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Nanobody-tethered transposition for dual profiling of chromatin accessibility and DNA methylation

GSE278068 Mus musculus (mouse) DNA methylation 201 samples Submitted 2026/01/10 Platform GPL24676Platform GPL24247
At a glance

DNA methylation · mouse · 201 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Mus musculus (mouse)
Samples
201 samples: 84 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
Nanobody-Tethered Transposition for Dual Profiling of Histone Modification and DNA MethylationJACS Au · 2026
Summary (written by the submitters)
DNA methylation and histone modifications are critical epigenetic regulators that orchestrate gene expression and modulate various physiological and pathological processes. However, existing methodologies for simultaneous profiling of these epigenetic marks often require high cell input and suffer from data loss due to bisulfite conversion.
Read the full summary ↓
In this study, we present advanced multimodal chromatin profiling methods, MethylTag and Multi-MethylTag, that address these challenges by integrating Tn5 transposase with methylated adaptors and optimizing post-bisulfite library preparation. These methods enable high-resolution, multi-dimensional chromatin profiling with reduced cell input and improved data integrity. We validated these techniques in various human and mouse cell lines, revealing complex interactions between DNA methylation and histone modifications. Our findings highlight the utility of these approaches in enhancing epigenetic research and deepening our understanding of the regulatory mechanisms underlying gene expression.
Published in
Nanobody-Tethered Transposition for Dual Profiling of Histone Modification and DNA Methylation
Liu J, Zhou J, Lu Z et al. · JACS Au 2026 · PMID 41614193 · doi:10.1021/jacsau.5c01492
This dataset
Open GSE278068 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 GSE278068_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 PRJNA1165323 and SRA study SRP534860. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41614193) ↗
Study design
84 conditions, mostly in duplicate
HEK293T,EX,H3K4ME3,5K,BS, ×3 HEK293T,EX,H3K4ME3,2W,BS, ×3 HEK293T,EX,H3K4ME3,5W,BS, ×3 HEK293T,EX,H3K4ME3,5K,IN, ×3 HEK293T,EX,H3K4ME3,2W,IN, ×3 HEK293T,EX,H3K4ME3,5W,IN, ×3 HEK293T,EX,H3K4ME3,5K,BS,spike, ×3 HEK293T,EX,H3K4ME3,2W,BS,spike, ×3 +81 more

Supports a between-group comparison across 196 samples.

How we read this: 84 replicated groups read from 201 sample titles; they account for 196 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

+ 161 more — browse all 201 samples with per-sample file links →

Datasets on a similar topic

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