Analyzing the impact of antibiotics treatment on lung inflammation in Mtb infected mouse lungs using bulk RNA transcriptomics
RNA-seq (gene expression) · mouse · 20 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
- 20 samples: 7 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.
- Paper
- Inflammatory Macrophages Associate With Tissue Injury and Fibrosis in a Mouse Model of TuberculosisThe Journal of infectious diseases · 2025
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE300035_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1278745 and SRA study SRP592753. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 7 replicated groups read from 20 sample titles; they account for 20 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.
- GSM9052724 Uninfected - biol rep 1 Uninfected - biol
- GSM9052725 Uninfected - biol rep 2 Uninfected - biol
- GSM9052726 Uninfected - biol rep 3 Uninfected - biol
- GSM9052727 12 weeks Mtb infected + 2 weeks carrier treated- biol rep 1 12 weeks Mtb infected +…
- GSM9052728 12 weeks Mtb infected + 2 weeks carrier treated- biol rep 2 12 weeks Mtb infected +…
- GSM9052729 12 weeks Mtb infected + 2 weeks carrier treated- biol rep 3 12 weeks Mtb infected +…
- GSM9052730 12 weeks Mtb infected + 2 weeks RIPE treated- biol rep 1 12 weeks Mtb infected +…
- GSM9052731 12 weeks Mtb infected + 2 weeks RIPE treated- biol rep 2 12 weeks Mtb infected +…
- GSM9052732 12 weeks Mtb infected + 2 weeks RIPE treated- biol rep 3 12 weeks Mtb infected +…
- GSM9052733 12 weeks Mtb infected + 4 weeks carrier treated- biol rep 1 12 weeks Mtb infected +…
- GSM9052734 12 weeks Mtb infected + 4 weeks carrier treated- biol rep 2 12 weeks Mtb infected +…
- GSM9052735 12 weeks Mtb infected + 4 weeks carrier treated- biol rep 3 12 weeks Mtb infected +…
- GSM9052736 12 weeks Mtb infected + 4 weeks RIPE treated- biol rep 1 12 weeks Mtb infected +…
- GSM9052737 12 weeks Mtb infected + 4 weeks RIPE treated- biol rep 2 12 weeks Mtb infected +…
- GSM9052738 12 weeks Mtb infected + 8 weeks carrier treated- biol rep 1 12 weeks Mtb infected +…
- GSM9052739 12 weeks Mtb infected + 8 weeks carrier treated- biol rep 2 12 weeks Mtb infected +…
- GSM9052740 12 weeks Mtb infected + 8 weeks carrier treated- biol rep 3 12 weeks Mtb infected +…
- GSM9052741 12 weeks Mtb infected + 8 weeks RIPE treated- biol rep 1 12 weeks Mtb infected +…
- GSM9052742 12 weeks Mtb infected + 8 weeks RIPE treated- biol rep 2 12 weeks Mtb infected +…
- GSM9052743 12 weeks Mtb infected + 8 weeks RIPE treated- biol rep 3 12 weeks Mtb infected +…
- GSE249963 Bulk RNA seq of sorted CD11c cells from lungs of uninfected and Mtb infected wild type mice. 10 samples shares infected, lungs, lung, bulk
- GSE263892 Single-cell analysis reveals Mycobacterium tuberculosis ESX-1-mediated accumulation of permissive macrophages in infected mouse lungs 6078 samples shares infected, lungs, lung
- GSE263891 Single-cell analysis reveals Mycobacterium tuberculosis ESX-1–mediated accumulation of permissive macrophages in infected mouse lungs 6072 samples shares infected, lungs, lung
- GSE319684 Timecourse of FACS sorted Ly6C+ monocytes, tissue resident alveolar macrophages (trAMs), monocyte derived alveolar macrophages (bmAMs) and epithelial cells from SARS-CoV-2 (maVie16) vs. IAV (PR8) infected mouse lungs 176 samples shares infected, lungs, lung
- GSE306035 scRNA-Seq of immune populations from nasal mucosa and lungs of C57BL/6 mice and BLT1 receptor deficient mice infected intranasally with MCMV K181 strain 20 samples shares infected, lungs, lung
- GSE332646 Bulk RNA-seq of juvenile mouse liver following NDMA or saline treatment in WT and Mgmt-/- genotypes across multiple timepoints 214 samples shares treatment, bulk
- GSE228456 Cell-intrinsic effect of IL-7R signaling of monocytes within C57BL/6J mouse ears infected with Leishmania major [bulk RNA-seq] 87 samples shares infected, bulk
- GSE331360 Bulk RNA sequencing of bone marrow-derived macrophages from WT and Ch25h-KO mice under different treatment conditions 24 samples shares treatment, bulk
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.