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Fig. S1. Intracellular pH measurement. Fig. S2. Characterization of Mycobacterium avium subsp. paratuberculosis-infected macrophages. Fig. S3. Transcriptional profiling of M. avium subsp. paratuberculosis infecting naïve and activated macrophages. Fig. S4. Hierarchical clustering analysis of the samples by Pearson correlation. Fig. S5. Comparative analysis of M. avium subsp. paratuberculosis transcriptomes growing under variable conditions. Fig. S6. Construction of the ΔsigH mutant using the wild-type M. avium subsp. paratuberculosis strain. Fig. S7. Microscopic observation of macrophage cell attachment. Fig. S8. Colonization of M. avium subsp. paratuberculosis strains in the liver. Fig. S9. qRT-PCR verification of the RNA-seq transcriptome studies.
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Table S1. Significant genes in intracellular conditions compared to RPMI-incubated control sample. Table S2. Significant genes common in all intracellular conditions. Table S3. Significant Mycobacterium avium subsp. paratuberculosis genes in infected IFN-γ-treated macrophages compared to infected naïve macrophages. Table S4. Normalized microarray hybridization mean intensities. Table S5. Genes differentially expressed between wild-type M. avium subsp. paratuberculosis and the ΔsigH mutant after exposure to diamide. Table S6. Genes differentially expressed between wild-type M. avium subsp. paratuberculosis and the ΔsigH mutant during standard physiological growth conditions. Table S7. Consensus promoter sequences of the target genes positively regulated by SigH in M. avium subsp. paratuberculosis. Table S8. qRT-PCR verification of the DNA microarray transcriptome studies. Table S9. Consensus promoter sequences of the target genes positively regulated by SigH in M. avium subsp. paratuberculosis.
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