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Transport stress induces immune dysregulation and exacerbates Mycobacterium tuberculosis infection in mice

GSE284562 Mus musculus (mouse) Single-cell RNA-seq 28 samples Submitted 2026/03/26 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 28 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. 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
28 samples: 12 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)
While transport stress (TS) is a well-known factor impacting immune function and infection, its cellular and molecular mechanisms remain elusive. In this study, we investigated the effects of TS on immune responses and its role in exacerbating Mycobacterium tuberculosis (Mtb) infection in mice. Behavioral assessments revealed that TS induced anxiety-like behaviors in mice.
Read the full summary ↓
Concomitantly, TS disrupted hypothalamic-pituitary-adrenal (HPA) axis homeostasis, altered hormone secretion patterns, and led to dysregulation of stress response genes (Egr1, Fos) and circadian regulators (Dbp, Per3). Single-cell RNA sequencing of the spleen revealed severe immune dysfunction, characterized by inhibition of Th17 differentiation, IL-17 signaling, and antigen presentation. Importantly, TS affects the crosstalk between the HPA axis and the spleen through ligand-receptor interactions, such as Pomc-Oprm1 and Gdf15-Tgfbr2. Furthermore, TS exacerbated the severity of Mtb infection, increased bacterial loads in the lungs and spleen, and attenuated infection-induced upregulation of immune genes (Tnfα, Il12b). Mechanistically, TS impairs adaptive immunity (Th1/Th2 differentiation) while amplifying neurotransmitter-related signaling, ultimately compromising host defenses. These findings highlight TS as a key contributor to neuroendocrine immune dysregulation, leading to increased susceptibility to infection. Addressing stress-related immune dysfunction may be crucial for improving outcomes in tuberculosis and other infectious diseases.
This dataset
Open GSE284562 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 GSE284562_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 PRJNA1173960 and SRA study SRP539802. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly in duplicate
hypothalamus, transport stress, ×2 hypothalamus, control, ×2 hypothalamus, transport stress+Mtb, ×2 hypothalamus, Mtb, ×2 hypophysis, transport stress, ×2 hypophysis, control, ×2 hypophysis, transport stress+Mtb, ×2 hypophysis, Mtb, ×2 +8 more

Supports a between-group comparison across 24 samples.

How we read this: 12 replicated groups read from 28 sample titles; they account for 24 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
Datasets on a similar topic

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