|
| Status |
Public on Dec 20, 2009 |
| Title |
benign nevus, 1 |
| Sample type |
RNA |
| |
|
| Source name |
FFPE benign nevus
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Benign nevus
|
| Treatment protocol |
Formalin-fixed paraffin-embedded (FFPE) tissues.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All samples contained at least 75% hyperplasia tissues without necrosis, which was confirmed by pathologist. The RecoverAll total RNA Isolation kit (Ambion, Streetsville, Canada) was used to extract total RNA (including miRNA) from FFPE samples.
|
| Label |
Cy3
|
| Label protocol |
100ng total RNA was dephosphorylated in the presence of calf intestine alkaline phsphatase, then a Cy3-pCp molecule was ligated to the 3' end of the RNA molecule according to Agilent miRNA protocol version 1.5.
|
| |
|
| Hybridization protocol |
Labeled RNA was hybridized to Agilent miRNA array (8 arrays per slide) at 55°C for 22h in rotisserie in a hybridization oven. Disassembled arrays were washed in GE wash buffer 1&2 for 5 minutes each.
|
| Scan protocol |
Images were scanned with Agilent scanner at 5µm resolution.
|
| Description |
JC-10
|
| Data processing |
The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate Gene View file, providing expression data for each gene probed on the array. Features interogating same miRNA were summarized together based on their weight. No interarray normalization method was employed.
|
| |
|
| Submission date |
Oct 09, 2009 |
| Last update date |
Jan 29, 2010 |
| Contact name |
Harriet Feilotter |
| Organization name |
Queen's University
|
| Department |
Pathology and molecular department
|
| Lab |
microarray facility
|
| Street address |
88 Stuart St
|
| City |
Kingston |
| State/province |
Ontario |
| ZIP/Postal code |
K7L 3N6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL9081 |
| Series (2) |
| GSE18509 |
miR-193b represses cell proliferation and regulates cyclin D1 in melanoma: benign nevi and metastatic melanoma |
| GSE18512 |
miR-193b represses cell proliferation and regulates cyclin D1 in melanoma |
|
