Transcriptome of chicken spleens with Escherichia coli infection

Purpose: the goals of this study was to find the differential genes of spleen in chickens infected with Escherichia coli Methods: The spleen samples from control group and the spleen samples from infection group were generated by deep sequencing using Illumina system with 9 biological repetitions and 2 technical repetitions, respectively. Results: Using an optimized data analysis workflow, we mapped about 68-91 million sequence reads per sample to the chicken spleens from the infection and control group by Hisat2. Approximately a quarter of the transcripts showed differential expression between the infection and control group, with a 5x SD fold change and p value <0.05. The one-day-old white leghorn SPF chickens were reared in isolators for 7 days, then these chickens were transferred to fumigated animal houses and reared for another 7 days. All the chickens were proved to be adapted to the breeding environment by 15 days old. After weighing, the chickens were randomly divided into two groups and 48 chickens in each group. The chickens in infection group were injected in the chest muscles with 0.5 mL of E. coli O78 bacterial fluid, while the chickens in control group were injected in the chest muscles with 0.5 mL sterile normal saline. At the time point of 72 h, the chickens for quantitative proteomics experiment were sacrificed, and spleens were dissected out and frozen at -80 ℃ for preservation. and part of the spleens were selected for transcriptomic analysis.