GEO series

Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling [single-nucleus Drop-seq]

GSE280192 Mus musculus (mouse) Single-nucleus RNA-seq 10 samples Submitted 2025/10/01 Platform GPL19057

At a glance

Single-nucleus RNA-seq · mouse · 10 samples

What it is: Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism: Mus musculus (mouse)
Samples: 10 samples: 3 × cortex_WT_control vs 3 × cortex_KO_control vs 2 × cortex_WT_seizure vs 2 × cortex_KO_seizureGroups 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: Histone variant H2BE controls activity-dependent gene expression and homeostatic scalingCell reports · 2026

Summary (written by the submitters)

A cell’s ability to respond and adapt to environmental stimuli relies in part on transcriptional programs controlled by histone proteins. Histones affect transcription through numerous mechanisms including through replacement with variant forms that carry out specific functions. We recently identified the first widely expressed H2B histone variant, H2BE and found that it promotes transcription and is critical for neuronal function and long-term memory.

Read the full summary ↓

However, how H2BE is regulated by extracellular stimuli and whether it controls activity-dependent transcription and cellular plasticity remain unknown. We used CUT&Tag and RNA-sequencing of primary neurons, single-nucleus sequencing of cortical tissue, and multielectrode array recordings to interrogate the expression of H2BE in response to stimuli and the role of H2BE in activity-dependent gene expression and plasticity. We find that unlike Further, we show that neurons lacking H2BE are unable to mount proper long-term activity-dependent transcriptional responses both in cultured neurons and in animal models. Lastly, we demonstrate that H2BE knockout neurons fail to undergo the electrophysiological changes associated with homeostatic plasticity in neurons after long-term stimulation. In summary, these data demonstrate that H2BE expression is inversely correlated to activity and necessary for long-term activity-dependent responses, revealing the first instance of a histone variant involved in the homeostatic plasticity response in neurons.

Published in

Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling

Feierman ER, Paranjapye A, Sangree AK et al. · Cell reports 2026 · PMID 41422507 · doi:10.1016/j.celrep.2025.116694

This dataset

Open GSE280192 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 GSE280192_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 PRJNA1176993 and SRA study SRP540487. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41422507) ↗

Study design

3 × cortex_WT_control vs 3 × cortex_KO_control vs 2 × cortex_WT_seizure vs 2 × cortex_KO_seizure

Supports a between-group comparison across 10 samples.

How we read this: 4 replicated groups read from 10 sample titles; they account for 10 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

GSM8591347 cortex_WT_control_rep1 cortex_WT_control
GSM8591348 cortex_WT_seizure_rep1 cortex_WT_seizure
GSM8591349 cortex_WT_control_rep2 cortex_WT_control
GSM8591350 cortex_WT_seizure_rep2 cortex_WT_seizure
GSM8591351 cortex_KO_control_rep1 cortex_KO_control
GSM8591352 cortex_KO_seizure_rep1 cortex_KO_seizure
GSM8591353 cortex_KO_control_rep2 cortex_KO_control
GSM8591354 cortex_KO_seizure_rep2 cortex_KO_seizure
GSM8591355 cortex_KO_control_rep3 cortex_KO_control
GSM8591356 cortex_WT_control_rep3 cortex_WT_control

Datasets on a similar topic

GSE280190 Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling [RNA-seq] 24 samples shares h2be, activity-dependent, homeostatic, controls, histone, variant
GSE280196 Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling. 43 samples shares h2be, activity-dependent, homeostatic, controls, histone, variant
GSE246688 CUT&Tag, ATAC-seq, bulk RNA-seq and single-nucleus RNA-seq analysis of histone variant H2BE in cortical neurons 67 samples shares h2be, single-nucleus, histone, variant
GSE282467 Age and cell type specific specific effects of histone variant H2BE in the brain [Intact_RNAseq] 12 samples shares h2be, histone, variant
GSE308556 RNA-seq analysis of neurons overexpressing histone variant H2BE and stimulated with BDNF 10 samples shares h2be, histone, variant
GSE282468 Age and cell type specific specific effects of histone variant H2BE in the brain [RNASeq] 3 samples shares h2be, histone, variant
GSE282578 Age and cell type specific specific effects of histone variant H2BE in the brain 47 samples shares h2be, histone, variant
GSE246739 ATAC-seq analysis of histone variant H2BE in neuronal chromatin 25 samples shares h2be, histone, variant

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