|
| Status |
Public on Dec 01, 2010 |
| Title |
BreastCancer-539 (mRNA)_115Sample dataset |
| Sample type |
RNA |
| |
|
| Source name |
Breast Primary Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast
disease state: Breast Primary Tumor
breast cancer subtype: Normal-like
tp53 mutation status: WT
death status: Alive
disease free survival time (months): 102.072368421053
estrogen receptor status: Negative
her2 (fish) status: Negative
|
| Treatment protocol |
fresh frozen in liquid nitrogen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol, following manufactors protocol
|
| Label |
Cy3
|
| Label protocol |
Agilent One-Color Microarray-Based Gene Expression Analysis, Protocol 5.5
|
| |
|
| Hybridization protocol |
Agilent One-Color Microarray-Based Gene Expression Analysis, Protocol 5.5
|
| Scan protocol |
Scanning on Agilent scanner G2565A.
|
| Description |
BC-M-539
This breast tumor sample has previously been assayed in Series GSE3985.
|
| Data processing |
Feature Extraction (FE) v9.5.3.1 was used to extract signals. Data were log2 transformed, non-uniform spots were excluded, and when averaging replicated probes, population outliers were excluded. Probes that are missing on more than 10 arrays were excluded.
Quantile normalization done in R using normalizeBetweenArrays from the limma library. Missing values imputed using LLS imputation (R: LLSimpute from the pcaMethod library with k=20).
|
| |
|
| Submission date |
Jan 13, 2010 |
| Last update date |
Apr 17, 2010 |
| Contact name |
Hilde Johnsen |
| E-mail(s) |
[email protected]
|
| Phone |
004722934421
|
| Fax |
004722934440
|
| Organization name |
Norwegian Radium Hospital
|
| Department |
Genetics
|
| Street address |
Montebello
|
| City |
Oslo |
| ZIP/Postal code |
0310 |
| Country |
Norway |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE19783 |
Molecular Characterization of Breast Cancer Subtypes from Joint Analysis of High Throughput miRNA and mRNA Data (II) |
|
