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DNA methylation profiles of brain samples from Down Syndrome subjects and controls.

GSE63347 Homo sapiens (human) DNA methylation 71 samples Submitted 2015/03/02 Platform GPL13534
At a glance

DNA methylation · human · 71 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Homo sapiens (human)
Samples
71 samples: 6 conditions, mostly with about 11 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed expression table (series matrix) and the array files, from NCBI.
Summary (written by the submitters)
Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 486,000 CpGs. Dataset included 71 samples from multiple brain regions (cerebellum, temporal/occipital/frontal cortex). The goal was to evalute the effect of trisomy 21 on DNA methylation levels and epigenetic age. Explanation of characteristics variables in supplementary file Explanation_of_characteristic_variables2.docx
This dataset
Open GSE63347 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 (GSE63347_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 PRJNA267550. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 25678027) ↗
Study design
6 conditions, mostly with about 11 replicates each
genomic DNA from Brain Frontal Cortex Sample ×21 genomic DNA from Brain CRBM Sample ×13 genomic DNA from Brain Temporal Cortex Sample ×11 genomic DNA from Brain Occipital Sample ×11 genomic DNA from Brain Hippocampus Sample ×9 genomic DNA from Brain MidBrain Sample ×6

Supports a between-group comparison across 71 samples.

How we read this: 6 replicated groups read from 71 sample titles; they account for 71 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

+ 31 more — browse all 71 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.