|
| Status |
Public on Apr 06, 2020 |
| Title |
HPV18-transfected human foreskin keratinocytes_line B_timepoint 2 |
| Sample type |
genomic |
| |
|
| Source name |
primary human foreskin keratinocytes transfected with HPV18
|
| Organism |
Homo sapiens |
| Characteristics |
transformation stage: extended lifespan
time point: 2
treatment: no treatment
|
| 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 |
genomic DNA |
| Extraction protocol |
Total DNA was isolated by standard proteinase K digestion followed by phenol-chloroform purification (van Zeeburg et al., Cancer Research 2005).
|
| Label |
Cy3
|
| Label protocol |
DNA was labeled using the CYTAG CGH Labeling kit (Enzo Life Sciences) according to the manufacturer's recommendations.
|
| |
|
| Hybridization protocol |
DNA was hybridized using the Agilent SurePrint G3 Human CGH Microarray Kit for the 4x180K Agilent platform (Agilent).
|
| Scan protocol |
Scanning was performed using a G2505B scanner (Agilent) using the protocol designed for the used platform by the manufacturer (Agilent).
|
| Description |
US22502676_252252210500_S01_CGH_107_Sep09_1_4.txt
|
| Data processing |
The pre-processing of CGH data comprised median normalization and segmentation using the circular binary segmentation method (Olshen et al., Biostatistics 2004).
|
| |
|
| Submission date |
Oct 10, 2019 |
| Last update date |
Apr 06, 2020 |
| Contact name |
Renske DM Steenbergen |
| E-mail(s) |
r.steenbergen@amsterdamumc.nl
|
| Organization name |
Amsterdam UMC, location VUmc
|
| Department |
Pathology
|
| Lab |
Molecular Pathology
|
| Street address |
De Boelelaan 1117
|
| City |
Amsterdam |
| ZIP/Postal code |
1081 HV |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16694 |
| Series (2) |
| GSE138081 |
Identification of deregulated pathways, key regulators, and novel miRNA-mRNA interactions in HPV-mediated transformation. |
| GSE138724 |
Identification of deregulated pathways, key regulators, and novel miRNA-mRNA interactions in HPV-mediated transformation. [CGH cell lines-Agilent] |
|
