Analysis of the swine tracheobronchial lymph node transcriptomic response to infection with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus
1 Virus and Prion Research Unit, National Animal Disease Center-USDA-ARS, Ames, Iowa, 50010, USA
2 Inter-departmental Genetics, Iowa State University, Ames, Iowa, 50011, USA
3 Department of Computer Science, Iowa State University, Ames, Iowa, 50011, USA
4 Infectious Bacterial Diseases Research Unit, National Animal Disease Center-USDA-ARS, Ames, Iowa, 50010, USA
5 Veterinary Diagnostic & Production Animal Medicine, Iowa State University, Ames, Iowa, 50011, USA
6 China Agricultural University, Beijing, China
BMC Veterinary Research 2012, 8:208 doi:10.1186/1746-6148-8-208Published: 30 October 2012
Additional file 1:
Cuffdiff output of all significant hits for comparison, using the HP-PRRSV rJXwn06 vs. control and the US PRRSV VR-2332 vs. control datasets, to test for differential expression and regulation amongst the two disease states. Gene annotation (symbol) was carried out using a MySQL database matching to the Ensembl Sscrofa9.56 reference genome currently supported by the Integrative Genomics Viewer (Broad Institute). Location (row.names); gene annotation (symbol); entrez gene name; treatment (sample_1, sample_2); status; abundance in FPKM (value_1, value_2); differential expression (log2_fold_change); test statistic (test_stat); p-value (p_value); false discovery rate (FDR)-adjusted p-value of the uncorrected test statistic (q_value); significance status after Benjamini-Hochberg correction for multiple-testing (significant).
Format: XLSX Size: 229KB Download file
Additional file 2:
Transcript sequences of all significant hits inthe HP-PRRSV rJXwn06 vs. control and the US PRRSV VR-2332 vs. control datasets.
Format: XLSX Size: 1009KB Download file