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Series GSE15220 Query DataSets for GSE15220
Status Public on Mar 18, 2009
Title Genome-wide analysis of differential methylation and gene expression in a testicular cancer cell line
Organism Homo sapiens
Experiment type Expression profiling by array
Methylation profiling by genome tiling array
Summary Aberrant methylation has been postulated to play an important role in tumorigenesis. We report the use of methylated DNA immunoprecipitation (MeDIP) and whole-genome tiling arrays to investigate methylation changes in testicular germ cell tumor (TGCT) cells. Coupled to expression profiling changes, we found that only 22-26% of differentially methylated genes were also expressed differentially. This phenomenon was independent of the presence of CpG islands in the promoter. Differential methylation and expression of some of these genes were confirmed in testicular tumor tissue. A substantial number of differentially methylated regions in the human genome were not linked to annotated gene loci. Subsequent analysis indicated several microRNAs and small nucleolar RNAs were regulated by these differentially methylated regions. Our results demonstrate the power of the combination of MeDIP-chip analysis and expression profiling for discovery in cancer cells of epigenetically regulated genes and non-coding RNAs in cancer cells.
Overall design MeDIP: Genomic DNA was extracted from the cultured TGCT cell line Ntera2 and a normal testis cell line (CRL-7002). Methylated DNA immunoprecipitation (MeDIP) was performed as previously described (Weber, et al, 2005). Methylation-enriched DNA was amplified and hybridized to Human Tiling Array 2.0R chips (Affymetrix). Triplicate sets of hybridization were performed from 3 independent MeDIP experiments for each cell line. The raw data were analyzed by Tiling Analysis Software (TAS). Arrays from each group (cancer vs normal) were quantile-normalized and differential methylation between groups of tumor and normal was compared by choosing the “two-sample comparison analysis” option in TAS. A two-sided test was performed to evaluate both hypermethylation and hypomethylation. Transfrags (or DMRs) were generated by Interval Analysis with a p-value cutoff at 20 (p < 0.01) and a bandwidth of 275. Transfrags generated by p-value cutoff with a positive signal difference were defined as hypermethylation while those of negative difference were defined as hypomethylation. Genomic bisulfite sequencing was performed to confirm the sensitivity of the observed DMRs.

Expression profiling: Total RNA was extracted from Ntera2 (cancer) and CRL-7002 (normal) cells. Triplicate sets of hybridization were performed for each cell line. Raw data were normalized and analyzed in Partek Genomics Suite Software. Differential gene expression was evaluated using one-way ANOVA.

The supplementary bed files contain 22,452 hypermethylated (GSE15220_Chip_ALL_HYPER.bed) and 12,756 hypomethylated (GSE15220_Chip_ALL_HYPO.bed) regions reported in the paper.
Contributor(s) Cheung H, Lee T, Davis AJ, Taft DH, Rennert OM, Chan W
Citation(s) 20051947
Submission date Mar 13, 2009
Last update date Mar 25, 2019
Contact name Hoi Hung Cheung
Phone 301-451-8368
Organization name NICHD
Lab Laboratory of Clinical and Developmental Genomics
Street address 49 Convent Dr, Rm.2C08 Bldg.49
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platforms (8)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL4910 [Hs35b_P01R] Affymetrix Human Tiling 2.0R Set, Array 1
GPL4911 [Hs35b_P02R] Affymetrix Human Tiling 2.0R Set, Array 2
Samples (13)
GSM380012 Testicular_cancer_cell_line_rep_1
GSM380048 Normal_testis_cell_line_rep_1
GSM380429 Normal_testis_cell_line_rep_2
BioProject PRJNA116469

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
GSE15220_Chip_ALL_HYPER.bed 539.3 Kb (ftp)(http) BED
GSE15220_Chip_ALL_HYPO.bed 310.4 Kb (ftp)(http) BED
GSE15220_RAW.tar 1.5 Gb (http)(custom) TAR (of BAR, CEL, CHP)
Processed data are available on Series record
Processed data provided as supplementary file
Processed data included within Sample table

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