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.
Complete Metadata
| 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 |
