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Bulk RNA-sequencing on sorted zebrafish macrophages based on novel irg1-knock-in reporter comparing control versus nlrc3l mutation under baseline and injury conditions

ABSTRACT: Using a GFP knock-in zebrafish targeting the irg1/acod1 locus, a gene highly induced in activated macrophages, we isolated macrophages based on high and low GFP levels by FACS to conduct bulk RNA-sequencing. Transcriptome analysis of macrophages showed nlrc3l mutants had constitutively activated macrophages that sustained elevated expression of pro-inflammatory genes, including irg1 and tnfa, and canonical and non-canonical NF-κB pathways genes. Furthermore, transcriptome analysis suggested that wild-type/control macrophages exhibited hybrid M1-like and M2-like characteristics during initial injury response, while nlrc3l mutant macrophages remained locked in a pro-inflammatory state. This analysis supports the rest of the functional experiments to demonstrate that chronic macrophage activation restricts functional plasticity associated with mrc1b deficiency and thereby hinders skeletal muscle repair.

ORGANISM(S): Danio rerio

PROVIDER: GSE283438 | GEO | 2025/12/06

REPOSITORIES: GEO

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