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Series GSE65027 Query DataSets for GSE65027
Status Public on Jan 15, 2016
Title Genome-wide methylation analysis and gene expression profiling identifies genes silenced in non-seminoma cell lines [methylation]
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Germ cell tumours (GCTs) are a complex group of malignancies. They are unique in developing from a pluripotent progenitor cell. The initial lesion is believed to be the relatively benign precursor lesion (ICGNU), from which either highly chemosensitive seminomas or the more aggressive non-seminomas develop. Previous analyses of selected genes have suggested that non-seminomas exhibit much higher levels of DNA methylation than seminomas. However, the genomic targets that are methylated, the extent to which this results in gene silencing and the identity of the silenced genes most likely to play a role in the tumours’ biology have not yet been established. Here genome-wide methylation and expression analysis of GCT cell lines was combined with gene expression data. This demonstrated that the seminoma cells exhibited very little aberrant DNA methylation while non-seminoma cells exhibited very high levels of DNA methylation. Large differences in the level of methylation of the CpG islands of individual genes between tumour cell lines correlated well with differential gene expression. Treatment of non-seminoma cells with 5-aza-2-deoxycytidine verified that methylation of all genes tested did indeed play a role in their silencing and many of these genes were also differentially expressed in primary tumours. Through this approach the genes silenced in the various GCT cell lines were identified. Conclusions: Several pluripotency-associated genes, never before implicated in this type of cancer, were identified as a major functional group of silenced genes. Silencing of these factors that normally suppress somatic differentiation might play an important role in the progression to non-seminoma formation.
Overall design Genomic DNA and RNA was extracted from cell lines representing four subtypes of GCT. RNA was subjected to Affymetric expression array analysis while DNA was bisulfite treated and analysed using Illumina Infinium 450K arrays. Statistical approaches were used to correlate methylation and expression for each gene.
Contributor(s) Noor DA, Jeyapalan JN, Alhazmi S, Carr M, Squibb B, Hughes J, Shipley J, Sheer D, Scotting PJ
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Submission date Jan 15, 2015
Last update date Mar 22, 2019
Contact name Paul J Scotting
Organization name University of Nottingham
Department School of Life Sciences
Lab D13
Street address Queen's Medical Centre
City Nottingham
ZIP/Postal code NG7 2UH
Country United Kingdom
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (4)
GSM1586008 TCam-2 - Seminoma cell line
GSM1586009 NT2D1 - Teratoma cell line
GSM1586010 GCT27 - Embryocarcinoma cell line
This SubSeries is part of SuperSeries:
GSE65028 Genome-wide methylation analysis and gene expression profiling identifies genes silenced in non-seminoma cell lines
BioProject PRJNA272734

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE65027_RAW.tar 183.1 Mb (http)(custom) TAR
GSE65027_methylated_and_unmethylated_signal.txt.gz 11.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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