## 5 Conclusions  
An infection with _A. salmonicida_ causes damages in rainbow trout aquaculture. To investigate the transcriptional profile of the skin and adhering skeletal muscle in response to _A. salmonicida_ infection in rainbow trout, the 4 \(\times\) 44 oligonucleotide microarray was applied. We identified differentially expressed genes at 2 and 6 days post infection. Further, we investigated the differences between moribund (2 dpi) and survivor (6 dpi) fish. Our results revealed a divergent expression of many genes involved in the fish immune system, mainly including inflammation, antimicrobial peptides, pattern recognition patterns, acute-phase response proteins, such as serum amyloids, lysozymes, cathelicidin, hepcidin and c-type lectins as well as genes involved in complement cascade after infection. Along with the immune response, we saw the up-regulation of leptin, prostaglandandins and eicosanoids related to metabolic reprogramming. Further, a gene expression analysis revealed the differential regulation of genes involved in programmed cell death (apoptosis, necrotosis and ferroptosis) and cytoskeleton and extracellular matrix remodeling. The results from this study confirm the complexity of the response to bacterial infection and constitute a source for further studies on furunculosis in rainbow trout. This is, to our knowledge, the first study that aimed to achieve the gene expression profiling of rainbow trout skin after an _A. salmonicida_ challenge. The following supporting information can be downloaded at [[https://www.mdpi.com/article/10.3390/app132312793/s1](https://www.mdpi.com/article/10.3390/app132312793/s1)]([https://www.mdpi.com/article/10.3390/app132312793/s1](https://www.mdpi.com/article/10.3390/app132312793/s1)), Table S1: List of differentially expressed genes with annotations identified in rainbow trout after infection with _A. salmonicida_ in moribund (2 dpi) and survivor (6 dpi) fish; Table S2: List of differentially expressed genes with annotations between moribund (2 dpi) and survivor (6 dpi) fish; Figure S1: GO enrichment analysis of moribund (2 dpi) group. Bubble plot presents top 10 GO subcategories with highest \(p\)-value in main categories: biological process (BP), cellular component (CC), molecular function (MF). (a) Up-regulated genes. (b) Down-regulated genes; Figure S2: GO enrichment analysis of survivor (6 dpi) group. Bubble plot presents top 10 GO subcategories with highest \(p\)-value in main categories: biological process (BP), cellular component (CC), molecular function (MF). (a) Penrose decreased over time. (b) Genes raised over time. Conceptualization, R.W. and M.M. ; methodology, R.W., A.K.S., S.D. and M.M. ; formal analysis, M.M. ; investigation, M.M., A.K.S., S.D. and R.W. ; resources, M.M., A.K.S., S.D. and R.W. ; writing--original draft preparation, M.M. and R.W. ; writing--review and editing, M.M., A.K.S., S.D. and R.W. ; visualization, M.M. ; supervision, R.W. ; validation, R.W. and M.M; funding acquisition, R.W. All authors have read and agreed to the published version of the manuscript. **Funding:** This study was partially funded by project no. 397/N-cGRASP/2009/0 of the Ministry of Science and Higher Education in Poland to RW and statutory task IV.1 in the IO PAS. **Institutional Review Board Statement:** All experimental procedures were performed in accordance with the three Rs for the humane use of animals in scientific research and were approved by the Local Ethics Committee on Animal Experimentation of the Inland Fisheries Institute of Olsztyn, Poland (approval code: Nr 20/2011; approval date: 30 March 2011). **Informed Consent Statement:** Not applicable. **Data Availability Statement:** The microarray data were deposited in the National Center for Biotechnology Information's Gene Expression Omnibus (NCBI GEO) under the accession number GEO: GSE230658. **Acknowledgments:** This research was supported in part by PL-Grid Infrastructure.