|
| Status |
Public on Apr 19, 2013 |
| Title |
163T_mRNA |
| Sample type |
RNA |
| |
|
| Source name |
Breast tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast
status: primary triple negative cancer
gender: Female
age at diagnosis: 45
best stage: 2A
grade: 4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from FFPE tissue using Recover ALL kit (Ambion)
|
| Label |
n/a
|
| Label protocol |
RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol by the Ohio State Microarray Core Facility
|
| |
|
| Hybridization protocol |
RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.
|
| Scan protocol |
Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.
|
| Data processing |
Data were collected as NanoString RCC files and provided as an Excel spreadsheet. The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using quantile normalization.
Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system.
|
| |
|
| Submission date |
Nov 19, 2012 |
| Last update date |
Apr 19, 2013 |
| Contact name |
Luciano Cascione |
| E-mail(s) |
luciano.cascione@ior.usi.ch
|
| Organization name |
IOR
|
| Department |
Lymphoma & Genomics Research Program
|
| Street address |
Via Chiesa 5
|
| City |
Bellinzona |
| State/province |
Ticino |
| ZIP/Postal code |
6500 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL16299 |
| Series (2) |
| GSE41970 |
Integrated microRNA and mRNA Signatures Associated with Survival in Triple Negative Breast Cancer |
| GSE45498 |
Integrated microRNA and mRNA Signatures Associated with Survival in Triple Negative Breast Cancer II |
|
