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Neuronal development shapes activity-dependent gene expression profiles in a stimulus-specific manner

GSE277512 Mus musculus (mouse) RNA-seq (gene expression) 55 samples Submitted 2025/09/17 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 55 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
55 samples: 21 conditions, mostly in triplicateGroups 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
Neuronal activity-dependent gene expression is stimulus-specific and changes with neuronal maturationFrontiers in molecular neuroscience · 2025
Summary (written by the submitters)
Neuronal activity-dependent gene expression is fundamental to a wide variety of brain functions. Transcriptional profile after in vitro stimulation has been assessed using different modalities to induce neuronal activity. In this work, we first investigate the influence of development on neuronal activity and activity-driven transcription.
Read the full summary ↓
We used an RNA sequencing approach over 7 days in vitro (DIV) or mature 21 DIV neurons after neuronal depolarization with potassium chloride (KCl)compared to Biccuculine application, a synaptic modality to induce neuronal activity. To further investigate how different activity patterns influence gene transcription in mature neurons, we performed a comparative analysis of global gene expression in neurons treated with extensively used activation protocols KCl, Bic, and TTX withdrawal. Our results demonstrate that different patterns of neuronal activity not only induce different transcriptional profiles but also exhibit distinct temporal dynamics for the same genes. These findings offer novel insights into the complex relationship between neuronal activity and gene expression, shedding light on the context-dependent nature of activity-dependent transcriptional responses.
Published in
Neuronal activity-dependent gene expression is stimulus-specific and changes with neuronal maturation
Lukin J, Beckel MS, Pedroncini O et al. · Frontiers in molecular neuroscience 2025 · PMID 41142683 · doi:10.3389/fnmol.2025.1609772
This dataset
Open GSE277512 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 GSE277512_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1162548 and SRA study SRP533434. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41142683) ↗
Study design
21 conditions, mostly in triplicate
21DIV_BasalTTX_0min ×4 7DIV_Basal_0min ×3 7DIV_KCl_15min ×3 7DIV_KCl_3h ×3 7DIV_4APBic_15min ×3 7DIV_4APBic_3h ×3 23DIV_Basal_0min ×3 23DIV_KCl_15min ×3 +13 more

Supports a between-group comparison across 55 samples.

How we read this: 21 replicated groups read from 55 sample titles; they account for 55 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

+ 15 more — browse all 55 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.