Authors’ information AC: Young researcher, Department of Biomedical Sciences, see more Division of Experimental and Clinical Microbiology, University of Sassari, ITALY. LAS: Full Professor, Department of Biomedical Sciences, Division ACY-241 order of Experimental and Clinical Microbiology, University of Sassari, ITALY. SZ: Full Professor, Department of Biomedical Sciences, Division of Experimental and Clinical Microbiology, University of Sassari, ITALY. VR: Young Researcher, Experimental Zooprophylactic

Institute of Sardinia, Department of Nuoro, ITALY. Acknowledgments This work was supported by the POR Sardegna “”Young Researchers, European Social Fund 2007–2013, L.R.7/ 2007 “Promotion of Scientific Research and Technological Innovation in Sardinia”". Project CRP1_9. Special thanks

go to Mr. Edmondo Manca for logistic assistance buy CB-5083 and Porto Conte Ricerche S.r.l – Alghero for array scanning instrumentation. Electronic supplementary material Additional file 1: Additional tables (Tables S1-S4). Table S1. Genes of M. avium subsp. paratuberculosis with significantly up-regulated expression levels in the acid-nitrosative stress (≥2 fold change). Table S2. Genes of M. avium subsp. paratuberculosis with significantly down- regulated expression levels in the acid-nitrosative stress (≤2 fold change). Table S3. Genes of M. avium subsp. paratuberculosis with significantly up-regulated expression levels in the infection of THP-1 cells (≥2 fold change). Table S4. Genes of M. avium subsp. paratuberculosis with significantly down-regulated

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