GEO series

RRBS profiling of mouse ESCs (wild type and DNMT KOs)

GSE67811 Mus musculus (mouse) DNA methylation 11 samples Submitted 2015/04/13 Platform GPL13112

At a glance

DNA methylation · mouse · 11 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Mus musculus (mouse)
Samples: 11 samples: 5 conditions, mostly in duplicateGroups 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; 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 key epigenetic modification involved in regulating gene expression and maintaining genomic integrity. Somatic patterns of DNA methylation are largely static, apart from focal dynamics at gene regulatory elements. To further advance our understanding of the role of DNA methylation in human development and disease, we inactivated all three catalytically active DNA methyltransferases in human embryonic stem cells (ESCs) using CRISPR/Cas9 genome editing.

Read the full summary ↓

Disruption of DNMT3A or DNMT3B individually, as well as of both enzymes in tandem, creates viable, pluripotent cell lines with distinct effects on their DNA methylation landscape as assessed by whole-genome bisulfite sequencing. Surprisingly, in contrast to mouse, deletion of DNMT1 resulted in rapid cell death in human ESCs. To overcome the immediate lethality, we generated a doxycycline (DOX) responsive tTA-DNMT1* rescue line and readily obtained homozygous DNMT1 mutant lines. However, DOX-mediated repression of the exogenous DNMT1* initiates rapid, global loss of DNA methylation, followed by extensive cell death, demonstrating that DNA methylation is essential for human ESCs cultured in standard conditions. In summary, our data provide a comprehensive characterization of DNMT mutant ESCs, including single base genome-wide maps of their targets.

This dataset

Open GSE67811 in finder → Find more mouse 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 GSE67811_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 PRJNA280974 and SRA study SRP057112. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 25822089) ↗

Study design

5 conditions, mostly in duplicate

WT_P ×2 Dnmt3aKO_P ×2 Dnmt3bKO_P ×2 Dnmt3a3bKO_P ×2 Dnmt1KO_P ×2 DnmtTKO ×1

Supports a between-group comparison across 10 samples.

How we read this: 5 replicated groups read from 11 sample titles; they account for 10 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

GSM1656422 WT_P4 WT_P
GSM1656423 WT_P14 WT_P
GSM1656424 Dnmt3aKO_P3 Dnmt3aKO_P
GSM1656425 Dnmt3aKO_P13 Dnmt3aKO_P
GSM1656426 Dnmt3bKO_P3 Dnmt3bKO_P
GSM1656427 Dnmt3bKO_P13 Dnmt3bKO_P
GSM1656428 Dnmt3a3bKO_P3 Dnmt3a3bKO_P
GSM1656429 Dnmt3a3bKO_P13 Dnmt3a3bKO_P
GSM1656430 Dnmt1KO_P7 Dnmt1KO_P
GSM1656431 Dnmt1KO_P17 Dnmt1KO_P
GSM1656432 DnmtTKO

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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.