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Combinational effect of the ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells

GSE238228 Mus musculus (mouse) DNA methylation 68 samples Submitted 2024/03/17 Platform GPL24247
At a glance

DNA methylation · mouse · 68 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Mus musculus (mouse)
Samples
68 samples: 12 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.
Paper
Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cellsNature communications · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells
Kubo N, Uehara R, Uemura S et al. · Nature communications 2024 · PMID 38627502 · doi:10.1038/s41467-024-47699-2
This dataset
Open GSE238228 in finder → Find more mouse RNA-seq 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 GSE238228_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 PRJNA998390 and SRA study SRP451389. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38627502) ↗
Study design
12 conditions, mostly in duplicate
RNA_WT_FGO ×18 RNA_WT_MII ×10 RNA_DNMT3L-ADD_FGO ×8 RNA_DNMT3A-ADD_FGO ×8 RNA_DNMT3A+DNMT3L-ADD_FGO ×8 RNA_DNMT3A+DNMT3L-ADD_E9_embryo ×3 WGBS_WT_FGO ×2 WGBS_DNMT3L-ADD_FGO ×2 +5 more

Supports a between-group comparison across 67 samples.

How we read this: 12 replicated groups read from 68 sample titles; they account for 67 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

+ 28 more — browse all 68 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq 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.