|
| Status |
Public on Oct 20, 2008 |
| Title |
Uvula normal squamous epithelium of the uvula VUMC_uvula1_b7_s |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
uvula
|
| Organism |
Homo sapiens |
| Characteristics |
normal squamous epithelium of the uvula
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol according to manufacturers' instructions
|
| Label |
Cy3
|
| Label protocol |
cDNA was prepared from 15 micrograms of total RNA using oligo-dT20-VN primer (Invitrogen) and coupled to Cy3 by enzymatic labelling with dUTP-Cy3
|
| |
|
| Channel 2 |
| Source name |
universal human reference RNA (Stratagene)
|
| Organism |
Homo sapiens |
| Characteristics |
Pooled RNA of 10 cell lines giving broad gene coverage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
see www.stratagene.com
|
| Label |
Cy5
|
| Label protocol |
as ch1, Cy5 in stead of Cy3
|
| |
|
| |
| Hybridization protocol |
Slides were pre-hybridised for 45 minutes at 37°C with a pre-hybridisation solution containing 30 micrograms of salmon sperm DNA (Gibco), 12 micrograms of poly A (Pharmacia), 60 micrograms of yeast tRNA (Sigma) and 24 micrograms of Cot-1 DNA (Invitrogen) dissolved in 127 microliter hybridisation mix (0.2% SDS, 8% glycerol, 50% formamide and 0.1% dextrane sulphate in 2x SSC). Pre-hybridisation was followed by probe hybridisation for 14 hours at 37°C. Both pre-hybridisation and hybridisation were performed in HybStation 12 (Perkin Elmer Life Sciences)
|
| Scan protocol |
as described by Buermans et al, Physiol Genomics, volume 21 (3), p 314-23
|
| Description |
normal squamous epithelium of the uvula of a non-cancer patient who underwent uvulopalatopharyngoplasty
|
| Data processing |
Spots were quantified in ImaGene 5.6.1 software using default settings. Microarray data were normalised using Lowess regression. When both intensities were below 50, hybridisation was assumed inefficient and the ratio value was considered ‘missing’. The cut-off “50” is based on technical reproducibility: intensities above 50 were reasonably reproducible for technical replicates on our platform. To obtain more stable ratios, intensity values below 50 were substituted by 50 when the other channel was above 50. Genes with missing ratio values in more than 20% of arrays were excluded from analysis. Remaining missings were imputed using K-nearest neighbour imputation.
|
| |
|
| Submission date |
Dec 07, 2006 |
| Last update date |
Oct 20, 2008 |
| 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 |
GPL3054 |
| Series (1) |
| GSE6473 |
Integrated genomic and transcriptional profiling yields putative marker genes for cervical cancer |
|
