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.
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Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[ "010:12" ] |
| contactPoint |
{ "fn": "Erik Hofmeister", "@type": "vcard:Contact", "hasEmail": "mailto:ehofmeister@usgs.gov" } |
| description | 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. |
| distribution |
[ { "@type": "dcat:Distribution", "title": "Digital Data", "format": "XML", "accessURL": "https://dx.doi.org/10.5066/F7G44NHF", "mediaType": "application/http", "description": "Landing page for access to the data" }, { "@type": "dcat:Distribution", "title": "Original Metadata", "format": "XML", "mediaType": "text/xml", "description": "The metadata original format", "downloadURL": "https://data.usgs.gov/datacatalog/metadata/USGS.592ee3ade4b092b266f13e74.xml" } ] |
| identifier | http://datainventory.doi.gov/id/dataset/USGS_592ee3ade4b092b266f13e74 |
| keyword |
[ "RNAseq", "Transcriptome", "USGS:592ee3ade4b092b266f13e74", "West Nile virus", "virus" ] |
| modified | 2020-10-06T00:00:00Z |
| publisher |
{ "name": "U.S. Geological Survey", "@type": "org:Organization" } |
| theme |
[ "geospatial" ] |
| title | Transcriptional response to West Nile virus infection in the zebra finch (Taeniopygia guttata), a songbird model for immune function |
