|
| Status |
Public on Apr 10, 2011 |
| Title |
C28 |
| Sample type |
RNA |
| |
|
| Source name |
colon
|
| Organism |
Homo sapiens |
| Characteristics |
localization: proximal
gender: female
relapse: yes
microsatellite status: MSS
age at diagnosis, years: 60
grading: G2
pt: 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For microarray analyses, snap frozen tissue specimens were cut into 7 µm-thick sections that were stained with haematoxylin & eosin (H&E). Stained sections were reviewed by a pathologist to identify areas of vital tumor cells and to ensure a tumor content of 80-90%. Corresponding tumor areas were macrodissected by vertical 3 mm incision into the frozen tissue specimens with a sterile blade. Incision was followed by a series of ten 20 μm frozen sections. Separated tumor areas were harvested by sterile micropipette tip and collected in a buffer (RLT buffer, RNeasy Mini Kit; Qiagen, Hilden, Germany). Each series of ten sections was followed by a 7 µm H&E stained section to control tissue composition. The number of tissue sections used to extract RNA was dependent on the expanse of the area of individual tumor tissue. Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions and quantified using the Nanodrop ND-1000 UV-vis spectrophotometer (Nanodrop Technologies, USA). The quality of the RNA was controlled using the BioAnalyzer (Agilent Technologies, USA) and exclusively high quality RNA was used for further analysis.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3ug total RNA
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2.0 arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Scanner G3000
|
| Description |
none
|
| Data processing |
Data were normalized with VSN (Bioconductor package vsn 3.2.1) and summarized with the median polish method. Data analysis and statistical computing were performed with R (2.6.0).
|
| |
|
| Submission date |
Sep 11, 2009 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Dido Lenze |
| E-mail(s) |
[email protected]
|
| Organization name |
Charité-Universitätsmedizin Berlin
|
| Department |
Pathologie, Campus Benjamin Franklin
|
| Street address |
Hindenburgdamm 30
|
| City |
Berlin |
| ZIP/Postal code |
12200 |
| Country |
Germany |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE18088 |
Correlation of molecular profiles and clinical outcome of stage UICC II colon cancer patients |
|
| Relations |
| Reanalyzed by |
GSE119087 |
