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.
Citation Information
| Publication Year | 2017 |
|---|---|
| Title | Transcriptional response to West Nile virus infection in the zebra finch (Taeniopygia guttata), a songbird model for immune function: Data |
| DOI | 10.5066/F7G44NHF |
| Authors | Erik K Hofmeister, Christopher N Balakrishnan, Daniel J Newhouse |
| Product Type | Data Release |
| Record Source | USGS Digital Object Identifier Catalog |
| USGS Organization | National Wildlife Health Center |
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