|
| Status |
Public on Feb 09, 2017 |
| Title |
FK18Bp143 |
| Sample type |
genomic |
| |
|
| Source name |
HPV-18-transfected human foreskin keratinocytes_line B
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary human foreskin keratinocytes transfected with HPV18
transformation stage: anchorage independent
|
| Treatment protocol |
No treatment was performed
|
| Growth protocol |
Establishment and culture of the HPV16 (FK16A and FK16B) and HPV18 (FK18A and FK18B) transformed keratinocyte cell lines and isolation and culture of primary human foreskin keratinocytes (HFKs) were described previously (Steenbergen et al, Oncogene 1996). The human cervical carcinoma cell lines SiHa, HeLa and CaSki were obtained from the American Type Culture Collection (Manassas, VA, USA) and cultured as described previously (Steenbergen et al, J Natl Cancer Inst 2001).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using the PurelinkTM Genomic DNA Minikit (Life Technologies) following the manufacturer's instructions. 500ng double stranded DNA was bisulfite converted using the EZ DNA Methylation kit (D5002, Zymo Research) according to the manufacturer's instructions.
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Labelling was done as described in the automated protocol of the Infinium HD assay methylation protocol guide (version: December 2010)
|
| |
|
| Hybridization protocol |
Hybridisation was done as described in the automated protocol of the Infinium HD assay methylation protocol guide (version: December 2010)
|
| Scan protocol |
Scanning was done as described in the automated protocol of the Infinium HD assay methylation protocol guide (version: December 2010)
|
| Data processing |
Data was processed and normalised using the pipeline described by Touleimat and Tost, which takes into account the different chemistry of class I and class II probes and returns Beta values representing the percentage of methylation for that particular CpG dinucleotide (Touleimat and Tost, Epigenomics 2012)
|
| |
|
| Submission date |
Feb 24, 2016 |
| Last update date |
Feb 09, 2017 |
| Contact name |
Daoud Sie |
| E-mail(s) |
d.sie@vumc.nl
|
| 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 |
GPL13534 |
| Series (2) |
| GSE78277 |
Aberrant methylation-mediated silencing of microRNAs contributes to HPV-induced anchorage independence [methylation-Illumina] |
| GSE78279 |
Aberrant methylation-mediated silencing of microRNAs contributes to HPV-induced anchorage independence |
|
