GEO series

SCoTCH-seq reveals that 5-hydroxymethylcytosine encodes regulatory information across DNA strands

GSE263772 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 2 samples Submitted 2025/07/16 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 2 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Mus musculus (mouse)
Samples: 2 samples: 2 samples, each with a distinct title — no replicated groupsGroups 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: SCoTCH-seq reveals that 5-hydroxymethylcytosine encodes regulatory information across DNA strandsProceedings of the National Academy of Sciences of the United States of America · 2025

Summary (written by the submitters)

In mammalian genomes, cytosine modifications form a layer of regulatory information alongside the genetic code. Decoding this information is crucial to our understanding of biology and disease. Established sequencing methods cannot simultaneously resolve cytosine’s three most common forms—cytosine (C), 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC)—across both strands of the DNA double helix.

Read the full summary ↓

Thus, how epigenetic information is distributed in DNA remains unclear. We present an accurate and quantitative, base-resolution approach to sequence genomes, together with mC and hmC, in both strands of the same DNA fragment. We show that different forms of cytosine combine across the double helix at CpG sites to form discrete information states in the mouse epigenome. These CpG states have distinct genomic distributions—including at promoters, enhancers, and gene bodies—and have different relationships with transcription. We show that while all possible forms of hydroxymethylation occur, hmC is predominantly asymmetric and that different forms of asymmetric hmC are not equivalent. Our findings demonstrate that 5-hydroxymethylcytosine combines with different cytosine variants across the DNA double helix to form distinct states of regulatory information.

Published in

SCoTCH-seq reveals that 5-hydroxymethylcytosine encodes regulatory information across DNA strands

Hardwick JS, Dhir S, Kirchner A et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 40743391 · doi:10.1073/pnas.2512204122

This dataset

Open GSE263772 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 GSE263772_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 peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1099216 and SRA study SRP501212. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40743391) ↗

Study design

2 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 2 sample titles: 2 distinct titles with little repetition. 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

GSM8198270 JSH9_E14 replicate 1
GSM8198271 JSH11_E14 replicate 2

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