|
| Status |
Public on May 31, 2013 |
| Title |
ProstateCancer_ETV4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Prostate cancer clinical specimen harboring suspected ETV4 rearrangement
|
| Organism |
Homo sapiens |
| Characteristics |
cancer subtype: Prostate cancer
cell line or clinical sample: clinical specimen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy mini kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
Sample labeling was performed using the Fairplay III Microarray Labeling Kit (Agilent). Briefly, 10ug of sample total RNA and 1ug of reference mRNA were differentially labeled with Cy5 and Cy3, respectively, and co-hybridized to the microarray.
|
| |
|
| Channel 2 |
| Source name |
Common mRNA reference (pooled from 11 diverse cell lines)
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Common mRNA reference (pooled from 11 diverse cell lines)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy mini kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Sample labeling was performed using the Fairplay III Microarray Labeling Kit (Agilent). Briefly, 10ug of sample total RNA and 1ug of reference mRNA were differentially labeled with Cy5 and Cy3, respectively, and co-hybridized to the microarray.
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.
|
| Scan protocol |
Microarrays were imaged using Agilent's High-Resolution C Scanner.
|
| Description |
Positive control sample 4, harbors a suspected gene fusion of ETV4, Untreated
|
| Data processing |
LOWESS normalized fluorescence ratios were extracted using Agilent Feature Extraction Software.
|
| |
|
| Submission date |
Jul 12, 2012 |
| Last update date |
May 31, 2013 |
| Contact name |
Craig Patrick Giacomini |
| E-mail(s) |
cpg17@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Pathology
|
| Lab |
Jonathan Pollack (M.D./Ph.D.) Laboratory
|
| Street address |
269 Campus Drive (CCSR 3245A)
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5176 |
| Country |
USA |
| |
|
| Platform ID |
GPL15797 |
| Series (2) |
| GSE39287 |
Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types (exon expression) |
| GSE45137 |
Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types |
|
