|
| Status |
Public on Feb 26, 2010 |
| Title |
case 12 microRNA |
| Sample type |
RNA |
| |
|
| Source name |
GCT patient case
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary intracranial pediatric germ cell tumor (GCT)
diagnosis: yolk sac tumor + germinoma
age: 14.5 years
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/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 to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 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 DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
miRNA expression data from CNS GCT patient
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (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.
|
| |
|
| Submission date |
Dec 07, 2009 |
| Last update date |
Feb 26, 2010 |
| Contact name |
Yu Hsuan Wu |
| E-mail(s) |
[email protected]
|
| Organization name |
National Yang-Ming University
|
| Street address |
No.155, Sec.2, Linong Street
|
| City |
Taipei |
| ZIP/Postal code |
112 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL8227 |
| Series (2) |
| GSE19347 |
microRNA expression data from pediatric primary intracranial germ cell tumor |
| GSE19350 |
Array-based bioinformatic analysis on pediatric primary central nervous system germ cell tumors |
|
