GEO series

Vitamin C induces Tet-dependent DNA demethylation in ES cells to promote a blastocyst-like methylome [MeDIP-Seq]

GSE46402 Mus musculus (mouse) DNA methylation 8 samples Submitted 2013/06/30 Platform GPL13112

At a glance

DNA methylation · mouse · 8 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Mus musculus (mouse)
Samples: 8 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)

DNA methylation is a heritable epigenetic modification involved in gene silencing, imprinting, and the suppression of retrotransposons. Global DNA demethylation occurs in the early embryo and the germline and may be mediated by Tet (ten-eleven-translocation) enzymes, which convert 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC).

Read the full summary ↓

Tet enzymes have been extensively studied in mouse embryonic stem (ES) cells, which are generally cultured in the absence of Vitamin C, a potential co-factor for Fe(II) 2-oxoglutarate dioxygenase enzymes like Tets. Here we report that addition of Vitamin C to ES cells promotes Tet activity leading to a rapid and global increase in hmC. This is followed by DNA demethylation of numerous gene promoters and up-regulation of demethylated germline genes. Tet1 binding is enriched near the transcription start site (TSS) of genes affected by Vitamin C treatment. Importantly, Vitamin C, but not other antioxidants, enhances the activity of recombinant human Tet1 in a biochemical assay and the Vitamin C-induced changes in hmC and mC are entirely suppressed in Tet1/2 double knockout (Tet DKO) ES cells. Vitamin C has the strongest effects on regions that gain methylation in cultured ES cells compared to blastocysts and in vivo are methylated only after implantation. In contrast, imprinted regions and intracisternal A-particle (IAP) elements, which are resistant to demethylation in the early embryo, are resistant to Vitamin C-induced DNA demethylation. Collectively, this study establishes that Vitamin C is a direct regulator of Tet activity and DNA methylation fidelity in ES cells.

This dataset

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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 GSE46402_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 PRJNA200282 and SRA study SRP021527. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 23812591) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 8 more — browse all 8 samples with per-sample file links →

Datasets on a similar topic

GSE46403 Vitamin C induces Tet-dependent DNA demethylation in ES cells to promote a blastocyst-like methylome 14 samples shares blastocyst-like, tet-dependent, demethylation, methylome, vitamin, induces, promote
GSE46319 Vitamin C induces Tet-dependent DNA demethylation in ES cells to promote a blastocyst-like methylome [Affymetrix] 6 samples shares blastocyst-like, tet-dependent, demethylation, methylome, vitamin, induces, promote
GSE192440 RNA m6A methylome in mouse oocytes and preimplantation embryos 24 samples shares methylome
GSE232810 Adverse maternal environments perturb hepatic DNA methylome and transcriptome prior to the adult-onset non-alcoholic fatty liver disease in mouse offspring [RRBS] 20 samples shares methylome
GSE273517 PROSER1 Modulates DNA Demethylation through Dual Mechanisms to Prevent Syndromic Developmental Malformations 41 samples shares demethylation
GSE280822 Dual DNA demethylation mechanisms implement epigenetic memory driven by the pioneer factor PAX7 38 samples shares demethylation
GSE242461 TET Proteins Control Early-Stage Stem Cell Differentiation via H3K27me3, Not DNA Demethylation 30 samples shares demethylation
GSE308674 Lactate as a metabolic-epigenetic signal linking high-intensity interval training (HIIT) to miRNA-Centered remodeling of the skeletal muscle methylome and transcriptome 28 samples shares methylome

Search all mouse methylation datasets in GEO →

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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.