GEO series

Methylation data from medulloblastoma tumor samples

GSE49576 Homo sapiens (human) DNA methylation 83 samples Submitted 2014/09/02 Platform GPL13534

At a glance

DNA methylation · human · 83 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Topic: MedulloblastomaThis series is part of our curated briefing on it.
Samples: 83 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Smoothened (SMO)-inhibitors recently entered clinical trials for sonic-hedgehog driven medulloblastoma (SHH-MB). Clinical response appears highly variable. To understand the mechanism(s) of primary resistance and to identify pathways co-operating with aberrant SHH-signaling, we sequenced a large cohort of SHH-MBs across all age groups by sequencing, DNA methylation and expression profiling.

Read the full summary ↓

Our data show that most adults but only half of the pediatric patients with SHH-MB will respond to SMO inhibition as predicted by molecular analysis of the primary tumor and tested in the SHH-xenografts, demonstrating that the next generation of SMO-inhibitor trials should be based on these predictive biomarkers. To further dissect the biological differences between the different age groups within SHH medulloblastomas, we looked at the DNA methylation profiles of SHH medulloblastoma samples.

This dataset

Open GSE49576 in finder → Find more human methylation datasets → Medulloblastoma landscape →

Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE49576_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA214321. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 24651015) ↗

Samples in this study

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+ 83 more — browse all 83 samples with per-sample file links →

More Medulloblastoma datasets

GSE10327 mRNA expression data of 62 human medulloblastoma tumors 62 samples same disease briefing · shares medulloblastoma
GSE294901 Measles oncolytic virus as an immunotherapy for recurrent/refractory pediatric medulloblastoma and atypical teratoid rhabdoid tumor: results from PNOC005 84 samples same disease briefing · shares medulloblastoma
GSE34258 Genome sequencing of childhood medulloblastoma brain tumors links chromothripsis with TP53 mutations 49 samples same disease briefing · shares medulloblastoma
GSE37385 Subgroup specific somatic copy number aberrations in the medulloblastoma genome 1382 samples same disease briefing · shares medulloblastoma
GSE270126 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency. 219 samples same disease briefing · shares medulloblastoma
GSE270125 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [CUT&Run] 169 samples same disease briefing · shares medulloblastoma
GSE21140 Genomics of medulloblastoma identifies four distinct molecular variants 103 samples same disease briefing · shares medulloblastoma
GSE243796 Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level 90 samples same disease briefing · shares medulloblastoma

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.