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Mycobacterium tuberculosis Co-opts Monocytic Niches to Evade Immunity in Lymph Nodes

GSE309019 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2026/06/19 Platform GPL34328
At a glance

RNA-seq (gene expression) · mouse · 20 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
20 samples: 7 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)
Mycobacterium tuberculosis (Mtb) not only establishes lung infection but also disseminates to lung-draining lymph nodes (LNs), where it can persist long-term. Paradoxically, these same LNs are critical for initiating protective T cell responses that help control infection. To understand how these divergent outcomes coexist within the same tissue, we examined the spatiotemporal dynamics of myeloid and CD4 T cell responses in the mediastinal LN (medLN) of mice after aerosol Mtb infection and BCG vaccination.
Read the full summary ↓
During early infection (2-3 weeks), Mtb disseminated to the medLN via conventional dendritic cells (cDC) and monocytes, which localized to the T cell zone and typically harbored single bacilli. This phase was marked by robust Th1 priming, driven by IL-12-producing cDC1 and type I IFN-induced inflammatory cDC2s. By 3-4 weeks, however, cDC migration declined and medLNs became dominated by large monocyte-derived aggregates containing multiple bacilli. These aggregates exhibited alternative activation profiles and coincided with reduced T cell priming and Th1 differentiation. Strikingly, Mtb-specific T cells appeared unable to engage these infected aggregates, suggesting immunological ‘blindness’ to this niche. BCG vaccination curtailed Mtb burden and limited monocyte aggregate formation in the medLN without significantly altering myeloid trafficking or T cell priming, suggesting that vaccination impairs the formation of the monocytic niche rather than initial dissemination. Together, these findings reveal a narrow temporal window for effective T cell priming in LNs and identify a later-arising monocytic niche that supports Mtb persistence while evading immune recognition, highlighting how spatially organized host-pathogen interactions govern both protection and persistence during tuberculosis.
This dataset
Open GSE309019 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 GSE309019_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 PRJNA1333800 and SRA study SRP626286. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
7 conditions, mostly in duplicate
blood.inf.d15 ×2 lung.neg.d15 ×2 mln.neg.d15 ×2 blood.inf.d28 ×2 lung.neg.d28 ×2 mln.neg.d28 ×2 mln.pos.d28 ×2 lung.pos.d15 ×1 +5 more

Supports a between-group comparison across 14 samples.

How we read this: 7 replicated groups read from 20 sample titles; they account for 14 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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