|
| Status |
Public on Nov 14, 2014 |
| Title |
Colorectal cancer tissue sample (FFPE) 84 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
colorectal cancer, CAIRO arm B
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colorectal cancer (FFPE)
study: CAIRO
study arm: B
progression-free survival first line (days): 29
progression: yes
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Brosens et al., J Pathol. 2010 (PMID 20593488).
|
| Label |
Cy3
|
| Label protocol |
DNA labeling protocol according to Enzo Life Sciences.
|
| |
|
| Channel 2 |
| Source name |
normal colorectum mucosa
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: normal colon mucosa
patient: same patient as in ch1
sample type: reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Brosens et al., J Pathol. 2010 (PMID 20593488).
|
| Label |
Cy5
|
| Label protocol |
DNA labeling protocol according to Enzo Life Sciences.
|
| |
|
| |
| Hybridization protocol |
Hybridization protocol available via www.agilent.com.
|
| Scan protocol |
Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.
|
| Description |
CAIRO arm B: capecitabine and irinotecan first line
Normal colon mucosa from the same patient as the tumor was used as reference in the aCGH experiments.
|
| Data processing |
The profiles were dewaved (van de wiel et al., Bioinformatics. 2009 (PMID 19276148)), median normalized and corrected for tumor cell percentage by using the R package CGHcall (van de Wiel et al., Bioinformatics. 2007 (PMID 17267432)).
|
| |
|
| Submission date |
Mar 27, 2012 |
| Last update date |
Nov 14, 2014 |
| Contact name |
Daoud Sie |
| E-mail(s) |
[email protected]
|
| Phone |
+31 20 4442428
|
| Organization name |
Vrije Universiteit Medical Center
|
| Department |
Pathology
|
| Lab |
Microarray Core Facility
|
| Street address |
De Boelelaan 1117
|
| City |
Amsterdam |
| ZIP/Postal code |
1081 HV |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL8687 |
| Series (2) |
| GSE36864 |
Genomic landscape of metastatic colorectal cancer |
| GSE63216 |
Recurrent breakpoint genes in colorectal cancer |
|
| Relations |
| Reanalyzed by |
GSM943166 |
