Brain tissue of BALB/c mouse inoculated with H5N6 influenza virus

In response to the increased interest to study the role of influenza virus respiratory infection on brain cells, we inoculated 4-6 weeks old female mice with influenza A virus (A/duck/Hubei/WH18/2015(H5N6)). A group of mice was intranasally (IN) infected with 105 TCID50 H5N6 influenza virus, while mice in the control group were mock-infected with phosphate-buffered saline (PBS), followed by brain collection at 3d.p.i. Total RNA was isolated and purified using TRIzol reagent. Moreover, RNA amount and purity of each sample was quantified using NanoDrop ND-1000, while the RNA integrity was assessed by Agilent 2100 with RIN number >7.0. cDNA library was constructed and sequenced with an illumine platform. The raw data output was further mapped and assembled by HISAT2 and StringTie, while differentially expressed genes were obtained using DESeq2 to screen for the altered biological processes in brain cells following intranasal influenza infection.