GEO series

KMT2C catalytic activity regulates enhancer H3K4me1 and synaptic gene expression in cortical excitatory neurons [CUT&Tag]

GSE336091 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 48 samples Submitted 2026/06/30 Platform GPL32159

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 48 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: 48 samples: 48 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.

Summary (written by the submitters)

Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental condition in which chromatin regulators represent some of the highest-confidence genetic risk factors. KMT2C encodes a COMPASS family histone methyltransferase that deposits H3K4me1 at enhancers, yet how its dysfunction contributes to ASD remains poorly understood.

Read the full summary ↓

Here, analysis of the SPARK cohort revealed a significant enrichment of ASD-associated variants within the catalytic SET domain of KMT2C. To determine the functional consequences of impaired catalytic activity, we selectively ablated the SET domain in cortical excitatory neurons. Loss of KMT2C catalytic function resulted in robust and persistent downregulation of genes involved in synapse assembly and synaptic signaling across developmental stages and in both sexes. These transcriptional deficits were accompanied by selective reductions in H3K4me1 at associated regulatory elements. Together, our findings demonstrate that KMT2C catalytic activity is required to maintain enhancer-associated H3K4me1 and sustain synaptic gene expression in cortical excitatory neurons.

This dataset

Open GSE336091 in finder → Find more mouse ChIP / ATAC / CUT&Tag 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 GSE336091_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 PRJNA1480682 and SRA study SRP711467. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

48 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 48 sample titles: 48 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

GSM9827142 neurons,WT,week18,female,rep1 (500_H3K27ac)
GSM9827143 neurons,WT,week18,female,rep1 (500_H3K4me1)
GSM9827144 neurons,WT,week18,female,rep1 (500_H3K4me2)
GSM9827145 neurons,WT,week18,female,rep1 (500_H3K4me3)
GSM9827146 neurons,WT,week18,female,rep2 (504_H3K27ac)
GSM9827147 neurons,WT,week18,female,rep2 (504_H3K4me1)
GSM9827148 neurons,WT,week18,female,rep2 (504_H3K4me2)
GSM9827149 neurons,WT,week18,female,rep2 (504_H3K4me3)
GSM9827150 neurons,WT,week18,female,rep3 (505_H3K27ac)
GSM9827151 neurons,WT,week18,female,rep3 (505_H3K4me1)
GSM9827152 neurons,WT,week18,female,rep3 (505_H3K4me2)
GSM9827153 neurons,WT,week18,female,rep3 (505_H3K4me3)
GSM9827154 neurons,cK2c,week18,female,rep1 (175_H3K27ac)
GSM9827155 neurons,cK2c,week18,female,rep1 (175_H3K4me1)
GSM9827156 neurons,cK2c,week18,female,rep1 (175_H3K4me2)
GSM9827157 neurons,cK2c,week18,female,rep1 (175_H3K4me3)
GSM9827158 neurons,cK2c,week18,female,rep2 (501_H3K27ac)
GSM9827159 neurons,cK2c,week18,female,rep2 (501_H3K4me1)
GSM9827160 neurons,cK2c,week18,female,rep2 (501_H3K4me2)
GSM9827161 neurons,cK2c,week18,female,rep2 (501_H3K4me3)
GSM9827162 neurons,cK2c,week18,female,rep3 (9776_H3K27ac)
GSM9827163 neurons,cK2c,week18,female,rep3 (9776_H3K4me1)
GSM9827164 neurons,cK2c,week18,female,rep3 (9776_H3K4me2)
GSM9827165 neurons,cK2c,week18,female,rep3 (9776_H3K4me3)
GSM9827166 neurons,WT,week18,male,rep1 (9278_H3K27ac)
GSM9827167 neurons,WT,week18,male,rep1 (9278_H3K4me1)
GSM9827168 neurons,WT,week18,male,rep1 (9278_H3K4me2)
GSM9827169 neurons,WT,week18,male,rep1 (9278_H3K4me3)
GSM9827170 neurons,WT,week18,male,rep2 (9768_H3K27ac)
GSM9827171 neurons,WT,week18,male,rep2 (9768_H3K4me1)
GSM9827172 neurons,WT,week18,male,rep2 (9768_H3K4me2)
GSM9827173 neurons,WT,week18,male,rep2 (9768_H3K4me3)
GSM9827174 neurons,WT,week18,male,rep3 (9771_H3K27ac)
GSM9827175 neurons,WT,week18,male,rep3 (9771_H3K4me1)
GSM9827176 neurons,WT,week18,male,rep3 (9771_H3K4me2)
GSM9827177 neurons,WT,week18,male,rep3 (9771_H3K4me3)
GSM9827178 neurons,cK2c,week18,male,rep1 (174_H3K27ac)
GSM9827179 neurons,cK2c,week18,male,rep1 (174_H3K4me1)
GSM9827180 neurons,cK2c,week18,male,rep1 (174_H3K4me2)
GSM9827181 neurons,cK2c,week18,male,rep1 (174_H3K4me3)

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

GSE335970 KMT2C catalytic activity regulates enhancer H3K4me1 and synaptic gene expression in cortical excitatory neurons [RNA-Seq] 39 samples shares h3k4me1, kmt2c, excitatory, catalytic, activity, enhancer, synaptic
GSE325799 KMT2C and KMT2D amplify GRHL2-driven enhancer activation [CUT&Tag] 80 samples shares kmt2c, cut, enhancer
GSE293129 Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging [CUT&RUN] 36 samples shares cut, enhancer
GSE290849 Acute intervention reveals critical roles of BAF, KMT2D and p300 in MyoD binding on enhancers 143 samples shares cut, enhancer
GSE304211 H4K16ac contributes to chromatin compartment reorganization during mitotic and meiotic transitions [CUTnTAG] 128 samples shares cut
GSE297309 SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [CUT&Tag] 108 samples shares cut
GSE289642 Noncanonical PRC2 chromatin association reveals a key role of EZHIP in intergenerational epigenetic memory transition [ChIP-Seq, Cut & Run] 107 samples shares cut
GSE303384 Mechanism of maintenance and establishment of repression by the Mtg16 tumor suppressor [CUT&RUN, ChIP-Seq] 92 samples shares cut

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