GEO series

Early immune responses in the lung and blood following a randomized controlled human inhaled infection with aerosolized attenuated Mycobacterium Bovis BCG in healthy, BCG-naïve, UK adults

GSE282132 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2025/04/28 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 12 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: Homo sapiens (human)
Samples: 12 samples: 3 × BAL, Saline D2, vs 3 × BAL, BCG D2, vs 3 × BAL, BCG D7, vs 3 × BAL, Saline D7,Groups 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: Early mucosal responses following a randomised controlled human inhaled infection with attenuated Mycobacterium bovis BCGNature communications · 2025

Summary (written by the submitters)

We utilise an aerosol mycobacterial human challenge model using attenuated M.bovis BCG, in BCG-naïve UK adult volunteers, to define the initial innate and adaptive immune events at the airway parenchymal interface, and in the blood. Blinded volunteers were randomised to inhale 1x10^7 CFU aerosolised BCG Danish or 0.9% saline (20:6); and sequentially allocated to bronchoscopy at day 2 or 7 post-inhalation (10 BCG, 3 saline each timepoint). scRNA-seq was conducted using the Bronchoalveolar lavage (BAL) samples collected 2 days and 7 days post-aerosol BCG infection and from the saline controls.

Published in

Early mucosal responses following a randomised controlled human inhaled infection with attenuated Mycobacterium bovis BCG

Marshall JL, Satti I, Surakhy M et al. · Nature communications 2025 · PMID 40442144 · doi:10.1038/s41467-025-60285-4

This dataset

Open GSE282132 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 GSE282132_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 PRJNA1185950 and SRA study SRP545165. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40442144) ↗

Study design

3 × BAL, Saline D2, vs 3 × BAL, BCG D2, vs 3 × BAL, BCG D7, vs 3 × BAL, Saline D7,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM8636641 BAL, Saline D2, rep 1 BAL, Saline D2,
GSM8636642 BAL, Saline D2, rep 2 BAL, Saline D2,
GSM8636643 BAL, BCG D2, rep 1 BAL, BCG D2,
GSM8636644 BAL, Saline D2, rep 3 BAL, Saline D2,
GSM8636645 BAL, BCG D2, rep 2 BAL, BCG D2,
GSM8636646 BAL, BCG D2, rep 3 BAL, BCG D2,
GSM8636647 BAL, BCG D7, rep 1 BAL, BCG D7,
GSM8636648 BAL, BCG D7, rep 2 BAL, BCG D7,
GSM8636649 BAL, BCG D7, rep 3 BAL, BCG D7,
GSM8636650 BAL, Saline D7, rep 1 BAL, Saline D7,
GSM8636651 BAL, Saline D7, rep 2 BAL, Saline D7,
GSM8636652 BAL, Saline D7, rep 3 BAL, Saline D7,

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