GEO series

Control of Mycobacterium abscessus pulmonary infection requires IFN- γ Induced formation of foam macrophages

GSE232854 Mus musculus (mouse) RNA-seq (gene expression) 22 samples Submitted 2026/05/18 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 22 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: 22 samples: 6 conditions, mostly with about 4 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)

To characterize the post infection responses of gene transcription in mice lungs after M. abscessus infection, we performed genome-wide transcriptional profiling analysis on lungs of WT and Rag2_KO mice after M. abscessus infection both in 7 dpi and 35dpi. The data revealed dynamic changes in lungs over a 35-day infection course. Four ‘‘functional’’ clusters were highlighted, including innate immunity function, adaptive immunity function, anti-microbial responses and inflammation & cell death.

This dataset

Open GSE232854 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 GSE232854_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 PRJNA974071 and SRA study SRP438531. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly with about 4 replicates each

Rag2_KO, Day7, ×4 WT, Day7, ×4 Rag2_KO, Day35, ×4 WT, Day35, ×4 Rag2_KO, Blank, ×3 WT, Blank, ×3

Supports a between-group comparison across 22 samples.

How we read this: 6 replicated groups read from 22 sample titles; they account for 22 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

GSM7384868 Rag2_KO, Blank, rep1 Rag2_KO, Blank,
GSM7384869 Rag2_KO, Blank, rep2 Rag2_KO, Blank,
GSM7384870 Rag2_KO, Blank, rep3 Rag2_KO, Blank,
GSM7384871 WT, Blank, rep1 WT, Blank,
GSM7384872 WT, Blank, rep2 WT, Blank,
GSM7384873 WT, Blank, rep3 WT, Blank,
GSM7384874 Rag2_KO, Day7, rep1 Rag2_KO, Day7,
GSM7384875 Rag2_KO, Day7, rep2 Rag2_KO, Day7,
GSM7384876 Rag2_KO, Day7, rep3 Rag2_KO, Day7,
GSM7384877 Rag2_KO, Day7, rep4 Rag2_KO, Day7,
GSM7384878 WT, Day7, rep1 WT, Day7,
GSM7384879 WT, Day7, rep2 WT, Day7,
GSM7384880 WT, Day7, rep3 WT, Day7,
GSM7384881 WT, Day7, rep4 WT, Day7,
GSM7384882 Rag2_KO, Day35, rep1 Rag2_KO, Day35,
GSM7384883 Rag2_KO, Day35, rep2 Rag2_KO, Day35,
GSM7384884 Rag2_KO, Day35, rep3 Rag2_KO, Day35,
GSM7384885 Rag2_KO, Day35, rep4 Rag2_KO, Day35,
GSM7384886 WT, Day35, rep1 WT, Day35,
GSM7384887 WT, Day35, rep2 WT, Day35,
GSM7384888 WT, Day35, rep3 WT, Day35,
GSM7384889 WT, Day35, rep4 WT, Day35,

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