GEO series

Methylation analysis of 81 glioma clinical samples (49 CIMP+ and 32 CIMP-) and 53 cell line samples

GSE30338 Homo sapiens (human) DNA methylation 134 samples Submitted 2012/02/16 Platform GPL13534

At a glance

DNA methylation · human · 134 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Samples: 134 samples: 27 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

Glioma CIMP (G-CIMP) is a powerful determinant of tumor pathogenicity but the molecular cause of G-CIMP is a fundamental question that is unresolved. Here, we show that mutation of a single gene, isocitrate dehydrogenase 1 (IDH1), directly causes the G-CIMP in gliomas by remodeling the methylome.

This dataset

Open GSE30338 in finder → Find more human methylation datasets →

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 (GSE30338_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 PRJNA154817. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 22343889) ↗

Study design

27 conditions, mostly in duplicate

Tumor ID ×81 P2Parental ×2 P2WT ×2 P2MUT ×2 P15Parental ×2 P15WT ×2 P15MUT ×2 P25Parental ×2 +20 more

Supports a case/control comparison: 81 samples read as cases, 8 as controls.

How we read this: 27 replicated groups read from 134 sample titles; they account for 133 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM752160 Tumor ID 21 Tumor ID
GSM752161 Tumor ID 22 Tumor ID
GSM752162 Tumor ID 23 Tumor ID
GSM752163 Tumor ID 18 Tumor ID
GSM752164 Tumor ID 17 Tumor ID
GSM752165 Tumor ID 19 Tumor ID
GSM752166 Tumor ID 1 Tumor ID
GSM752167 Tumor ID 2 Tumor ID
GSM752168 Tumor ID 5 Tumor ID
GSM752169 Tumor ID 4 Tumor ID
GSM752170 Tumor ID 6 Tumor ID
GSM752171 Tumor ID 3 Tumor ID
GSM752172 Tumor ID 7 Tumor ID
GSM752173 Tumor ID 10 Tumor ID
GSM752174 Tumor ID 11 Tumor ID
GSM752175 Tumor ID 8 Tumor ID
GSM752176 Tumor ID 28 Tumor ID
GSM752177 Tumor ID 12 Tumor ID
GSM752178 Tumor ID 9 Tumor ID
GSM752179 Tumor ID 13 Tumor ID
GSM752180 Tumor ID 29 Tumor ID
GSM752181 Tumor ID 31 Tumor ID
GSM752182 Tumor ID 30 Tumor ID
GSM752183 Tumor ID 16 Tumor ID
GSM752184 Tumor ID 32 Tumor ID
GSM752185 Tumor ID 33 Tumor ID
GSM752186 Tumor ID 37 Tumor ID
GSM752187 Tumor ID 35 Tumor ID
GSM752188 Tumor ID 34 Tumor ID
GSM752189 Tumor ID 36 Tumor ID
GSM752190 Tumor ID 41 Tumor ID
GSM752191 Tumor ID 42 Tumor ID
GSM752192 Tumor ID 43 Tumor ID
GSM752193 Tumor ID 27 Tumor ID
GSM752194 Tumor ID 44 Tumor ID
GSM752195 Tumor ID 40 Tumor ID
GSM752196 Tumor ID 45 Tumor ID
GSM752197 Tumor ID 47 Tumor ID
GSM752198 Tumor ID 49 Tumor ID
GSM752199 Tumor ID 48 Tumor ID

+ 94 more — browse all 134 samples with per-sample file links →

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GSE36278 Methylation data from glioblastoma tumor samples 142 samples shares methylation
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GSE277273 Multi-omics Sequencing reveals Epigenetic Regulation in Actinic Keratosis and Cutaneous Squamous Cell Carcinoma [850K DNA methylation array] 20 samples shares methylation
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Search all human methylation datasets in GEO →

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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.