|
| Status |
Public on Aug 02, 2011 |
| Title |
Control 08 baseline Squamous Metaplasia |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Bronchial tissue, AFB-visualized
|
| Organism |
Homo sapiens |
| Characteristics |
case number: Control 08
baseline/follow-up: baseline
disease status: Squamous Metaplasia
tissue: bronchial
gender: female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation protocol as described by van Zeeburg et al, Cancer Res 2005; 65(4):1271-1276
|
| Label |
Cy5
|
| Label protocol |
DNA labeling protocol according to Enzo Life Sciences
|
| |
|
| Channel 2 |
| Source name |
blood, pooled DNA from 19 individuals
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
gender: male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation protocol as described by van Zeeburg et al, Cancer Res 2005; 65(4):1271-1276
|
| Label |
Cy5
|
| 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 v9.5.1 (Agilent Technologies) using the Agilent CGH-v4_95 protocol with default settings
|
| Description |
Pooled DNA from the blood of 18 healthy individuals was used as reference in the aCGH experiments; across array CGH comparisons were made as described by Buffart et al, Genes, Chromosomes description = 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 |
Aug 16, 2010 |
| Last update date |
Aug 02, 2011 |
| 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 |
GPL8841 |
| Series (1) |
| GSE23644 |
DNA copy number alterations in endobronchial squamous metaplastic lesions predict lung cancer |
|
