GEO series

RNA-seq analysis of neurons overexpressing histone variant H2BE and stimulated with BDNF

GSE308556 Mus musculus (mouse) Single-nucleus RNA-seq 10 samples Submitted 2026/01/02 Platform GPL30172

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). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 10 samples: 3 × BDNF_N vs 3 × Control_N vs 2 × H2BE_N vs 2 × H2BE-BDNF_NGroups 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 GSE308556 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 GSE308556_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 PRJNA1330875 and SRA study SRP622018. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41422507) ↗

Study design

3 × BDNF_N vs 3 × Control_N vs 2 × H2BE_N vs 2 × H2BE-BDNF_N

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

GSM9247987 BDNF_N1 BDNF_N
GSM9247988 BDNF_N2 BDNF_N
GSM9247989 BDNF_N3 BDNF_N
GSM9247990 Control_N1 Control_N
GSM9247991 Control_N2 Control_N
GSM9247992 Control_N3 Control_N
GSM9247993 H2BE_N2 H2BE_N
GSM9247994 H2BE_N3 H2BE_N
GSM9247995 H2BE-BDNF_N2 H2BE-BDNF_N
GSM9247996 H2BE-BDNF_N3 H2BE-BDNF_N

Datasets on a similar topic

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, rna-seq, neurons, histone, variant
GSE308557 CUT&Tag seq analysis of histone variant H2BE in stimulated neurons 10 samples shares h2be, stimulated, neurons, histone, variant
GSE280190 Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling [RNA-seq] 24 samples shares h2be, rna-seq, histone, variant
GSE246618 CUT&Tag seq analysis of histone variant H2BE in neurons 6 samples shares h2be, neurons, 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
GSE280192 Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling [single-nucleus Drop-seq] 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

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