|
| Status |
Public on Sep 30, 2013 |
| Title |
miRNA-tumour-P49_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
frozen_breast_tumour
|
| Organism |
Homo sapiens |
| Characteristics |
pam50 subtype assignment: PAM50_Basal
patient id: P49
path. review % of tumour cells: NA
ihc_pr: 0
ihc_er: 0
ihc_her2: 0
node positive: TRUE
grade: 3
traditional histological type: NST
diag_tumour_size: 3.2
mets_dd_after_diagnosis: NA
death_dd_after_diagnosis: NA
mets_count: 0
cause_of_death: NA
age_at_diagnosis: 50
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction from fresh-frozen samples was performed after tissue homogenization with Qiagen miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) completed with optional on-column DNase digestion carried out by RNase-Free DNase Set (Qiagen GmbH).
|
| Label |
Cy3
|
| Label protocol |
Total RNA was dephosphorylated, denaturated and Cyanine3-pCp ligated according to the manufacturer’s instructions using miRNA Complete Labeling and Hyb Kit (Agilent Tech. Inc.).
|
| |
|
| Hybridization protocol |
Samples were hybridized to Agilent Human miRNA Microarray Rel12.0 (Agilent Tech. Inc.) at 55oC, for 20 hours according to the manufacturer’s instructions.
|
| Scan protocol |
After washing microarray slides array scanning was performed by Agilent DNA Microarray Scanner G2565BA (Agilent Tech. Inc.).
|
| Data processing |
Feature extraction and data processing was performed with default scenario for Agilent Human MiRNA Microarray Rel12.0 by Feature Extraction Software 9.5.3 (Agilent Tech. Inc.) to calculate gProcessed signal. miRNA data were then post-processed using the AgiMicroRna (www.aroma-project.org) R package. Quality of individual arrays was assessed by visual evaluation of RLE (relative log expression), NUSE (normalised unscaled standard error) and hierarchical clustering plots. Robust Multichip Analysis (RMA) methodology was used to remove the array signal background, followed by quantile normalisation to correct for inter-arrays global differences and by miRNA level summarisation. miRNAs not detected or having saturated signal in more than 10 samples were filtered out. Replicated samples for the same patient were averaged.
|
| |
|
| Submission date |
Aug 21, 2012 |
| Last update date |
Feb 27, 2014 |
| Contact name |
Emanuele de Rinaldis |
| E-mail(s) |
emanuele_derinaldis@merck.com
|
| Organization name |
IRBM (MERCK)
|
| Street address |
Via Pontina
|
| City |
Pomezia(Rome) |
| ZIP/Postal code |
00100 |
| Country |
Italy |
| |
|
| Platform ID |
GPL10850 |
| Series (1) |
| GSE40267 |
miRNA analysis of triple-negative breast cancers in association with clinical and molecular phenotypes |
|
