|
| Status |
Public on Feb 09, 2017 |
| Title |
FK16BT4+ |
| Sample type |
RNA |
| |
|
| Source name |
primary human foreskin keratinocytes transfected with HPV16
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HPV16-transfected human foreskin keratinocytes_line B
transformation stage: anchorage independent
timepoint: timepoint 4
treatment: 5000 nM 5-aza-2’-deoxycytidine (DAC)
|
| Treatment protocol |
cells were treated with 5000 nM 5-aza-2’-deoxycytidine (DAC; Sigma-Aldrich, Zwijndrecht, The Netherlands) dissolved in PBS for 5 days. DAC was added to the cells every day.
|
| Growth protocol |
Establishment and culture of the HPV16 (FK16A and FK16B) and HPV18 (FK18A and FK18B) transformed keratinocyte cell lines was described previously (Steenbergen et al, Oncogene 1996).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol Reagent according to the manufacturer’s instructions (Life Technologies).
|
| Label |
Cy3
|
| Label protocol |
According to manufacturer's instructions: miRNA Microarray System with miRNA Complete Labeling and Hyb Kit version 2.4 from September 2011
|
| |
|
| Hybridization protocol |
According to manufacturer's instructions: miRNA Microarray System with miRNA Complete Labeling and Hyb Kit version 2.4 from September 2011
|
| Scan protocol |
protocol name: miRNA_107_Sep09. Scanning is done according to manufacturer's instructions: miRNA Microarray System with miRNA Complete Labeling and Hyb Kit version 2.4 from September 2011
|
| Description |
HPV16-transfected human foreskin keratinocytes_line B_timepoint 4_DAC treated
|
| Data processing |
Probes corresponding to human miRNAs were selected and replicates weakly correlating to all other replicates of the same probe were removed. Data was normalized per treatment group using the robust quantile method (Bolstad et al, Bioinformatics 2003) and transformed using the variance stabilizing transformation (Huber, Bioinformatics 2002). The obtained values were averaged per probe for further analysis.
|
| |
|
| 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 |
GPL15159 |
| Series (2) |
| GSE78278 |
Aberrant methylation-mediated silencing of microRNAs contributes to HPV-induced anchorage independence [miR-Agilent] |
| GSE78279 |
Aberrant methylation-mediated silencing of microRNAs contributes to HPV-induced anchorage independence |
|
