ds into severe immunosuppression and hence secondary infections may result in infected chickens. Infectious bursal disease virus is the causative agent of the disease. Two serotypes are identified in which serotype 1 comprises pathogenic strains, whereas serotype 2 strains cause neither disease nor protection against serotype 1 strains in chickens. It is demonstrated that the virus propagates in the actively proliferating IgM-bearing B-lymphocytes and hence induces apoptotic effects. Though the pathogenicity and epizootiology have been studied for a certain period of time, the molecular interactions between the host cells and the viruses have not been well defined yet. In recent years studies have started to focus on the molecular mechanisms involved in the host responses upon IBDV infection. Quantitative RT-PCR and microarray assays are increasingly SB366791 site employed to reveal the PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19691102/ transcriptional changes of the host cells in response to IBDV infections. While some studies also utilize proteomic approaches to identify the differentially expressed protein during the course of IBDV infection. Majority of these studies emphasized the cytokine responses including interleukin and interferon expressions, whereas some of these studies revealed expression of mRNA related to apoptotic mechanisms. Up to now, however, there is no comprehensive transcriptional landscape described in the cells upon IBDV infection. In order to explore the differential expression pattern in the event of IBDV infection, RNA sequencing was employed to assay the transcript variations across the entire chicken genome. RNA-Seq reveals a high overall sensitivity on differentially expressed gene level compared with other whole-transcriptome expression quantification platforms including microarrays. The prerequisite of hybridization-based microarray assays relies on existing knowledge about genome sequences and hence limits the detection of novel, rare transcript species exist in the transcriptome. Whereas RNA-Seq takes an advantage not only in determining the differential expression level of transcripts, but it also provides evidence on transcript splice-variants, isoforms and single nucleotide polymorphism PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19690518 . It has also been demonstrated that RNA-Seq is highly accurate for determining gene expression levels as performed with qPCR. Background levels resulting from cross-hybridization is also much lower than occurred in microarray assay. Taking these advantages, in this study we made use of RNA-Seq to unveil the transcriptomic dynamics upon caIBDV infection in DF-1 cells and to reveal a more comprehensive molecular interactions between the host cells and the virus. Materials and Methods Cell culture and virus Chicken embryonic fibroblast cells DF-1 were maintained and cultured with high glucose Dulbecco’s Modified Eagle Medium DMEM-HG supplemented with 10% fetal bovine serum at 37C, 5% CO2. Celladapted IBDV was generated with propagating IBDV vaccine strain D78 in secondary chicken embryonic fibroblast cells, followed by purification with CsCl gradient and 20% sucrose gradient as described previously. The quantity of the purified virus was determined by standard plaque assay. 2 / 
17 DE Profile of DF-1 Cells Infected with caIBDV Virus inoculation DF-1 cells were seeded into each well of 6-well plate at 1 104 cells at 24 hrs prior to virus inoculation. A total of six individual wells were prepared for each sampling time point of both mock- and caIBDV- infected groups. The purified caIBD