|
| Status |
Public on Dec 03, 2013 |
| Title |
Case 01 baseline premalignancy |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Bronchial tissue, AFB-visualized
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bronchial
gender: male
case or control: case
|
| 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 100 healthy individuals
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Pooled DNA from the blood of 100 healthy individuals
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
|
| |
|
| |
| 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_107_Sep09 protocol with default settings
|
| Description |
ch1 raw data file: MACF_251495027272_S01_CGH_107_Sep09_1_1.txt
ch2 raw data file: MACF_251495027272_S01_CGH_107_Sep09_1_3.txt
Pooled DNA from the blood of 100 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
|
| 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. We use the sex difference as an internal quality control measure to check for experiment errors.
Dual channel hybs were analysed as single channel and compared as listed above. All raw data file designations are provided in the description field, and the files are available on the Series record (to avoid duplication).
|
| |
|
| Submission date |
Mar 19, 2013 |
| Last update date |
Dec 03, 2013 |
| 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) |
| GSE45287 |
DNA copy number profiles of premalignant endobronchial lesions: a validated predictor for endobronchial cancer |
|
