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DNA methylation profiles of human saliva

GSE78874 Homo sapiens (human) DNA methylation 259 samples Submitted 2016/07/13 Platform GPL13534
At a glance

DNA methylation · human · 259 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Homo sapiens (human)
Samples
259 samples: 259 × genomic DNA from saliva of subjectGroups 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)
Human DNA methylation Beadchip v1.2 was used to analyze n=259 human saliva samples from Caucasians (non-Hispanic whites) and Hispanics collected from the PEG study (directed by Dr Beate Ritz). The main goal of the study was to measure the epigenetic age (also known as DNA methylation age) of saliva. To measure DNA methylation age, we used the epigenetic clock software described in Horvath S (n=2013) DNA methylation age of human tissues and cell types. Genome Biology.2013, 14:R115. DOI: 10.1186/10.1186/gb-2013-14-10-r115 PMID: 24138928.
This dataset
Open GSE78874 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 (GSE78874_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 PRJNA314259. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 27511193) ↗
Study design
259 × genomic DNA from saliva of subject

Supports a between-group comparison across 259 samples.

How we read this: 1 replicated groups read from 259 sample titles; they account for 259 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

+ 219 more — browse all 259 samples with per-sample file links →

Datasets on a similar topic

Search all human methylation datasets in GEO →

Share this dataset

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.