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Series GSE121348 Query DataSets for GSE121348
Status Public on Jul 17, 2019
Title Transcriptomics of the Avian Immune Response in Hypothalamus, Spleen, and Red Blood Cells using RNA-seq
Organism Taeniopygia guttata
Experiment type Expression profiling by high throughput sequencing
Summary The goal of this research is to better understand the transcriptomic response in peripheral and neural tissue of zebra finch to lipopolysaccharide (LPS) challenge using RNASeq. The acute phase response (APR) is the initial reaction of the immune system to infection, and is triggered by pro-­inflammatory cytokines or exposure to immunogens, such as bacterial LPS. The APR also inhibits reproduction and induces a number of physiological and behavioral symptoms, such as fever and sickness behavior. Through RNAseq, we can better understand the transcriptomic response of genes that are important for response to infection in a wild species such as the Zebra Finch. This has implications for disease surveillance programs that monitor the epidemiology of zoonotic diseases, like avian influenza and West Nile virus. We examine the transcriptomic response in Zebra Finch spleen and hypothalumus to lipopolysaccharide (LPS) challenge; however, unlike mammals, with the exception of the camel, avian species have red blood cells that contain a nucleus, and will have gene regulation depending on the physiological needs of the organism. Therefore, we also took the opportunity to investigate the transcriptomic response of nucleated red blood cells to lipopolysaccharide (LPS) challenge.
 
Overall design A comparison was made of the transcriptomic response to lipopolysccharide challenge (Escherishia Coli) of Zebra Finch hypothalamus, spleen, and red blood cells using birds injected with saline as experimental controls.
 
Contributor(s) Ashley N, Scalf CS, Chariker JH, Rouchka EC
Citation(s) 31412766
NIH grant(s)
Grant ID Grant title Affiliation Name
P20 GM103436 KY IDeA Networks of Biomedical Research Excellence UNIVERSITY OF LOUISVILLE RESEARCH FOUNDATION NIGEL G.F. COOPER
Submission date Oct 16, 2018
Last update date Oct 16, 2019
Contact name Eric Christian Rouchka
E-mail(s) eric.rouchka@louisville.edu
Organization name University of Louisville
Department Biochemistry and Molecular Genetics
Lab KY INBRE Bioinformatics Core
Street address 522 East Gray Street
City Louisville
State/province Kentucky
ZIP/Postal code 40292
Country USA
 
Platforms (1)
GPL22780 Illumina NextSeq 500 (Taeniopygia guttata)
Samples (24)
GSM3431859 NA-01-1-SAL-HYP_S1
GSM3431860 NA-02-2-SAL-HYP_S2
GSM3431861 NA-03-3-SAL-HYP_S3
Relations
BioProject PRJNA497105
SRA SRP165902

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE121348_FPKM_geneMatrix_NORMALIZED.txt.gz 1.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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