GEO series

The genomic and epigenomic landscape of atypical teratoid rhabdoid tumors

GSE70460 Homo sapiens (human) Genome variation profiling by genome tiling array 150 samples Submitted 2016/03/02 Platform GPL13534

At a glance

human · 150 samples

Organism: Homo sapiens (human)
Samples: 150 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

Atypical teratoid/rhabdoid tumor (ATRT) is one of the most common brain tumors in infants. Although the prognosis of ATRT patients is poor, some patients respond favorably to current treatments, suggesting molecular inter-tumor heterogeneity. To investigate this further, we genetically and epigenetically analyzed a large series of human ATRTs.

Read the full summary ↓

Three distinct molecular subgroups of ATRTs, associated with differences in demographics, tumor location, and type of SMARCB1 alterations, were identified. Whole-genome DNA and RNA sequencing found no recurrent mutations in addition to SMARCB1 that would explain the differences between subgroups. Whole-genome bisulfite sequencing and H3K27Ac chromatin-immunoprecipitation sequencing of primary tumors, however, revealed clear differences, leading to the identification of subgroup-specific regulatory networks and potential therapeutic targets.

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 (GSE70460_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 ↓

Also filed as BioProject PRJNA288790. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 26923874) ↗

Samples in this study

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+ 150 more — browse all 150 samples with per-sample file links →

Datasets on a similar topic

GSE282972 An in vitro pharmacogenomic approach reveals subtype-specific therapeutic vulnerabilities in atypical teratoid/rhabdoid tumors (AT/RT) [RNASeq] 13 samples shares atypical, teratoid, rhabdoid
GSE231287 Investigation of genetic dependencies in atypical teratoid rhabdoid tumors 40 samples shares atypical, teratoid, rhabdoid
GSE197569 Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors 31 samples shares atypical, teratoid, rhabdoid
GSE230742 Investigation of genetic dependencies in atypical teratoid rhabdoid tumors (ATRTs) [I] 21 samples shares atypical, teratoid, rhabdoid
GSE231286 Investigation of genetic dependencies in atypical teratoid rhabdoid tumors (ATRTs) [II] 12 samples shares atypical, teratoid, rhabdoid
GSE283843 A cycling, progenitor-like cell population at the root of atypical teratoid rhabdoid tumor subtype differentiation trajectories 56 samples shares atypical, teratoid, rhabdoid
GSE213248 Inhibiting EZH2 Targets Atypical Teratoid Rhabdoid Tumor by Triggering Viral Mimicry via Both RNA and DNA Sensing Pathways [CUT&RUN] 24 samples shares atypical, teratoid, rhabdoid
GSE276501 Atypical Teratoid Rhabdoid Tumours Are Susceptible to Panobinostat-Mediated Differentiation Therapy 18 samples shares atypical, teratoid, rhabdoid

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