GEO series

PD-1 Deficiency Exacerbates Mycobacterium abscessus Lung Infection via Dysregulated T Cell Responses

GSE317833 Mus musculus (mouse) RNA-seq (gene expression) 30 samples Submitted 2026/04/14 Platform GPL34290

At a glance

RNA-seq (gene expression) · mouse · 30 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: 30 samples: 6 conditions, mostly with about 5 replicates eachGroups 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)

A PD-1-deficient Mycobacterium abscessus -infected mouse model was established. The impact of PD-1 on bacterial clearance, immune cell activity, and metabolism was evaluated via colony counting, histopathology, flow cytometry, multiplex immunofluorescence and transcriptomics. We fonud that PD-1−/− mice exhibited increased susceptibility to MAB. Early infection showed elevated lung CD4⁺ T cells, reduced neutrophils, and higher blood cytokines (IFN-γ, IL-21, IL-6, IL-27).

This dataset

Open GSE317833 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 GSE317833_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 PRJNA1411448. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly with about 5 replicates each

lung, WT mice, MAB infection, day 3, ×5 lung, WT mice, MAB infection, day 7, ×5 lung, WT mice, MAB infection, day 14, ×5 lung, PD-1-Deficient Mice, MAB infection, day… ×5 lung, PD-1-Deficient Mice, MAB infection, day… ×5 lung, PD-1-Deficient Mice, MAB infection, day… ×5

Supports a between-group comparison across 30 samples.

How we read this: 6 replicated groups read from 30 sample titles; they account for 30 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

GSM9479894 lung, WT mice, MAB infection, day 3, rep1 lung, WT mice, MAB infe…
GSM9479895 lung, WT mice, MAB infection, day 3, rep2 lung, WT mice, MAB infe…
GSM9479896 lung, WT mice, MAB infection, day 3, rep3 lung, WT mice, MAB infe…
GSM9479897 lung, WT mice, MAB infection, day 3, rep4 lung, WT mice, MAB infe…
GSM9479898 lung, WT mice, MAB infection, day 3, rep5 lung, WT mice, MAB infe…
GSM9479899 lung, WT mice, MAB infection, day 7, rep1 lung, WT mice, MAB infe…
GSM9479900 lung, WT mice, MAB infection, day 7, rep2 lung, WT mice, MAB infe…
GSM9479901 lung, WT mice, MAB infection, day 7, rep3 lung, WT mice, MAB infe…
GSM9479902 lung, WT mice, MAB infection, day 7, rep4 lung, WT mice, MAB infe…
GSM9479903 lung, WT mice, MAB infection, day 7, rep5 lung, WT mice, MAB infe…
GSM9479904 lung, WT mice, MAB infection, day 14, rep1 lung, WT mice, MAB infe…
GSM9479905 lung, WT mice, MAB infection, day 14, rep2 lung, WT mice, MAB infe…
GSM9479906 lung, WT mice, MAB infection, day 14, rep3 lung, WT mice, MAB infe…
GSM9479907 lung, WT mice, MAB infection, day 14, rep4 lung, WT mice, MAB infe…
GSM9479908 lung, WT mice, MAB infection, day 14, rep5 lung, WT mice, MAB infe…
GSM9479909 lung, PD-1-Deficient Mice, MAB infection, day 3, rep1 lung, PD-1-Deficient Mi…
GSM9479910 lung, PD-1-Deficient Mice, MAB infection, day 3, rep2 lung, PD-1-Deficient Mi…
GSM9479911 lung, PD-1-Deficient Mice, MAB infection, day 3, rep3 lung, PD-1-Deficient Mi…
GSM9479912 lung, PD-1-Deficient Mice, MAB infection, day 3, rep4 lung, PD-1-Deficient Mi…
GSM9479913 lung, PD-1-Deficient Mice, MAB infection, day 3, rep5 lung, PD-1-Deficient Mi…
GSM9479914 lung, PD-1-Deficient Mice, MAB infection, day 7, rep1 lung, PD-1-Deficient Mi…
GSM9479915 lung, PD-1-Deficient Mice, MAB infection, day 7, rep2 lung, PD-1-Deficient Mi…
GSM9479916 lung, PD-1-Deficient Mice, MAB infection, day 7, rep3 lung, PD-1-Deficient Mi…
GSM9479917 lung, PD-1-Deficient Mice, MAB infection, day 7, rep4 lung, PD-1-Deficient Mi…
GSM9479918 lung, PD-1-Deficient Mice, MAB infection, day 7, rep5 lung, PD-1-Deficient Mi…
GSM9479919 lung, PD-1-Deficient Mice, MAB infection, day 14, rep1 lung, PD-1-Deficient Mi…
GSM9479920 lung, PD-1-Deficient Mice, MAB infection, day 14, rep2 lung, PD-1-Deficient Mi…
GSM9479921 lung, PD-1-Deficient Mice, MAB infection, day 14, rep3 lung, PD-1-Deficient Mi…
GSM9479922 lung, PD-1-Deficient Mice, MAB infection, day 14, rep4 lung, PD-1-Deficient Mi…
GSM9479923 lung, PD-1-Deficient Mice, MAB infection, day 14, rep5 lung, PD-1-Deficient Mi…

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