protein digestion and absorption, and IL-17 signaling pathway. The pathways that had been drastically enriched inside the DEGs from comparison group Z_Z vs. Z_B mostly included protein digestion and absorption, chemical carcinogenesis, metabolism of xenobiotics by cytochrome P450, and glycolysis/gluconeogenesis. KEGG pathways that had been considerably enriched in additional than 3 comparison groups included NF-kappa B signaling pathway, IL-17 signaling pathway, protein digestion and absorption, NOD-like PAK5 Formulation receptor signaling pathway, metabolism of xenobiotics by cytochrome P450, chemical carcinogenesis, retinol metabolism, and glutathione metabolism. PI3K-Akt, NOD-like receptor, HIF-1, MAPK, and TNF signaling pathways play crucial roles in immune-related molecular Nav1.1 medchemexpress pattern recognition, signal transduction, and host immune system regulation. These final results deliver critical insights in to the transcriptional mechanism of intestinal diarrhea induced by a no-antibiotic diet in rabbits. 3.6. Gene Expression Levels Are Constant in Each qRT-PCR and RNA-Seq To validate the reproducibility and repeatability of DEGs identified from transcriptome sequencing, we randomly chosen ten genes, namely, CELA1, S100A8, FABP6, EAF2, S100A9, LOC100349113, IL1A, SHH, and JCHAIN, for RT-qPCR evaluation (Figure 7). Our outcomes showed that these genes were considerably differentially expressed and have been consistently upregulated or downregulated with the gene expression modifications depending on RNA-seq, which indicated that the RNA-seq information had been trusted.Biosensors 2021, 11, x FOR PEER REVIEW14 ofBiosensors 2021, 11,11,FOR PEER Assessment Animals 2021, x14 of 10 of 17Figure five. Cont.Biosensors 2021, 11,11,FOR PEER Overview Animals 2021, x15 of 11 of 17Figure 5. KEGG pathway enrichment evaluation of DEGs in unique comparison groups. S_Z vs. S_B (A), K_Z vs. K_B (B), Animals 2021, 11, x FOR PEER Assessment M_B (D), J_Z vs. J_B (E), and Z_Z vs. Z_B (F). The names of KEGG pathways are on the10 of 16 H_Z vs. H_B (C), M_Z vs. x-axis. S_Z: the duodenum of healthier rabbits, S_B: diarrhea inside the duodenum of rabbits, H_Z: healthful rabbit ileum, H_B: diarrheal rabbit ileum, K_Z: healthful rabbit jejunum, K_B: rabbits with diarrheal jejunum, M_Z: wholesome cecum of rabbits, M_B: rabbits with diarrheal cecum, J_Z: healthy rabbit colon, J_B: colon of rabbits with diarrhea, Z_Z: healthful rabbit rectum, Z_B: rectum of rabbits with diarrhea.Figure 6. The considerably enriched pathways in DEGs from diverse intestinal segment comparison groups. S: duodenum; H: ileum; significantly cecum; colon; Z: in DEGs from diverse intestinal segment comparison groups. S: Figure 6. The K: jejunum; M:enrichedJ: pathwaysrectum. duodenum; H: ileum; K: jejunum; M: cecum; J: colon; Z: rectum.3.six. Gene Expression Levels Are Constant in Each qRT-PCR and RNA-Seq To validate the reproducibility and repeatability of DEGs identified from transcriptome sequencing, we randomly selected ten genes, namely, CELA1, S100A8, FABP6, EAF2, S100A9, LOC100349113, IL1A, SHH, and JCHAIN, for RT-qPCR evaluation (FigureAnimals 2021, 11, x FOR PEER Evaluation Animals 2021, 11,11 of 16 12 ofon RNA-seq, which indicated that the RNA-seq information were dependable.Figure 7. Expression level of genes CELA1, S100A8, FABP6, EAF2, S100A9, LOC100349113, IL1A, Figure 7. Expression degree of genes CELA1, S100A8, FABP6, EAF2, S100A9, LOC100349113, IL1A, CYP4B1, SHH, and JCHAIN validated by RT-qPCR. The -actin gene was employed as an internal handle CYP4B1, SHH, and JCHAIN validated
