Transcriptional response to West Nile virus infection in the zebra finch (Taeniopygia guttata), a songbird model for immune function

The data set contains paired-end, 100 nucleotide long RNA sequencing reads for each sample. Raw sequencing reads ranged from 18-30million reads per sample. Quality trimmed reads were mapped to the Zebra Finch reference genome with an average of 79.0-80.8% mapping rate, corresponding to 18,618 Ensembl gene IDs. Of these, 14,114 genes averaged at least 5 mapped reads across all samples and were utilized for differential expression (DE) analyses. DE analyzed two ways: as pairwise comparisons between treatments to identify specific genes with DEseq2 and as a time course grouping genes into expression paths with EBSeqHMM.