|
| Status |
Public on Dec 10, 2007 |
| Title |
53A;pretreatment;female;breast tumor; nonresponder |
| Sample type |
RNA |
| |
|
| Source name |
53A;pretreatment;female;breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
53A;pretreatment;female;breast tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Biopsies were snap-frozen after collection and stored in liquid nitrogen. Frozen sections were taken prior to RNA extraction to confirm the presence of cancerous tissue within the specimens. Only samples in which the malignant component comprised at least 20% of the section area were used in further analyses. Immediately before RNA extraction the biopsies were pulverised using U2 micro-dismembranator U (Braun Biotech). Total RNA was extracted from the resultant frozen tissue powder using TRI-reagent (Sigma) according to the manufacturer's recommendations. Extracted RNA was additionally purified on RNeasy mini columns (Qiagen). RNA quantity and quality was verified on Bioanalyser 2100 (Agilent).
|
| Label |
biotin
|
| Label protocol |
Approximately 500 ng of total RNA was processed to produce biotinylated cRNA targets using protocol described in Biotechniques. 2003 Mar;34(3):546-50, 552-4, 556
|
| |
|
| Hybridization protocol |
standard Affymetrix procedures except for use of a custom 24-channel fluidics machine and GCS2500 scanner
|
| Scan protocol |
standard Affymetrix procedures
|
| Description |
breast tumor biopsy
|
| Data processing |
MAS5
|
| |
|
| Submission date |
Aug 04, 2006 |
| Last update date |
Oct 13, 2010 |
| Contact name |
John R Walker |
| E-mail(s) |
jwalker@gnf.org
|
| Phone |
858-812-1636
|
| Organization name |
Genomics Institute of the Novartis Research Foundation
|
| Lab |
Genetics Core
|
| Street address |
10675 John Jay Hopkins
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92121 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (2) |
| GSE5462 |
Letrozole (Femara) early response to treatment |
| GSE20181 |
Letrozole (Femara) early and late responses to treatment |
|
