|
| Status |
Public on Nov 30, 2012 |
| Title |
HPV- HNSCC sample FFPE 42 |
| Sample type |
genomic |
| |
|
| Source name |
HNSCC
|
| Organism |
Homo sapiens |
| Characteristics |
tumour site: tonsil/base of tongue
tissue: HPV- HNSCC tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The QIAamp DNA FFPE Tissue Kit (QIAGEN) was used for the DNA extraction of laser dissected FFPE samples.
|
| Label |
Biotin
|
| Label protocol |
DNAs were prepared in a total volume of 20 µl (2 µg for FFPE DNA per sample) using a previously optimized protocol (Thirlwell et al. 2010) in conjunction with the REPLIg FFPE kit (Qiagen GmbH D-40724 Hilden, cat No. 150243) and EZ DNA Methylation kit (Zymo Research Corp, Orange, CA 92867, USA, cat No. D5001). The latter was modified to improve bisulphite conversion efficiency by inclusion of a cyclic denaturation step as described previously (Thirlwell et al. 2010).
|
| |
|
| Hybridization protocol |
The Infinium HumanMethylation450 BeadChips were processed by the UCL Genomics core facility according to the manufacturer’s recommendation.
|
| Scan protocol |
The Infinium HumanMethylation450 BeadChips were processed by the UCL Genomics core facility according to the manufacturer’s recommendation.
|
| Description |
Ligated BS-converted DNA
|
| Data processing |
The scanned data and image output files were managed with the Genomestudio software (version 1.9.0) (Illumina®, Inc., San Diego, CA 92121, USA).
|
| |
|
| Submission date |
May 25, 2012 |
| Last update date |
Nov 30, 2012 |
| Contact name |
Matthias Lechner |
| E-mail(s) |
m.lechner@ucl.ac.uk
|
| Organization name |
University College London
|
| Department |
UCL Cancer Institute
|
| Lab |
Medical Genomics
|
| Street address |
Gower Street
|
| City |
London |
| ZIP/Postal code |
WC1E 6BT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE38266 |
450k Analysis of 42 FFPE HPV+ and HPV- HNSCC samples |
| GSE38271 |
FF and FFPE HPV+ and HPV- HNSCC and HNSCC cell lines |
|
