GEO series

Gene expression data from ATRT tumor samples

GSE70678 Homo sapiens (human) Expression microarray 49 samples Submitted 2016/03/02 Platform GPL570

At a glance

Expression microarray · human · 49 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 49 samples
Data you can get: A processed expression table (series matrix) and the array 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 (GSE70678_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: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA289342. 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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+ 49 more — browse all 49 samples with per-sample file links →

Datasets on a similar topic

GSE230742 Investigation of genetic dependencies in atypical teratoid rhabdoid tumors (ATRTs) [I] 21 samples shares atrt
GSE231286 Investigation of genetic dependencies in atypical teratoid rhabdoid tumors (ATRTs) [II] 12 samples shares atrt
GSE301405 Disordered DNA methylation leads to targetable transcriptional plasticity in ATRT [RNA-seq] 48 samples shares atrt
GSE273455 SIRT2 is a regulator of the differentiation block driven by SMARCB1 loss in ATRT. 32 samples shares atrt
GSE274373 SIRT2 is a regulator of the differentiation block driven by SMARCB1 loss in ATRT [bulk RNA-seq] 12 samples shares atrt
GSE273418 SIRT2 is a regulator of the differentiation block driven by SMARCB1 loss in ATRT. [CUT&Run] 10 samples shares atrt
GSE273417 SIRT2 is a regulator of the differentiation block driven by SMARCB1 loss in ATRT. [RNA-Seq] 8 samples shares atrt
GSE278558 SIRT2 is a regulator of the differentiation block driven by SMARCB1 loss in ATRT [scRNA-seq] 2 samples shares atrt

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