|
| Status |
Public on Jul 22, 2011 |
| Title |
Benign Breast Core_037_Baseline_Placebo |
| Sample type |
RNA |
| |
|
| Source name |
Benign Breast Core,Baseline,Placebo
|
| Organism |
Homo sapiens |
| Characteristics |
subjectid: 037
tissue: Benign Breast Core
time: Baseline
treatment: Placebo
menopausal_status: POST
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from snap frozen breast tissue core samples (Qiazol and the RNeasy Micro Kit, Qiagen) and amplified once, (TargetAmp Biotin-aRNA Amplification Kit, Epicentre Biotechnologies).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
1888857166_E
|
| Data processing |
Analysis was performed using GeneSpring 11.0.1 as follows. Flags were set to present for entities with detection P-values < 0.2 and absent for entities with detection P-values > 0.4. Raw signal values < 1 were reset to 1. Quantile normalization was used and baseline transformation performed based on the median expression level for all entities. Matrix non-normalized is average raw intensity; Matrix normalized is thresholded, median transformed, and quantile normalized mean intensity. The microdissected lobule data was normalized and processed independent of the whole breast tissue core data.
|
| |
|
| Submission date |
May 17, 2011 |
| Last update date |
Jul 22, 2011 |
| Contact name |
David Euhus |
| E-mail(s) |
david.euhus@utsouthwestern.edu
|
| Phone |
214-648-6467
|
| Fax |
214-648-7965
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Surgery
|
| Street address |
5323 Harrry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9155 |
| Country |
USA |
| |
|
| Platform ID |
GPL13376 |
| Series (1) |
| GSE29338 |
Benign Breast Cores from Healthy Women Treated with Tamoxifen or Placebo |
|
