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Series GSE44684 Query DataSets for GSE44684
Status Public on Jun 12, 2013
Title DNA methylation data from pilocytic astrocytoma tumor samples and normal cerebellum controls
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Pilocytic astrocytomas (PA) are the most common brain tumor in pediatric patients and can cause significant morbidity, including chronic neurological deficiencies. They are characterized by activating alterations in the mitogen-activated protein kinase (MAPK) pathway, but little else is known about their development. To map the global DNA methylation profiles of these tumors, we analysed 61 PAs and 6 normal cerebellum samples using Illumina's Infinium HumanMethylation450 BeadChips. These data revealed two subgroups of PA that separate according to tumor location (infratentorial versus supratentorial), and identified key neural developmental genes that are differentially methylated between the two groups. Integration with transcriptome microarray data highlighted significant expression differences, which were unexpectedly associated with a strong positive correlation between methylation and expression. Differentially methylated probes were often identified within the gene body and/or regions up- or downstream of the gene, rather than at the transcription start site. We also identified a large number of differentially methylated genes between cerebellar PAs and normal cerebellum, which included additional developmental genes.
Overall design Bisulphite converted DNA from 61 PA tumours (fresh frozen) and 6 normal cerebellum (from commerical sources) were hybridised to the Illumina Infinium HumanMethylation450 BeadChips.
Contributor(s) Lambert SR, Witt H, Hovestadt V, Zucknick M, Kool M, Pearson DM, Korshunov A, Ryzhova M, Ichimura K, Jabado N, Fontebasso A, Lichter P, Pfister SM, Collins VP, Jones DT
Citation(s) 23660940
Submission date Feb 26, 2013
Last update date Mar 22, 2019
Contact name Sally R Lambert
Organization name Queen Mary, University of London
Department Centre for Cutaneous Research
Street address Blizard Institute, 4 Newark Street
City London
ZIP/Postal code E1 2AT
Country United Kingdom
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (67)
GSM1088869 PA_01
GSM1088870 PA_02
GSM1088871 PA_03
BioProject PRJNA190897

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
GSE44684_RAW.tar 183.1 Mb (http)(custom) TAR
GSE44684_beta.txt.gz 137.5 Mb (ftp)(http) TXT
GSE44684_signals.txt.gz 284.8 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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