GEO series

H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium (scRNA-Seq)

GSE249086 Mus musculus (mouse) Single-cell RNA-seq 1 samples Submitted 2024/10/25 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 1 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 1 samples
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: H3K36 methylation regulates cell plasticity and regeneration in the intestinal epitheliumNature cell biology · 2025

Summary (written by the submitters)

Cell plasticity is needed during development and homeostasis to generate diverse cell types from stem and progenitor cells. Following differentiation, plasticity must be restricted in specialized cells to maintain tissue integrity and function. For this reason, specialized cell identity is highly stable under homeostatic conditions; however, cells in some tissues regain plasticity during injury-induced regeneration.

Read the full summary ↓

While precise gene expression is needed to control these processes, the regulatory mechanisms that restrict or promote cell plasticity are poorly understood. Here, we use the mouse small intestine as a model system to study cell plasticity. We find that H3K36 methylation reinforces expression of cell type-associated genes to maintain specialized cell identity in intestinal epithelial cells. Depleting H3K36 methylation leads to defects in lineage commitment and activates a plastic, regenerative gene expression signature. Correspondingly, we observe rapid and reversible remodeling of H3K36 methylation following injury-induced regeneration. Together, these data suggest a fundamental role for H3K36 methylation in regulating cell plasticity and regeneration.

Published in

H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium

Pashos ARS, Meyer AR, Bussey-Sutton C et al. · Nature cell biology 2025 · PMID 39779942 · doi:10.1038/s41556-024-01580-y

This dataset

Open GSE249086 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 GSE249086_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1047143 and SRA study SRP475174. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39779942) ↗

Samples in this study

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+ 1 more — browse all 1 samples with per-sample file links →

Datasets on a similar topic

GSE275296 H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium [cutandtag_enzyme_profiling] 12 samples shares h3k36, regeneration, methylation, plasticity, intestinal, epithelium
GSE292289 H3K79 methylation and H3K36 trimethylation synergistically regulate gene expression in pluripotent stem cells 94 samples shares h3k36, methylation
GSE338640 Vascular function underlies enhanced intestinal regeneration after FLASH radiation 26 samples shares regeneration, intestinal
GSE337790 Vascular function underlies enhanced intestinal regeneration after FLASH radiation [bulk RNAseq] 18 samples shares regeneration, intestinal
GSE326641 Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation [scRNA-seq] 8 samples shares regeneration, scrna-seq
GSE297315 Crotonate-activated histone H3K14 crotonylation enhances intestinal regeneration after injury 41 samples shares regeneration, intestinal
GSE285237 R-loop maintains the deposition of H3K36me3 to prevent invasion of H3K4me3 during SN-oocyte development [3] 15 samples shares h3k36
GSE229903 CUT&Tag analysis of H3K4me3, H3K27Ac,H2A119Ub, H3K27me3 and H3K36me3 in KPC1199 murine PDAC cell line 10 samples shares h3k36

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