GEO series

Single-cell transcriptomics reveals probiotic reversal of neonatal morphine-induced gene disruptions underlying adolescent pain hypersensitivity.

GSE298919 Mus musculus (mouse) Single-cell RNA-seq 13 samples Submitted 2025/10/24 Platform GPL34290

At a glance

Single-cell RNA-seq · mouse · 13 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: 13 samples: 5 × Morphine vs 4 × Control vs 4 × Morphine+probioticsGroups 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: Single-cell transcriptomics reveals probiotic reversal of neonatal morphine-induced gene disruptions underlying adolescent pain hypersensitivityCommunications biology · 2025

Summary (written by the submitters)

Neonatal morphine is commonly administered in the Neonatal Intensive Care Unit (NICU) to manage pain. However, its long-term effects on neurodevelopment of pain pathways, remain a significant concern. The midbrain is a core region that plays a central role in pain processing and opioid-mediated analgesia. Here, we performed single-cell RNA sequencing to study gene expression in 107,427 midbrain single cells from adolescent mice neonatally exposed to either saline, morphine, or morphine with the probiotic Bifidobacterium infantis (B.

Read the full summary ↓

infantis). We found broad alterations in transcriptomics within neurons, astrocytes, oligodendrocytes, and microglial cells. Analysis of differentially regulated genes revealed down regulation of HOX genes and upregulation of pathways related to neurotransmitter signaling and pain in adolescence that were neonatally treated with morphine. Interestingly, neonatal probiotic supplementation mitigated these morphine-induced alterations on the transcriptome. This study presents the first single-cell RNA sequencing dataset of the adolescent midbrain following neonatal morphine exposure and probiotic intervention. These findings offer new insights into the neurodevelopmental impact of early opioid exposure and highlight the therapeutic potential of microbiome-targeted interventions.

Published in

Single-cell transcriptomics reveals probiotic reversal of neonatal morphine-induced gene disruptions underlying adolescent pain hypersensitivity

Tao J, Antoine D, Jalodia R et al. · Communications biology 2025 · PMID 41372449 · doi:10.1038/s42003-025-09150-0

This dataset

Open GSE298919 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 GSE298919_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 PRJNA1260540 and SRA study SRP585315. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41372449) ↗

Study design

5 × Morphine vs 4 × Control vs 4 × Morphine+probiotics

Supports a between-group comparison across 13 samples.

How we read this: 3 replicated groups read from 13 sample titles; they account for 13 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

GSM9026016 Control1 Control
GSM9026017 Control2 Control
GSM9026018 Control3 Control
GSM9026019 Control4 Control
GSM9026020 Morphine-1 Morphine
GSM9026021 Morphine-2 Morphine
GSM9026022 Morphine-3 Morphine
GSM9026023 Morphine-4 Morphine
GSM9026024 Morphine-5 Morphine
GSM9026025 Morphine+probiotics1 Morphine+probiotics
GSM9026026 Morphine+probiotics2 Morphine+probiotics
GSM9026027 Morphine+probiotics3 Morphine+probiotics
GSM9026028 Morphine+probiotics4 Morphine+probiotics

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