IFN-γ induced the formation of foamy macrophages by CD40 signaling control during Mycobacterium abscessus pulmonary infection
RNA-seq (gene expression) · mouse · 17 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
- 17 samples: 5 × IFN_gamma_MAB vs 4 × Uninfected vs 4 × IFN_gamma vs 4 × MABGroups 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
- Bufei Jiedu Formula enhances CD40 activation and macrophage polarization to eliminate intracellular MRSA persistersFrontiers in immunology · 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 GSE287681_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 PRJNA1214242 and SRA study SRP559113. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 17 samples.
How we read this: 4 replicated groups read from 17 sample titles; they account for 17 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.
- GSM8749777 Uninfected_rep1 Uninfected
- GSM8749778 Uninfected_rep2 Uninfected
- GSM8749779 Uninfected_rep3 Uninfected
- GSM8749780 Uninfected_rep4 Uninfected
- GSM8749781 IFN_gamma_rep1 IFN_gamma
- GSM8749782 IFN_gamma_rep2 IFN_gamma
- GSM8749783 IFN_gamma_rep3 IFN_gamma
- GSM8749784 IFN_gamma_rep4 IFN_gamma
- GSM8749785 MAB_rep1 MAB
- GSM8749786 MAB_rep2 MAB
- GSM8749787 MAB_rep3 MAB
- GSM8749788 MAB_rep4 MAB
- GSM8749789 IFN_gamma_MAB_rep1 IFN_gamma_MAB
- GSM8749790 IFN_gamma_MAB_rep2 IFN_gamma_MAB
- GSM8749791 IFN_gamma_MAB_rep3 IFN_gamma_MAB
- GSM8749792 IFN_gamma_MAB_rep4 IFN_gamma_MAB
- GSM8749793 IFN_gamma_MAB_rep5 IFN_gamma_MAB
- GSE324935 IFN-γ and TLR9 signaling reprogram tumor-associated macrophages to promote antitumor immunity in melanoma 20 samples shares ifn, macrophages
- GSE325803 CD40-induced humoral immunity 18 samples shares cd40, induced
- GSE243269 The RNA binding protein HNRNPA2B1 regulates IFNG signaling in macrophages 12 samples shares ifn, macrophages
- GSE303772 Ontogenically distinct alveolar macrophages mediate cigarette smoke-induced inflammation and damage [RNA-Seq] 24 samples shares macrophages, induced
- GSE282695 STAT3 regulates pathogen control and clearance in macrophages by reprogramming inflammation-induced microbial defense response 18 samples shares macrophages, induced
- GSE317613 pH-Responsive Nanostructured Calcium Phosphate Microrods as Pulmonary Delivery Platform: Fabrication, Characterization, and Comparative Assessment of Cytotoxic and Transcriptomic Responses in Alveolar Macrophages 15 samples shares macrophages, pulmonary
- GSE302734 Single-Cell RNA Sequencing Unravels Interactions between Macrophages and Fibroadipogenic Progenitors during Ectopic Bone Formation in FOP Mice 12 samples shares macrophages, formation
- GSE283664 RNA Sequencing of macrophages harboring redox-diverse Mycobacterium tuberculosis. 12 samples shares mycobacterium, macrophages
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.