|
| Status |
Public on Nov 01, 2012 |
| Title |
Colorectal cancer CRC10 [aCGH] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
colorectal carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
age: 87
crc location: Rectum-Ca
ms status: microsatellite stable (MSS)
kras- and braf mutational status: KRAS-mut; BRAF-wt
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Colorectal cancer samples were collected from 17 patients who underwent colon resection for biopsy-proven invasive colorectal adenocarcinoma at the University of Regensburg. The study was performed in agreement with the Institutional ethical review board of the University of Regensburg (05/003). DNA from frozen colon tissues was isolated using the PUREGENE™ DNA Purification Kit (Gentra, Minneapolis, USA) according to the supplier’s recommendation.
Human peripheral blood monocytes were separated by leukapheresis of healthy donors followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge (Beckman Instruments) or by magnetic bead separation from buffy coats of healthy donors using CD14 antibodies. DNA from monocytes was prepared using Qiagen Blood & Cell Culture DNA Kit. Leukapharesis was performed in agreement with the Institutional ethical review board of the University of Regensburg.
|
| Label |
Cy 5–dUTP
|
| Label protocol |
Genome-wide analysis of unbalanced chromosomal changes was done by microarray-based Comparative Genomic Hybridization (aCGH). CRC DNA (1 µg) as well as normal reference DNA (mixed normal human monocytes, 1 µg) were labelled using the Genomic DNA Enzymatic Labeling Kit (Agilent)
|
| |
|
| Channel 2 |
| Source name |
normal monocyte
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male
sample: normal monocytes; mixture of six donors
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Colorectal cancer samples were collected from 17 patients who underwent colon resection for biopsy-proven invasive colorectal adenocarcinoma at the University of Regensburg. The study was performed in agreement with the Institutional ethical review board of the University of Regensburg (05/003). DNA from frozen colon tissues was isolated using the PUREGENE™ DNA Purification Kit (Gentra, Minneapolis, USA) according to the supplier’s recommendation.
Human peripheral blood monocytes were separated by leukapheresis of healthy donors followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge (Beckman Instruments) or by magnetic bead separation from buffy coats of healthy donors using CD14 antibodies. DNA from monocytes was prepared using Qiagen Blood & Cell Culture DNA Kit. Leukapharesis was performed in agreement with the Institutional ethical review board of the University of Regensburg.
|
| Label |
Cy 3–dUTP
|
| Label protocol |
Genome-wide analysis of unbalanced chromosomal changes was done by microarray-based Comparative Genomic Hybridization (aCGH). CRC DNA (1 µg) as well as normal reference DNA (mixed normal human monocytes, 1 µg) were labelled using the Genomic DNA Enzymatic Labeling Kit (Agilent)
|
| |
|
| |
| Hybridization protocol |
Labelled samples were hybridized on Human 4x180K CGH SurePrint G3 Microarrays (Agilent, GPL10123) according to the manufacturer’s instructions.
|
| Scan protocol |
Images were scanned after washing using a DNA microarray scanner (Agilent)
|
| Description |
Comparative genomic hybridization of CRC DNA samples against a common reference
|
| Data processing |
Image data was processed using Feature Extraction Software 10 (Agilent) and analyzed using Agilent Genomic Workbench
|
| |
|
| Submission date |
Nov 09, 2010 |
| Last update date |
Nov 01, 2012 |
| Contact name |
Michael Rehli |
| E-mail(s) |
michael.rehli@klinik.uni-r.de
|
| Organization name |
University Hospital Regensburg
|
| Department |
Internal Med III
|
| Street address |
F.-J.-Strauss-Allee 11
|
| City |
Regensburg |
| ZIP/Postal code |
93042 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10123 |
| Series (2) |
| GSE25228 |
Chromosomal abnormalities in colorectal cancer |
| GSE25229 |
Genome-wide analysis of unbalanced chromosomal changes in colorectal carcinoma |
|
