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Transcriptomic profiling of morphine and LPS exposure across mouse brain regions

GSE332798 Mus musculus (mouse) RNA-seq (gene expression) 208 samples Submitted 2026/06/17 Platform GPL34290

At a glance

RNA-seq (gene expression) · mouse · 208 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: 208 samples: 71 conditions, mostly in duplicateGroups 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)

We profiled genome-wide gene expression across four brain regions (hippocampus, prefrontal cortex, striatum, and hypothalamus) in male and female C57BL/6NTac mice using a perinatal morphine exposure model of Neonatal Opioid Withdrawal Syndrome (NOWS). Mice received morphine or saline perinatally, then were challenged with LPS or saline in adulthood, yielding four groups (SAL-SAL, SAL-LPS, MOR-SAL, MOR-LPS).

Read the full summary ↓

NeuN+ neuronal nuclei (~5,000 per sample) were isolated by FACS from PFC, hippocampus, hypothalamus, and striatum and profiled by RNA-seq (Illumina NovaSeq X Plus, paired-end 150 bp). RNA-seq identified differentially expressed genes enriched in immune and metabolic pathways, with the hypothalamus displaying the most pronounced transcriptional response to perinatal morphine exposure.

This dataset

Open GSE332798 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 GSE332798_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 PRJNA1469105 and SRA study SRP702674. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

71 conditions, mostly in duplicate

RNA-seq hippocampus, SAL-LPS, male, replicate… ×3 RNA-seq hippocampus, SAL-SAL, female, replica… ×3 RNA-seq hippocampus, SAL-SAL, male, replicate… ×3 RNA-seq hypothalamus, MOR-LPS, female, replic… ×3 RNA-seq hypothalamus, SAL-LPS, female, replic… ×3 RNA-seq hypothalamus, SAL-LPS, male, replicat… ×3 RNA-seq striatum, MOR-LPS, female, replicate … ×3 RNA-seq striatum, MOR-LPS, male, replicate 6 ×3 +117 more

Supports a between-group comparison across 154 samples.

How we read this: 71 replicated groups read from 208 sample titles; they account for 154 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

GSM9753585 RNA-seq hippocampus, MOR-LPS, female, replicate 12-0 RNA-seq hippocampus, MO…
GSM9753586 RNA-seq hippocampus, MOR-LPS, female, replicate 12-2 RNA-seq hippocampus, MO…
GSM9753587 RNA-seq hippocampus, MOR-LPS, female, replicate 15-1 RNA-seq hippocampus, MO…
GSM9753588 RNA-seq hippocampus, MOR-LPS, female, replicate 15-3 RNA-seq hippocampus, MO…
GSM9753589 RNA-seq hippocampus, MOR-LPS, female, replicate 16-2 RNA-seq hippocampus, MO…
GSM9753590 RNA-seq hippocampus, MOR-LPS, female, replicate 16-4 RNA-seq hippocampus, MO…
GSM9753591 RNA-seq hippocampus, MOR-LPS, female, replicate 18-1
GSM9753592 RNA-seq hippocampus, MOR-LPS, female, replicate 7-1
GSM9753593 RNA-seq hippocampus, MOR-LPS, male, replicate 13-0 RNA-seq hippocampus, MO…
GSM9753594 RNA-seq hippocampus, MOR-LPS, male, replicate 13-2 RNA-seq hippocampus, MO…
GSM9753595 RNA-seq hippocampus, MOR-LPS, male, replicate 14-2 RNA-seq hippocampus, MO…
GSM9753596 RNA-seq hippocampus, MOR-LPS, male, replicate 14-4 RNA-seq hippocampus, MO…
GSM9753597 RNA-seq hippocampus, MOR-LPS, male, replicate 17-1 RNA-seq hippocampus, MO…
GSM9753598 RNA-seq hippocampus, MOR-LPS, male, replicate 17-3 RNA-seq hippocampus, MO…
GSM9753599 RNA-seq hippocampus, MOR-LPS, male, replicate 6-2
GSM9753600 RNA-seq hippocampus, MOR-LPS, male, replicate 8-3
GSM9753601 RNA-seq hippocampus, MOR-SAL, female, replicate 15-2 RNA-seq hippocampus, MO…
GSM9753602 RNA-seq hippocampus, MOR-SAL, female, replicate 15-4 RNA-seq hippocampus, MO…
GSM9753603 RNA-seq hippocampus, MOR-SAL, female, replicate 16-1
GSM9753604 RNA-seq hippocampus, MOR-SAL, female, replicate 18-0
GSM9753605 RNA-seq hippocampus, MOR-SAL, female, replicate 7-2 RNA-seq hippocampus, MO…
GSM9753606 RNA-seq hippocampus, MOR-SAL, female, replicate 7-3 RNA-seq hippocampus, MO…
GSM9753607 RNA-seq hippocampus, MOR-SAL, male, replicate 13-1 RNA-seq hippocampus, MO…
GSM9753608 RNA-seq hippocampus, MOR-SAL, male, replicate 13-3 RNA-seq hippocampus, MO…
GSM9753609 RNA-seq hippocampus, MOR-SAL, male, replicate 17-2 RNA-seq hippocampus, MO…
GSM9753610 RNA-seq hippocampus, MOR-SAL, male, replicate 17-4 RNA-seq hippocampus, MO…
GSM9753611 RNA-seq hippocampus, MOR-SAL, male, replicate 6-1
GSM9753612 RNA-seq hippocampus, MOR-SAL, male, replicate 8-0
GSM9753613 RNA-seq hippocampus, SAL-LPS, female, replicate 10-0 RNA-seq hippocampus, SA…
GSM9753614 RNA-seq hippocampus, SAL-LPS, female, replicate 10-4 RNA-seq hippocampus, SA…
GSM9753615 RNA-seq hippocampus, SAL-LPS, female, replicate 2-0 RNA-seq hippocampus, SA…
GSM9753616 RNA-seq hippocampus, SAL-LPS, female, replicate 2-2 RNA-seq hippocampus, SA…
GSM9753617 RNA-seq hippocampus, SAL-LPS, female, replicate 3-1
GSM9753618 RNA-seq hippocampus, SAL-LPS, female, replicate 4-0 RNA-seq hippocampus, SA…
GSM9753619 RNA-seq hippocampus, SAL-LPS, female, replicate 4-4 RNA-seq hippocampus, SA…
GSM9753620 RNA-seq hippocampus, SAL-LPS, female, replicate 9-3
GSM9753621 RNA-seq hippocampus, SAL-LPS, male, replicate 1-0 RNA-seq hippocampus, SA…
GSM9753622 RNA-seq hippocampus, SAL-LPS, male, replicate 1-2 RNA-seq hippocampus, SA…
GSM9753623 RNA-seq hippocampus, SAL-LPS, male, replicate 1-4 RNA-seq hippocampus, SA…
GSM9753624 RNA-seq hippocampus, SAL-LPS, male, replicate 11-0

+ 168 more — browse all 208 samples with per-sample file links →

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GSE290810 ALS/FTD-linked TBK1 deficiency in microglia induces an aged-like microglial signature and drives social recognition deficits [FACS_SpinalCord_Microglia & LPS_Brain_SpinalCord] 35 samples shares lps, brain
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Search all mouse RNA-seq datasets in GEO →

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