|
| Status |
Public on Jan 16, 2013 |
| Title |
SCC of the vulva 02-1060 expression |
| Sample type |
RNA |
| |
|
| Source name |
tumor
|
| Organism |
Homo sapiens |
| Characteristics |
differentiation: moderately differentiated
individual: 02-1060
tissue: squamous cell carcinoma tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent. Using the Illumina TotalPrep RNA Amplification Kit, 500ng were reversely transcribed, amplified and Biotin-16-UTP-labeled. The amount and quality of labeled CDNA were measured using both a NanoDrop spectrophotometer and an Agilent 2100 Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Using the Illumina TotalPrep RNA Amplification Kit, 500ng were reversely transcribed, amplified and Biotin-16-UTP-labeled.
|
| |
|
| Hybridization protocol |
750 ng of biotin-labeled cRNA was hibridized to the HumanHT-12 v.4 Illumina Sentrix BeadCHip according to the manufacturer's instructions.
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Data processing |
Bead summary data was imported into GenomeStudio to remove control probes and to produce a text file containing the signal and detection p-values per probe for all samples, as well as imputing missing data using the k-nearest neighbor algorithm (Tech note: Inputing HumanHT-12 Expression BeadChip Data; Illumina, Inc.). The text file was imported into J-Express Pro 2011, and signal intensity values were quantile normalized (Bolstad et al. 2003) and log transformed (base 2). Significance Analysis of Microarrays (SAM) was used to look for differentially expressed genes. To obtain manageable datasets, differentially expressed genes were defined by a fold change ≥2 and q-value = 0.
|
| |
|
| Submission date |
May 24, 2012 |
| Last update date |
Jan 16, 2013 |
| Contact name |
Francesca Micci |
| E-mail(s) |
francesca.micci@medisin.uio.no
|
| Organization name |
Oslo Universitetssykehus
|
| Department |
Institute for medical informatics
|
| Lab |
cancer cytogenetics
|
| Street address |
Ullernchausseen 70
|
| City |
oslo |
| ZIP/Postal code |
0310 |
| Country |
Norway |
| |
|
| Platform ID |
GPL10558 |
| Series (2) |
| GSE38228 |
Expression analysis of 13 squamous cell carcinomas arising in the vulva |
| GSE38230 |
SCC of the vulva |
|
