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RNA sequencing and data analysis.

CZ Cong Zhang
YZ Yuqing Zhang
YQ Yuhao Qin
QZ Qingchao Zhang
QL Qiang Liu
DS Daozhen Shang
HL Huijun Lu
XL Xiao Li
CZ Congzhao Zhou
FH Fengming Huang
NJ Ningyi Jin
CJ Chengyu Jiang
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Lung tissue and blood from mice treated with drug or vehicle were obtained at 3 days after H5N1 infection. Total RNA was isolated from lung tissue and blood using TRIzol (Invitrogen, CA, USA). High-throughput strand-specific RNA sequencing was performed using an Illumina HiSeq 2500 platform (Berry Genomics, Beijing, China). Following quality control of the RNA sequencing reads by FastQC (version 0.11.2), the reads were mapped to the mouse genome (version mmc10; http://hgdownload.cse.ucsc.edu/downloads.html) with Bowtie2 (version 2.1.0) and TopHat2 (version 2.0.11). We then assembled the transcription units to calculate the number of mapped fragments per kilobase per million (FPKM) and analyzed the differentially expressed genes (DEGs) between samples using Cufflinks (version 2.2.1), Cuffmerge (version 2.2.1), and Cuffdiff (version 2.2.1). The functional pathways of DEGs between animals administered drug or vehicle were analyzed using Metacore.

Copyright and License information:  ©2019 Zhang et al.
This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.This content is distributed under the terms of the Creative Commons Attribution 4.0 International license.

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