|
| Status |
Public on Jul 23, 2008 |
| Title |
Breast tumor sample (test) 13 |
| Sample type |
RNA |
| |
|
| Source name |
breast cancer sample
|
| Organism |
Homo sapiens |
| Characteristics |
Tissue: breast
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Synthesis of biotin-labeled cRNA from cDNA was performed using the GeneChip Expression 3’ Amplification Reagents IVT labelling kit (Affymetrix, Inc., Santa Clara, CA) at 37oC for 16 hours. Total RNA clean-up was performed using the Qiagen RNeasy kit (Qiagen, Inc., Valenica, CA) prior to synthesis of double stranded cDNA.
|
| |
|
| Hybridization protocol |
The biotin- labelled cRNA (20 µg) was fragmented at 94oC for 60 min to generate 50 to 200-base fragments. Following fragmentation, Array was hydrated with water and incubated at 65oC for 10 min prior to priming with pre-hybridization solution at 45oC for 30 min. Biotin-labelled fragmented cRNAs (5 µg, 50 ng/µl) were hybridized to the array and incubated at 45oC for 16 hours with gentle rotation.
|
| Scan protocol |
GeneChips were scanned using the GenePix 4000B scanner
|
| Description |
Gene expression data from breast cancer (test set)
|
| Data processing |
The data were analyzed with Microarray Imager software and customized program.
The related GPL5022 Platform includes only ~200 gene signatures, which vary from sample to sample in breast cancer. In other words, these samples are supposed to show various median expression levels based on the small scale of 200 genes. For this reason, control genes are used for normalization, rather than global normalization.
|
| |
|
| Submission date |
Apr 02, 2007 |
| Last update date |
Jul 22, 2008 |
| Contact name |
Kun Yu |
| E-mail(s) |
yukun@omniarray.com
|
| Phone |
+65 64368390
|
| Organization name |
National Cancer Centre
|
| Department |
Cellular & Molecular Research
|
| Street address |
|
| City |
Singapore |
| ZIP/Postal code |
169610 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL5022 |
| Series (1) |
| GSE7422 |
Clinical validation of a customized multiple signature microarray for breast cancer |
|
