|
| Status |
Public on Dec 01, 2010 |
| Title |
BreastCancer-246 (mRNA)_114Sample dataset |
| Sample type |
RNA |
| |
|
| Source name |
Breast Primary Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast
disease state: Breast Primary Tumor
breast cancer subtype: Basal
tp53 mutation status: Mut
death status: Alive
disease free survival time (months): 114.046052631579
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-246
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.
Data in Sample tables were not normalized across samples. We did a further processing of the 114 mRNA samples: RMA normalization and averaging per Gene Symbol in our analysis. See supplementary file (GSE19536_final_processed_mRNAdata.txt) on GSE19536 record.
|
| |
|
| Submission date |
Jan 13, 2010 |
| Last update date |
Apr 17, 2010 |
| Contact name |
Hilde Johnsen |
| E-mail(s) |
hilde.johnsen@rr-research.no
|
| 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) |
| GSE19536 |
Molecular Characterization of Breast Cancer Subtypes Derived from Joint Analysis of High Throughput miRNA and mRNA Data |
|
