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Lung mucosal and systemic responses at single-cell resolution in an aerosolised Mycobacterium bovis BCG human challenge model

GSE301133 Homo sapiens (human) Single-cell RNA-seq 159 samples Submitted 2026/04/13 Platform GPL34284Platform GPL24676
At a glance

Single-cell RNA-seq · human · 159 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Samples
159 samples: 35 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.
Summary (written by the submitters)
The development of an effective vaccine against tuberculosis (TB) is hindered by the limited understanding of the dynamics of cellular responses to Mycobacterium tuberculosis infection in humans. Here, in our aerosolised Mycobacterium bovis BCG human challenge study, we used single-cell and bulk immune profiling of bronchoalveolar lavage and blood samples to temporally resolve the dynamics of immune responses in BCG-naïve individuals.
Read the full summary ↓
We observed a rapid change in cellular composition and gene expression in both the lung mucosa and blood. TB-specific gene signatures were observed on days 2 and 7 following aerosol challenge. T cell receptor (TCR) clones that expanded in the blood seven days post-challenge (BCG-expanded TCR clones) persisted in the lung mucosa for up to 56 days post-challenge, with most of these detectable in the blood prior to challenge. Pre-existing BCG-expanded TCR clones were more likely to be activated CD4⁺ T cells and were more enriched in the lung mucosa than newly expanded TCR clones. Only a small proportion of mycobacterial antigen-reactive TCR clones in the blood, detected by the activation-induced marker assay, were enriched in the lung mucosa. Several public BCG-expanded TCR clones across individuals were identified in the lung mucosa and shown to be reactive to mycobacterial antigens using artificial antigen-presenting cells and reporter T cells. Overall, our study provides crucial insights into the dynamics of human mucosal and systemic immunity following aerosolised BCG challenge, informing the design of more effective TB vaccines.
This dataset
Open GSE301133 in finder → Find more human 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 GSE301133_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 PRJNA1281703. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
35 conditions, mostly in triplicate
PBMC TCR, BCG, TBT04301051-D ×6 PBMC TCR, BCG, TBT04301058-D ×6 PBMC TCR, BCG, TBT04301059-D ×6 PBMC TCR, BCG, TBT04301062-D ×6 PBMC TCR, BCG, TBT04301072-D ×6 PBMC TCR, BCG, TBT04301097-D ×6 PBMC TCR, BCG, TBT04301083-D ×4 PBMC TCR, BCG, TBT04301086-D ×4 +71 more

Supports a between-group comparison across 115 samples.

How we read this: 35 replicated groups read from 159 sample titles; they account for 115 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

+ 119 more — browse all 159 samples with per-sample file links →

Datasets on a similar topic

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