|
| Status |
Public on Nov 05, 2011 |
| Title |
col096 |
| Sample type |
RNA |
| |
|
| Source name |
Primary tumor resection
|
| Organism |
Homo sapiens |
| Characteristics |
disease status: AJCC stage II CRC
tissue: primary tumor resection
age at diagnosis: 61,91
Sex: m
meta or recurrence within 3 years: no
time to meta or recurrence: 1147
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
|
| Label |
biotin
|
| Label protocol |
RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
|
| |
|
| Hybridization protocol |
10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
|
| Scan protocol |
Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol
|
| Description |
COL096.CEL
|
| Data processing |
Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix)
|
| |
|
| Submission date |
Oct 20, 2011 |
| Last update date |
Mar 18, 2013 |
| Contact name |
Richard Volckmann |
| E-mail(s) |
r.volckmann@amsterdamumc.nl
|
| Organization name |
Academic Medical Centre, University of Amsterdam
|
| Department |
Department of Oncogenomics
|
| Street address |
P.O. Box 22700
|
| City |
Amsterdam |
| ZIP/Postal code |
1100DE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE33113 |
AMC colon cancer AJCCII |
| GSE33114 |
Methylation of Cancer Stem Cell-associated Wnt target genes predicts poor prognosis in colorectal cancer patients |
|
