Dataset of proinflammatory cytokine and cytokine receptor gene expression in rainbow trout (Oncorhynchus mykiss) measured using a novel GeXP multiplex, RT-PCR assay

Ivan Kutyrev,Beth Cleveland,Timothy Leeds,Gregory D Wiens

doi:10.1016/j.dib.2017.02.014

Ivan Kutyrev, Beth Cleveland + Show 2 more

Open Access

https://doi.org/10.1016/j.dib.2017.02.014

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Abstract

A GeXP multiplex, RT-PCR assay was developed and optimized that simultaneously measures expression of a suite of immune-relevant genes in rainbow trout (Oncorhynchus mykiss), concentrating on tumor necrosis factor and interleukin-1 ligand/receptor systems and acute phase response genes. The dataset includes expression values for drpt, il11a, il1b1, il1b2, il1b3, il1r-like-1(e3-5), il1r-like-1(e9-11), il1r1-like-a, il1r1-like-b, il1r2, saa, tnfa1, tnfa2, tnfa3, tnfrsf1a, tnfrsf1a-like-a, tnfrsf1a-like-b, tnfrsf5, and tnfrsf9. Gene expression was measured at four time-points post-challenge in both a resistant line (ARS-Fp-R) and a susceptible line (ARS-Fp-S) of rainbow trout. In addition, fish body weight, spleen index and the Flavobacterium psychrophilum load are reported. These data are an extension of information presented and discussed in “Proinflammatory cytokine and cytokine receptor gene expression kinetics following challenge with Flavobacterium psychrophilum in resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss)” (Kutyrev et al., 2016) [1].

Highlights

Dataset of proinflammatory cytokine and cytokine receptor gene expression in rainbow trout (Oncorhynchus mykiss) measured using a novel GeXP multiplex, reverse transcription (RT)-PCR assay
Gene expression was measured at four time-points post-challenge in both a resistant line (ARS-Fp-R) and a susceptible line (ARS-Fp-S) of rainbow trout
Fish body weight, spleen index and the Flavobacterium psychrophilum load are reported. These data are an extension of information presented and discussed in “Proinflammatory cytokine and cytokine receptor gene expression kinetics following challenge with Flavobacterium psychrophilum in resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss)” (Kutyrev et al, 2016) [1]

Summary

Data accessibility

Figures GeXP multiplex, RT-PCR assay (Genome Lab GeXP genetic analysis system; Beckman Coulter Inc.; Pasadena, CA, USA). qPCR (ABI 7900HT real-time thermal cycler; Applied Biosystems). Raw Challenge: Flavobacterium psychrophilum strain CSF259-93 or PBS Sampling timepoints: 6 h, 24 h, 48 h and 144 h post-injection Genetic line: ARS-Fp-R (resistant) and ARS-Fp-S (susceptible) Tanks: 1–8 RNA extraction batch: 1–8 GeXP run: 1–3 Tanks were randomly assigned to treatment. The dataset includes assay optimization and meta-data associated with measuring gene expression kinetics of bacterial cold water disease resistant and susceptible genetic lines of rainbow trout (Oncorhynchus mykiss) following challenge with Flavobacterium psychrophilum [1]. The GeXP assay primer dilutions were optimized and the predicted PCR products matched their elution peak in single reactions (Table 1). The complete gene expression dataset includes the meta-data of tank number, sample order, RNA extraction batch, GeXP run and normalized gene expression value (Supplemental Data Table 1). Kanr RNA is an independent template used as a positive control for RT and PCR reactions

Gene expression analysis

Real time RT-PCR