|
| Status |
Public on Jul 01, 2011 |
| Title |
patient6_OXFU_138 |
| Sample type |
RNA |
| |
|
| Source name |
primary breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary breast cancer
treatment: 0
age at operation: 55
menopause status: post
histology: infiltrating ductal
tumor size: 3
histological grade: 3
genomic grade: 1
estrogen receptor status: 1
nodal status: 0
rfs status: 0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from tumor cryostat sections using the Trizol method according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
7.5 µg total RNA was labeled with Cy3 dye using the miRVana labeling kit according to the manufacturer's instructions (Ambion).
|
| |
|
| Hybridization protocol |
Hybridization on mirVana miRNA Bioarrays V2 were performed according to the manufacturer’s recommendations (Ambion).
|
| Scan protocol |
Hybridization signals were detected at 532 nm using a GenePix 4000B scanner and quantified by GenePix Pro 4.0 software.
|
| Description |
MiRNA labeling and hybridization on mirVana miRNA Bioarrays V2 were performed according to the manufacturer’s recommendations using 7.5 µg of total RNA and the mirVana miRNA labeling kit.
|
| Data processing |
The signal intensity of each spot was calculated by subtracting the local background from the mean signal. After averaging replicate spots, a global scaling normalization was applied, as suggested by Ambion. This normalization consisted of the following steps: 1) thresholding, for which intensities below the background (set to 2 times the signal of empty spots) were set to 1; 2) scaling, which involved ranking the intensities of each sample separately and dividing them by the 30th intensity value; and 3) log 2 transformation. The normalized intensities were used for further analyses.
|
| |
|
| Submission date |
Apr 01, 2011 |
| Last update date |
Jul 01, 2011 |
| Contact name |
Françoise Rothé |
| Organization name |
Jules Bordet Institute
|
| Lab |
Breast cancer translational research laboratory
|
| Street address |
boulevard de waterloo 127
|
| City |
brussels |
| ZIP/Postal code |
1000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL5106 |
| Series (1) |
| GSE28321 |
Global MicroRNA Expression Profiling Identifies MiR-210 Associated with Tumor Proliferation, Invasion and Poor Clinical Outcome in Breast Cancer |
|
