Additional File 4:

Figure S2. Regulatory network of CHv-encoded miRNAs and CHv genes. a Gene regulatory network formed by CHv-encoded miRNAs (red ellipses) and their target genes (yellow ectangles). b Gene regulatory network of CHv-encoded miRNAs (red ellipses) and their target immediate-early(IE) genes (yellow rectangles) (PDF 401 kb

Additional file 9: of Virulent duck enteritis virus infected DEF cells generate a unique pattern of viral microRNAs and a novel set of host microRNAs

Table S7. Differentially expressed host alignment miRNA in CHv-infected DEF cells. Fold-change = log2 (infected/mock in expression) > 1 or < − 1, and p-value < 0.05 indicated significance differentially expressed miRNA. Fold-change < − 1 indicates down-regulated, Fold-change > 1 indicates up-regulated. (XLSX 12 kb

Additional file 7: of Virulent duck enteritis virus infected DEF cells generate a unique pattern of viral microRNAs and a novel set of host microRNAs

Table S5. Novel duck miRNA expressed in DEF cells. The 386 mature sequence and sequence read count of novel duck miRNAs predicted with miRDeep in each sequenced sample of DEF cells. (XLSX 26 kb

Additional file 5: of Virulent duck enteritis virus infected DEF cells generate a unique pattern of viral microRNAs and a novel set of host microRNAs

Table S3. Predicted host target genes of DEV miRNAs. Host target genes were predicted using PITA and RNAhybrid software. (XLSX 832 kb

Additional file 2: of Virulent duck enteritis virus infected DEF cells generate a unique pattern of viral microRNAs and a novel set of host microRNAs

Table S2. Distribution of sRNAs in DEV-infected and uninfected samples. (DOCX 15 kb

Additional File 10:

Figure S3. Regulatory network of DEF miRNAs and CHv genes. a Gene regulatory network formed by differentially-expressed DEF miRNAs (blue ellipses) and their target genes (yellow rectangles). b Gene regulatory network of differentially-expressed DEF miRNAs (blue circles) and target immediate-early (IE) genes (yellow rectangles). (PDF 353 kb

Additional file 1: of Virulent duck enteritis virus infected DEF cells generate a unique pattern of viral microRNAs and a novel set of host microRNAs

Table S1. Primers used to amplify virus and host miRNAs by stem-loop RT-qPCR. Stem-loop RT-qPCR was conducted using miRNA specific stem-loop RT primers together with corresponding miRNA specific forward (F) primers and universal reverse (UR) primer. (DOCX 15 kb

Additional file 6: of Virulent duck enteritis virus infected DEF cells generate a unique pattern of viral microRNAs and a novel set of host microRNAs

Table S4. Gene ontology analysis on host targets of the viral miRNAs (XLSX 23 kb

Additional File 3:

The expression profiling of CHv miRNAs and pre-miRNA secondary structures. MiRNA sequences and their coresponding reads mapped on the precursors of CHv miRNA genes. Opening parentheses indicate pairing nucleotides. Inside the closed parentheses indicate the minimum free energy for the secondary structure of the miRNA. The number of reads mapped to the miRNA precursors is indicated in the right side. Mature miRNAs are denoted in red. The hairpin structures of pre-miRNA is shown at the back. (PDF 649 kb

Additional file 8: of Virulent duck enteritis virus infected DEF cells generate a unique pattern of viral microRNAs and a novel set of host microRNAs

Table S6. Novel duck miRNA expressed in DEF cells. The 212 mature sequence and sequence read count of novel duck miRNAs predicted with miRDeep in each sequenced sample of DEF cells. (XLSX 15 kb