|
| Status |
Public on Aug 13, 2010 |
| Title |
Tissue_BC_Tamoxifen_680 |
| Sample type |
RNA |
| |
|
| Source name |
tissue from breast tumor excision
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: 680
profiling lab: JBI
tissue: breast cancer
estrogen receptor (er) status: ER+
endocrine therapy: Tamoxifen treatment for 5 years
nodal status (0=negative, 1=positive, na=not applicable): 1
distant relapse (1=dr, 0 censored): 1
event time (years): 6.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from fresh frozen tissue specimens from breast cancer patients using Qiagen RNeasy columns.
|
| Label |
biotin
|
| Label protocol |
A single-round of T7 amplification was used to generate biotin-labeled cRNA for hybridization. At least 1 ug of RNA was used for cRNA synthesis.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A or Plus2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX (MDA) or 3000 (JBI).
|
| Description |
680.CEL
|
| Data processing |
Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html). MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 1322 breast cancer specific genes.
|
| |
|
| Submission date |
Aug 18, 2009 |
| Last update date |
Sep 06, 2013 |
| Contact name |
Christos Hatzis |
| E-mail(s) |
[email protected]
|
| Phone |
781-938-3830
|
| URL |
http://www.nuverabio.com
|
| Organization name |
Nuvera Biosciences
|
| Street address |
400 West Cummings Park, Suite 5350
|
| City |
Woburn |
| State/province |
MA |
| ZIP/Postal code |
01801 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE17705 |
Endocrine Sensitivity Index Validation Dataset |
|
| Relations |
| Reanalyzed by |
GSE50564 |
