GEO series

RNA methylation destabilizes developmental regulators in murine embryonic stem cells (MoGene-2)

GSE46879 Mus musculus (mouse) DNA methylation 26 samples Submitted 2014/01/06 Platform GPL16570

At a glance

DNA methylation · mouse · 26 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Mus musculus (mouse)
Samples: 26 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Recent methylome studies have located N6-methyladenosine (m6A) RNA modification on thousands of mammalian transcripts. However, its functional mechanism remains unclear. In this study, we examined the role of m6A methylation in mouse embryonic stem cells. To gain an understanding of dynamic changes in cells depleted with (proposed) methyltranferases at molecular level, we examined the time-series gene expression pattern in mESC lines using microarray analysis.

This dataset

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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 (GSE46879_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 PRJNA202907. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 24394384) ↗

Samples in this study

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+ 26 more — browse all 26 samples with per-sample file links →

Datasets on a similar topic

GSE243566 Systematic perturbations of SETD2, NSD1, NSD2, NSD3 and ASH1L reveal their distinct contributions to H3K36 methylation 125 samples shares methylation, stem
GSE292289 H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells 94 samples shares methylation, stem
GSE272913 Dnmt3a Controls Hematopoietic Stem Cells via DNA Methylation-Independent Regulation of Telomeres 66 samples shares methylation, stem
GSE284988 Epigenetic profiling of hematopoietic stem cells identifies KDR and PU.1 as regulators of aging transcriptome and caloric restriction response 58 samples shares regulators, stem
GSE292282 H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells [RNA-Seq] 44 samples shares methylation, stem
GSE274865 Epigenetic regulators of clonal hematopoiesis control CD8 T cell stemness during immunotherapy [CUT&Tag] 36 samples shares regulators, stem
GSE242461 TET Proteins Control Early-Stage Stem Cell Differentiation via H3K27me3, Not DNA Demethylation 30 samples shares methylation, stem
GSE267262 Genetic variation modulates aberrant DNA hypomethylation in naïve pluripotent stem cells. 12 samples shares methylation, stem

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