|
Status |
Public on Aug 01, 2015 |
Title |
TCam-2-2w-1 |
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
|
Description |
biological replicate 1
|
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)
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|
|
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 |
|