RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection

Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis, as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up- or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA-seq was conducted using a low dose infection (approximately 30 CFU) at 4 weeks post infection, from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Identification of the up- and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed, from three to nine biological replicates in each group. Wild type (WT) sibling fish were used as a control. The groups were WT PBS injected, mutant PBS injected, WT M. marinum infected, mutant M. marinum infected.