|
| Status |
Public on Aug 01, 2015 |
| Title |
TCam-2 in vitro |
| Sample type |
genomic |
| |
|
| Source name |
Seminoma-like cell line
|
| Organism |
Homo sapiens |
| Characteristics |
strain: CD1 nude mice
age: 6 weeks at start of xenografting
tissue: Seminoma-like
|
| Growth protocol |
cultivation protocol: TCam-2 and 2102EP cells were cultivated as published (Nettersheim et al., 2013, PubMed ID: 24386123)
xenografting protocol: 1x10^7 TCam-2 and 2102EP cells were xenografted in CD1 nude mice as published previously (Nettersheim et al., 2012, Pubmed ID: 22489004)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated by phenol / chloroform / isoamylalcohol isolation as published (Nettersheim et al., 2013, Pubmed ID: 24386123). Quality control was performed with Agilent Bioanalyser.
bisulfite convesion: Genomic DNA was bisulfite converted using the EZ DNA methylation kit according to the manual (Zymo Research) and as published (Nettersheim et al., 2013, Pubmed ID: 24386123)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Data processing |
A subset quantile normalization approach developed by N. Touleimat & J. Tost was applied (Touleimat, Tost, 2012, Pubmed ID: 22690668 ). This processing pipeline includes signal correction for the adjustment of the color balance and background level correction as well as the Infinium I/Infinium II shift correction between sample normalization. Technical quality parameters such as hybridization, extension, bisulfite conversion and specificity were evaluated using the ‚Genome Studio’ software. Beta-value signal distributions were inspected by density plots. Data was analysed using ‚Bioconductor R’ (http://www.bioconductor.org). To increase performance in terms of detection and true positive rate of highly methylated and unmethylated CpG-sites, beta-values were transformed to M-values (Du et al., 2010, Pubmed ID: 21118553)
|
| |
|
| Submission date |
Aug 26, 2014 |
| Last update date |
Aug 01, 2015 |
| Contact name |
Daniel Nettersheim |
| E-mail(s) |
Daniel.nettersheim@med.uni-duesseldorf.de
|
| Organization name |
University Hospital Düsseldorf
|
| Department |
Urology
|
| Lab |
Urological Research Lab, Translational Urooncology
|
| Street address |
Universitätsstr. 1
|
| City |
Düsseldorf |
| State/province |
NRW |
| ZIP/Postal code |
40225 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE60787 |
Genome-wide DNA methylation analysis of seminoma-like TCam-2 cells during transition into an embryonal carcinoma-like state |
|
