|
| Status |
Public on Oct 20, 2014 |
| Title |
adenocarcinoma 9d |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Colorectal tissue, m-FCM sorted nuclei
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Colorectal tissue, m-FCM sorted nuclei
ploidy status: diploid
gender: F
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Multiple haematoxylin-eosin stained cryostatic sections were used as references to increase the epithelian cell component. DAPI stained nuclei suspentions were prepared and measured by multiparameter FACS 440-Sorted. DNA was extracted using Archive Pure DNA kit (5 Prime), amplified with Enzo Bioscore Screening and Amplification kit and Whole Genome Amplification kit WGA2 (Sigma-Aldrich) and purified with QIAquick Purification kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
DNA labeling protocol according to Enzo Life Sciences.
|
| |
|
| Channel 2 |
| Source name |
Fresh/frozen DNA pool from different organs of non-cancer individuals
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Fresh/frozen DNA pool from different organs of non-cancer individuals
gender: M/F
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Multiple haematoxylin-eosin stained cryostatic sections were used as references to increase the epithelian cell component. DAPI stained nuclei suspentions were prepared and measured by multiparameter FACS 440-Sorted. DNA was extracted using Archive Pure DNA kit (5 Prime), amplified with Enzo Bioscore Screening and Amplification kit and Whole Genome Amplification kit WGA2 (Sigma-Aldrich) and purified with QIAquick Purification kit (Qiagen).
|
| Label |
Cy3
|
| 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 G2505B micro-array scanner. Image data acquisition was performed in feature extraction software v10.5 (Agilent Technologies) using the Agilent CGH-105_Dec08 protocol with default settings
|
| Description |
Pooled DNA (fresh/frozen) of different organs of non-cancer individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes & Cancer 2008, 47(11): 994-1004
|
| Data processing |
Median Signal intensity minus median Background intensity; excluding negative values. To overcome potential wave bias due to differences in GC-content of the different chromosomal regions, a smoothing algorithm was applied on our dataset as described by van de Wiel et al, Bioinformatics 2009; 25(9):1099-1104.
|
| |
|
| Submission date |
May 21, 2013 |
| Last update date |
Oct 20, 2014 |
| Contact name |
Daoud Sie |
| E-mail(s) |
d.sie@vumc.nl
|
| 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 (1) |
| GSE47148 |
Chromosome 20 Aberrations at the Diploid-Aneuploid Transition in Sporadic Colorectal Cancer |
|
