To understand if the delay in TFEB nuclear entry by stationary-grown Salmonella reprogrammed lysosome and autophagy gene expression relative to infection with late-log Salmonella, we quantified by quantitative real-time PCR (qRT-PCR) the expression of the model genes, LC3, LAMP1, and cathepsin D. We used wild-type, tfeb–/–, and tfeb–/–tfe3–/– RAW cells, previously described (17). Here, MAP1LC3A is linked to infection.