|
Status |
Public on Oct 04, 2012 |
Title |
flat adenoma 120 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
Colorectal tissue, macrodissected [test]
|
Organism |
Homo sapiens |
Characteristics |
gender: M paris classification: IIa
|
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.
|
|
|
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_252252210213_S01_CGH_105_Dec08_1_3.txt raw data ch2: US22502676_252252210055_S01_CGH_105_Dec08_1_1.txt FLAT_ADE_120
|
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.
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|
|
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 |
|