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Systems biology mapping of rBCG-LTAK63-induced protection against tuberculosis reveals the significance of autophagy and circadian rhythm regulation by cAMP

GSE278523 Mus musculus (mouse) RNA-seq (gene expression) 126 samples Submitted 2025/09/01 Platform GPL23479
At a glance

RNA-seq (gene expression) · mouse · 126 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
126 samples: 126 samples, each with a distinct title — no replicated groupsGroups 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
rBCG-LTAK63 enhances protection against tuberculosis by inducing autophagy and circadian gene regulationFrontiers in immunology · 2025
Summary (written by the submitters)
Using systems biology and RNA sequencing data from lung cells, we investigated the immune mechanisms of protection induced by this vaccine in mice, both after immunization and following challenge. The RNA-seq data were analyzed using IPA (Ingenuity Pathways Analysis), CEMiTools (modular co-expression analysis). The RNA-seq derived results were analysed through correlation with immune response and disease outcomes, such as bacillary load, pathology score (infiltrated cell number, inflammatory area, and functional area).
Published in
rBCG-LTAK63 enhances protection against tuberculosis by inducing autophagy and circadian gene regulation
Marques-Neto LM, Trentini MM, Moreno ACR et al. · Frontiers in immunology 2025 · PMID 41208953 · doi:10.3389/fimmu.2025.1695560
This dataset
Open GSE278523 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 GSE278523_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 PRJNA1159865 and SRA study SRP534644. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41208953) ↗
Study design
126 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 126 sample titles: 126 distinct titles with little repetition. 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

+ 86 more — browse all 126 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.