Gene expression by RNA-seq in purified paneth cells in antibiotics microbiome depleded mice

The study of how gene expression in paneth cells changes after TNF admistration in mice were the microbiome has been depleted with broad spectrum antibiotics. The depletion of the microbiome excludes the occurence of indirect effects mediated through it by TNF on PC gene expression, only direct TNF effecs on crypt cells are measured Overall design: To investigate the effects of TNF on PCs without microbiome, PCs were purified from mice treated with antibiotics for 2 weeks and treated with 1µg/g TNF or PBS (control) by IP injection for 3 hours. A total of 4 biological replicates were used for each condition for a total of 8 samples