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Series GSE56597 Query DataSets for GSE56597
Status Public on Nov 30, 2014
Title Wide methylation analysis in vestibular schwannoma [Affymetrix exon level analysis]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Vestibular schwannomas are intracranial tumors that affects unilateral and sporadically or bilateral when is associated to Neurofibromatosis type 2 syndrome. The hallmark of the disease is the biallelic inactivation by NF2 gene mutation or LOH of chromosome 22q, where this gene harbors. In this work, we used Infinium HumanMethylation 450K BeadChip microarrays in a series of 36 vestibular schwannomas, 4 non-vestibular schwannomas and 5 healthy nerves. Our results shows a trend to hypomethylation in schwannomas. Furthermore, HOX genes, located at 4 clusters in the genome, displayed hypomethylation in numerous CpG sites in vestibular but not in non-vestibular schwannomas. Additionally, several microRNA and protein-coding genes were found hypomethylated at promoter regions and confirmed by expression analysis; including miRNA-199a1, miRNA-21, MET and PMEPA1. We also detected methylation patterns that might be involved in alternative transcripts of several genes such as NRXN1 or MBP; that would increase the complexity of methylation-expression. Overall, our results shows specific epigenetic signatures in several coding genes and microRNA that could be used in the finding of potential therapeutic targets.
Overall design Microarrays of vestibular and 4 non-vestibular schwannomas were used in Affymetrix Human Gene 1.0 ST, at exon level. Batch correction was performed between tumors and controls to avoid batch effect.
Contributor(s) Torres-Martin M, Lassaletta L, Melendez B, Rey JA
Citation(s) 25533176
Submission date Apr 08, 2014
Last update date Jan 25, 2019
Contact name Miguel Torres-Martin
Organization name Hospital Universitari Germans Trias i Pujol
Department Clinical Genomics Unit
Street address Carretera de Canyet, s/n
City Badalona
State/province Barcelona
ZIP/Postal code 08916
Country Spain
Platforms (1)
GPL10739 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [probe set (exon) version]
Samples (44)
GSM1365195 NonV1
GSM1365196 NonV2
GSM1365197 NonV3
This SubSeries is part of SuperSeries:
GSE56598 Wide methylation analysis in vestibular schwannoma
BioProject PRJNA244046

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
GSE56597_ExonProcessedAdjusted.txt.gz 61.1 Mb (ftp)(http) TXT
GSE56597_RAW.tar 192.7 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
Processed data are available on Series record

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