|
| Status |
Public on Oct 04, 2012 |
| Title |
flat adenoma 66 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Colorectal tissue, macrodissected [test]
|
| Organism |
Homo sapiens |
| Characteristics |
gender: M
paris classification: IIc
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Laser capture microdissection was performed on haematoxylin stained tissue section to obtain the dysplastic cells. Tissues were incubated overnight 37°C in 1M NaSCN. Subsequently, samples were treated with proteinase K for 5 days. DNA was extracted using the DNA Qiagen micro kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
DNA labeling protocol according to Enzo Life Sciences.
|
| |
|
| Channel 2 |
| Source name |
FFPE colon DNA pool from healthy individuals [reference]
|
| Organism |
Homo sapiens |
| Characteristics |
gender: M
reference description: Pooled DNA (FFPE) of 10 healthy 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
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Laser capture microdissection was performed on haematoxylin stained tissue section to obtain the dysplastic cells. Tissues were incubated overnight 37°C in 1M NaSCN. Subsequently, samples were treated with proteinase K for 5 days. DNA was extracted using the DNA Qiagen micro 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 |
raw data ch1: US22502676_252252210153_S01_CGH_105_Dec08_1_2.txt
raw data ch2: US22502676_252252210153_S01_CGH_105_Dec08_1_1.txt
FLAT_ADE_66
|
| 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 |
Jul 07, 2011 |
| Last update date |
Oct 04, 2012 |
| 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 (1) |
| GSE30479 |
DNA copy number changes in colorectal flat adenomas |
|
