Tehran University of Medical Sciences Iranian Journal of Microbiology 2008-3289 13 1 2021 02 10 17 22 Shabnam Hashemi Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran Seyed Masoud Hosseini Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran Arash Ghalyanchilangeroudi Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran Nariman Sheikhi Department of Clinical Sciences, College of Veterinary, Tehran Sciences and Research Branch, Islamic Azad University, Tehran, Iran 2020 11 08 2020 11 21 Background and Objectives: Infection with Infectious bronchitis virus (IBV) and avian pathogenic Escherichia coli (APEC) is an important respiratory infection worldwide. Apoptosis is a physiological process of cell death that occurs as part of normal development and responds to a variety of physiological and pathophysiological stimuli. The identification of molecular mechanisms of action or inaction of key apoptotic proteins is important. This study aimed to investigate apoptotic related genes in the trachea tissue of infected (IBV variant 2, and APEC serotype O78: K80) SPF chickens group compared to the control group. Materials and Methods: Forty SPF chickens was divided into 2 groups. Differential transcriptional profile in the infected SPF chickens trachea tissue was compared to those of control group in the early stage of infection by Illumina RNA-seq technique paired-end and strand-specific sequencing. Differentially expressed genes (DEGs) of transcriptome profiling of the trachea from the infected group were identified. Gene ontology category, KEGG pathway, and STRING analysis were analyzed to identify relationships among differentially expressed genes. Results: Twenty-eight apoptotic genes were identified. They consisted of six pathways related to cell death: the extrinsic pathway, intrinsic pathway, endoplasmic reticulum stress pathway, MAPK signaling pathway, and cell death by NFkB and activates mTOR pathway and some regulator and apoptosis inhibitors. Conclusion: All of the apoptotic genes in our study were up-regulated. Among these genes, the more fold change value was for TRADD and BCL2A1 genes, and the less fold change value was for MAP3K14, NFKB1, PIK3CB, and ITPR2 genes. https://ijm.tums.ac.ir/index.php/ijm/article/view/2847 https://ijm.tums.ac.ir/index.php/ijm/article/download/2847/1311