Differential expression of Mtb genes during BMM infection. Total Mtb RNA was isolated from CDC1551 or HN878-infected BMM at 24 and 48 hpi and the level of expression of Mtb genes involved in pathways including hypoxia, general stress response and fatty acid/lipid metabolism was determined by qRT-PCR. The amount of transcripts for each Mtb gene was normalized to 16S rRNA levels and relative fold change in gene expression was calculated by comparing the expression level at 24 and 48 hpi with T0 levels. (A and B) Intracellular mRNA levels of Mtb genes involved in mycobacterial survival during hypoxia expressed by CDC1551 or HN878 at 24 (A) and 48 (B) hpi. (C and D) Transcript levels of Mtb genes involved in fatty acid/lipid metabolism expressed by CDC1551 or HN878 at 24 (C) and 48 (D) hpi of BMM. (E and F) mRNA levels of Mtb genes involved in general stress response expressed by intracellular CDC1551 or HN878 at 24 (E) and 48 (F) hpi. (G and H) Intracellular mRNA levels of Mtb genes involved in iron metabolism and peptidases involved in acid shock response expressed by CDC1551 or HN878 at 24 (G) and 48 (H) hpi. The results are means ± standard deviation from three independent samples per experimental group per time point repeated at least twice. * P ≤ 0.05.