|
| Status |
Public on Mar 12, 2009 |
| Title |
VUMC_HNSCC_11 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
Head and Neck Squamous cell carcinoma
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen tumor samples were used for HPV analysis and for all tumor samples microdissection was performed to enrich for tumor tissue. DNA and RNA was extracted as described by Tabor et al. (Tabor M. Clin. Cancer Res., 7, 1523-1532)
|
| Label |
Cy3
|
| Label protocol |
as described by Snijders et al, Nat Genetics, volume 29, p263-4
|
| |
|
| Channel 2 |
| Source name |
Pooled reference DNA
|
| Organism |
Homo sapiens |
| Characteristics |
Pooled DNA from blood of 10 normal individuals
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen tumor samples were used for HPV analysis and for all tumor samples microdissection was performed to enrich for tumor tissue. DNA and RNA was extracted as described by Tabor et al. (Tabor M. Clin. Cancer Res., 7, 1523-1532)
|
| Label |
Cy5
|
| Label protocol |
as described by Snijders et al, Nat Genetics, volume 29, p263-4
|
| |
|
| |
| Hybridization protocol |
Hybridisations were performed as described by Snijders et al, Nat Genetics, volumn 29, p 263-4. Both pre-hybridisation and hybridisation were performed in a hybridisation station (HybStation12 - Perkin Elmer Life Sciences).
|
| Scan protocol |
Microarray Scanner G2505B (Agilent Technologies), default settings
|
| Description |
as described by S.J.Smeets et al. Oncogene 2006, 25(17):2558-64
|
| Data processing |
Spots were quantified in ImaGene 5.6.1 software using default settings. BAC clones were positioned along the genome according to the May 2004 freeze. After exclusion of flagged spots, the average of the triplicate spots was calculated for each BAC clone and 2log ratios (tumour/normal reference signal) were normalized by subtraction of the mode value of BAC clones on chromosome 1-22. BAC clones with flagged spots were excluded from analysis.
|
| |
|
| Submission date |
Jun 29, 2008 |
| Last update date |
Mar 12, 2009 |
| 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 |
GPL2843 |
| Series (2) |
| GSE11929 |
Identification of a subgroup of head and neck cancers lacking numerical chromosomal aberrations |
| GSE12020 |
Head and neck squamous cell carcinomas |
|
