GEO series

Illumina Infinium 450K array data for Diffuse Intrinsic Pontine Glioma

GSE50022 Homo sapiens (human) DNA methylation 28 samples Submitted 2014/03/31 Platform GPL16304

At a glance

DNA methylation · human · 28 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Samples: 28 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children with no effective treatment and near 100% fatality. The failure of most therapies can be attributed to the delicate location of these tumors and choosing therapies based on assumptions that DIPGs are molecularly similar to adult disease.

Read the full summary ↓

Recent studies have unraveled the unique genetic make-up of this brain cancer with nearly 80% harboring a K27M-H3.3 or K27M-H3.1 mutation. However, DIPGs are still thought of as one disease with limited understanding of the genetic drivers of these tumors. To understand what drives DIPGs we integrated whole-genome-sequencing with methylation, expression and copy-number profiling, discovering that DIPGs are three molecularly distinct subgroups (H3-K27M, Silent, MYCN) and uncovering a novel recurrent activating mutation in the activin receptor ACVR1, in 20% of DIPGs. Mutations in ACVR1 were constitutively activating, leading to SMAD phosphorylation and increased expression of downstream activin signaling targets ID1 and ID2. Our results highlight distinct molecular subgroups and novel therapeutic targets for this incurable pediatric cancer.

This dataset

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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 (GSE50022_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 PRJNA215837. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 24705254) ↗

Samples in this study

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+ 28 more — browse all 28 samples with per-sample file links →

Datasets on a similar topic

GSE39198 Genome-scale methylome profiling of pheochromocytomas and paragangliomas with Illumina Infinium 27k Human Methylation arrays 148 samples shares illumina, infinium, glioma, array
GSE250464 Oncohistone H3.3K27M-driven CREB5/ID1 Axis Mediates the Malignant Cell States of Diffuse Intrinsic Pontine Glioma (DIPG) [CUT&Tag] 26 samples shares intrinsic, diffuse, pontine, glioma
GSE288070 Radiotherapy plus neoadjuvant and concomitant IL-13Rα2-directed immunotoxin therapy for diffuse intrinsic pontine glioma 19 samples shares intrinsic, diffuse, pontine, glioma
GSE225029 SUV39H1 inhibition by Chaetocin targets stemness and oncogenic networks and synergizes with ONC201 against Diffuse intrinsic pontine gliomas 12 samples shares intrinsic, diffuse, pontine, glioma
GSE215220 RNA-Seq of VUMC-DIPG10 and HSJD-DIPG007 human diffuse intrinsic pontine glioma cells treated with a copper chelator 12 samples shares intrinsic, diffuse, pontine, glioma
GSE250466 Oncohistone H3.3K27M-driven CREB5/ID1 Axis Mediates the Malignant Cell States of Diffuse Intrinsic Pontine Glioma (DIPG) [RNA-seq] 10 samples shares intrinsic, diffuse, pontine, glioma
GSE48472 Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array 56 samples shares 450k, illumina, array
GSE65820 Whole genome characterisation of chemoresistant ovarian cancer [Illumina_450K_Methylation] 121 samples shares 450k, illumina

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