GEO series

Conservation and divergence of methylation patterning in plants and animals

GSE21152 Oryza sativa; Danio rerio; Populus trichocarpa; Apis mellifera; Arabidopsis thaliana; Ciona intestinalis; Mus musculus; Chlamydomonas reinhardtii DNA methylation 14 samples Submitted 2010/04/09 Platform GPL9100Platform GPL9909Platform GPL10284Platform GPL9302Platform GPL9147Platform GPL10164Platform GPL9185Platform GPL9062Platform GPL9311

At a glance

DNA methylation · Oryza sativa; Danio rerio; Populus trichocarpa; Apis mellifera; Arabidopsis thaliana; Ciona intestinalis; Mus musculus; Chlamydomonas reinhardtii · 14 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Oryza sativa; Danio rerio; Populus trichocarpa; Apis mellifera; Arabidopsis thaliana; Ciona intestinalis; Mus musculus; Chlamydomonas reinhardtii
Samples: 14 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. While DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here, we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes.

Read the full summary ↓

We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylation throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most of the organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honeybee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, we demonstrate that the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes.

This dataset

Open GSE21152 in finder → Find more methylation datasets →

Download · which file do I need?

Direct links to NCBI and ENA, 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, or the whole study as GSE21152_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA126633 and SRA study SRP002239. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 20395551) ↗

Samples in this study

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+ 14 more — browse all 14 samples with per-sample file links →

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.