GEO series

Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

GSE75073 Homo sapiens (human) DNA methylation 7 samples Submitted 2015/12/18 Platform GPL21145Platform GPL13534

At a glance

DNA methylation · human · 7 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Samples: 7 samples: 7 samples, each with a distinct title — no replicated groupsGroups 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)

DNA methylation is the most well-known epigenetic mark and CpG methylation is critical for many cellular processes and human disorders. Cancer has highlighted the relevance of an aberrant DNA methylation landscape, including promoter CpG island hypermethylation-associated silencing of tumor suppressor genes and the presence of DNA hypomethylation blocks, but an altered DNA methylome is also now evident in other pathologies.

Read the full summary ↓

However, progresses in delivering complete DNA methylation maps are compromised by the high price and labor and interpretation-consuming aspects of the single nucleotide methods nowadays used for whole genome bisulfite sequencing analyses. Following the success of the industry-leading HumanMethylation450 BeadChip (Infinium) methylation microarray that assess close to 450,000 CpG sites (450K), we have biologically and technically validated the newly developed MethylationEPIC BeadChip (Infinium) microarray that covers over 850,000 CpG methylation sites (850K). The 850K microarray contains >90% of the original 450K methylation sites, but add new 350,000 CpGs located in enhancers regions identified by the ENCODE and FANTOM5 projects. Herein, we show that the 850K DNA methylation array demonstrates high reproducibility for the previously analyzed CpG sites included in the 450K microarray; it is consistent among technical replicates; it is reliable in the matched study of fresh frozen vs formalin-fixed paraffin-embeded samples; and it is useful for both 5-methylcytosine and 5-hydroxymethylcytosine determination. The provided validation milestones highlights the value of the MethylationEPIC BeadChip as an informative and useful tool for the analyses of the DNA methylation profile of the human genome.

This dataset

Open GSE75073 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 (GSE75073_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 PRJNA302389. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 26673039) ↗

Study design

7 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 7 sample titles: 7 distinct titles with little repetition. 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

GSM1942152 RCC9_FF_450k
GSM1942153 NC22A_850k
GSM1942154 NC22A_bis_850k
GSM1942155 NCC9_FF_850k
GSM1942156 NCC9_FFPE_850k
GSM1942157 H229_BS_850k
GSM1942158 H229_oxBS_850k

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