Genome-wide methylomic and transcriptomic analyses identify subtype-specific epigenetic signatures commonly dysregulated in GBM and GSCs

  • Tianzhi Huang (Northwestern University) (Contributor)
  • Angel A Alvarez (Contributor)
  • Rajendra P. Pangeni (Contributor)
  • Taiping Shi (Contributor)
  • Namratha Sastry (Contributor)
  • Songjian Lu (Contributor)
  • John Kessler (Contributor)
  • Ichiro Nakano (Contributor)
  • Xinghua Lu (Contributor)
  • Charles David James (Contributor)
  • Bo Hu (Contributor)
  • Shi-Yuan Cheng (Contributor)



Accession Number: GSE90498

GPL13534: Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)

Organism: Homo sapiens

Published on 2017-11-22

Genome-wide DNA methylation and trancription profiling of different subtypes in GBM (TCGA) and glioma stem cells (GSCs) were carried out using Illumina BeadChip HumanMethylation 450K array (450K array) to analyse over 485K CpG sites accross each samples. 450K array data for 94 GBM samples comprising 4 different subtypes i.e. Proneural (PN), Mesenchymal (MES), Classical (CL) and Neural (N) were used for GBM analysis. Similarly, 450K array for 23 GSCs and 1NHA, RNA seq for 29 GSCs and affimetrix microarray gene expression array for 12 GSCs were used for GBM data analyses.

Overall Design:
Bisulphite converted DNA from the for 23 GSCs and a NHA used used for Illumina Infinium 450k Human Methylation array.Differential methylation between the subtype(s) were carried out to generate subtype-specific DNA methylation signatues which were then compared to RNA seq and/or gene expression data.

Name: Rajendra Prasad Pangeni
Organization: Northwestern University
Laboratory: Cheng's Lab, Lurie 6-250
Deparment: Neurology
Address: 303 Chicago IL 60611 USA
Phone: 5312-503-5314

Organization: Illumina Inc.
Address: 9885 Towne Centre Drive San Diego CA 92121 USA
Phone: 1 800 809 4566
Date made available2017
PublisherGene Expression Omnibus

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