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Evaluation of the Infinium Methylation 450K technology

GSE29290 Homo sapiens (human) DNA methylation 22 samples Submitted 2011/12/15 Platform GPL13534
At a glance

DNA methylation · human · 22 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Homo sapiens (human)
Samples
22 samples: 8 × genomic DNA of normal sample N vs 8 × genomic DNA of tumor sample BCGroups 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)
Genome-wide DNA methylation profiling of HCT116 WT, HCT116 DNMT1 and DNMT3B double KO, and breast cancer tumors by next generation Infinium assay
This dataset
Open GSE29290 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 (GSE29290_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 PRJNA138615. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 22126295) ↗
Study design
8 × genomic DNA of normal sample N vs 8 × genomic DNA of tumor sample BC

Supports a case/control comparison: 8 samples read as cases, 11 as controls.

How we read this: 2 replicated groups read from 22 sample titles; they account for 16 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
Datasets on a similar topic

Search all human methylation datasets in GEO →

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