public on Jun 17, 2015 |
| Title |
normal5 |
| Sample type |
RNA |
| |
|
| Source name |
normal control
|
| Organism |
Homo sapiens |
| Characteristics |
subject gender: female
subject group: healthy control
tissue: urine
|
| Treatment protocol |
urine was collected and directly stored -80℃.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The mirVana miRNA isolation kit (Ambion Inc, Austin, TX) was used for theextraction of total RNA from urine according to the manufacturer’s protocol. For each subject, 400 uL of urine was used for miRNA extraction.
|
| Label |
cy3-pCp
|
| Label protocol |
Microarray experiments were conducted according to the manufacturer's instructions. Briefly, the miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (100 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays. Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.
|
| |
|
| Hybridization protocol |
Equilibrate water bath or heat block to 100°C. Resuspend the dried sample in 17 μL of nuclease-free water when the Spike-In solution is used and 18 μL. Add 1.0 μL of the Hyb Spike-In solution (3rd Dilution) to each sample.Add 4.5 μL of the 10X GE Blocking Agent to each sample.Add 22.5 μL of 2X Hi-RPM Hybridization Buffer to each sample for a total of 45 μL.Mix well but gently on a vortex mixer. hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting for 1x44k 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
N5
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software (V.10.7) (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Pleaes note that the complete data matrix including control probesets (2,028 data rows) is linked to Series records.
|
| |
|
| Submission date |
Jun 16, 2014 |
| Last update date |
Jun 17, 2015 |
| Contact name |
Jun Zhou |
| Organization name |
urine
|
| Department |
Central South University
|
| Lab |
Pathology
|
| Street address |
172 Tongzipo Road
|
| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410011 |
| Country |
China |
| |
|
| Platform ID |
GPL18402 |
| Series (1) |
| GSE58517 |
Detection of urinary microRNAs from epithelial ovarian cancer patients as biomarker |
|
