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

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

Dates

Publication Date
Start Date
2013-08-14
End Date
2016-10-15

Citation

Hofmeister, E.K., Newhouse, D.J., and Balakrishnan, C.N., 2017, Transcriptional response to West Nile virus infection in the zebra finch (Taeniopygia guttata), a songbird model for immune function: U.S. Geological Survey data release, https://dx.doi.org/10.5066/F7G44NHF.

Summary

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.

Contacts

Point of Contact :
Erik K Hofmeister
Originator :
Erik K Hofmeister, Daniel J Newhouse, Christopher N Balakrishnan
Metadata Contact :
Erik K Hofmeister
Distributor :
U.S. Geological Survey - ScienceBase
USGS Mission Area :
Ecosystems
SDC Data Owner :
National Wildlife Health Center

Attached Files

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Transcriptional_response_to_West_Nile_virus_infection_in_the_zebra_finch_Taeniopygia_guttat_a_sngbird_model_for_immune_function.xml
Original FGDC Metadata
View 		23.27 KB application/fgdc+xml
DEseq2_GO.csv 76.51 KB text/csv
SignificantDEsep2_Genes.csv 29.22 KB text/csv
WBseqHMM_GoTerms.csv 221.23 KB text/csv

Purpose

The data set contains results for RNAseq analysis of RNA extracted from zebra finches experimentally infected 2 and 4 days earlier with West Nile virus or control virus diluent. The purpose of the study was to determine if WNV infection elicited differential expression of innate or acquired immune response genes as compared to uninfected birds.

Communities

  • National Wildlife Health Center
  • USGS Data Release Products

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DOI https://www.sciencebase.gov/vocab/category/item/identifier doi:10.5066/F7G44NHF

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