|
| Status |
Public on Feb 18, 2017 |
| Title |
H05.8088 |
| Sample type |
genomic |
| |
|
| Source name |
Base of tongue
|
| Organism |
Homo sapiens |
| Characteristics |
anatomical site: Base of tongue
tissue storage: fresh frozen
hpv status: Positive
center: CAL
gender: M
organ group: Oropharynx
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
QIAamp DNA mini kit (Qiagen)
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450k Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged with standard recommended Illumina scanner settings
|
| Description |
9721365162_R03C02
|
| Data processing |
Idat files were loaded into R and analyzed with R/Bioconductor packages
Normalized betas (FunNorm normalization - minfi R package). Probes were filtered out for SNPs, XY chromosomes and cross-reactive probes.
|
| |
|
| Submission date |
Feb 17, 2017 |
| Last update date |
Feb 18, 2017 |
| Contact name |
Zdenko Herceg |
| E-mail(s) |
HercegZ@iarc.fr
|
| Organization name |
IARC
|
| Department |
EGM
|
| Lab |
Epigenomics and mecanisms
|
| Street address |
150 Cours Albert Thomas
|
| City |
Lyon |
| ZIP/Postal code |
69372 CEDEX 08 |
| Country |
France |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE95036 |
Unique DNA methylation signature in HPV-positive head and neck squamous cell carcinomas |
|
