Open Access Research article

Analysis of the swine tracheobronchial lymph node transcriptomic response to infection with a Chinese highly pathogenic strain of porcine reproductive and respiratory syndrome virus

Laura C Miller1*, Damarius Fleming2, Andrew Arbogast3, Darrell O Bayles4, Baoqing Guo5, Kelly M Lager1, Jamie N Henningson1, Sarah N Schlink1, Han-Chun Yang6, Kay S Faaberg1 and Marcus E Kehrli1

Author Affiliations

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

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BMC Veterinary Research 2012, 8:208  doi:10.1186/1746-6148-8-208

Published: 30 October 2012

Additional files

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

Open Data

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

Open Data