Characterisation of the horse transcriptome from immunologically active tissues

Moreton, Joanna; Malla, Sunir; Aboobaker, A. Aziz; Tarlinton, Rachael; Emes, Richard D.

doi:10.7717/peerj.382

Cited by 6 publications

(6 citation statements)

References 30 publications

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“…Tissue samples for RNAseq: details of these samples, generation of RNAseq data and mapping to the horse genome have been published previously [ 27 , 28 ]. Briefly, the samples consisted of five tissue samples (kidney, jejunum, liver, spleen and mesenteric lymph node) collected from an aged gelding, lymphocytes isolated by Ficoll Paque (GE healthcare) from a healthy 11 year old welsh mountain pony gelding and RNA from lymphocytes isolated from a healthy thoroughbred mare (the same horse whose DNA the horse genome is derived from) (Additional file 1 : Table S2).…”

Section: Methodsmentioning

confidence: 99%

“…The RNA samples were extracted, prepared and sequenced on a SOLiD 3 ABi sequencer to generate 50 bp reads. These reads were mapped to the equine reference genome EquCab2 and the transcriptome data was generated as in Moreton et al [ 27 ]. The data for the TLR genes was retrieved from the annotated transcriptome [data available at EBI sequence read archive (SRA) under the study accession number ERP001116 and at 10.7717/peerj.382/supp-6].…”

Section: Methodsmentioning

confidence: 99%

“…Ethical approval was obtained from the University of Nottingham, school of Veterinary Medicine and Science Clinical Ethical Review panel. Data from another study (Moreton et al [ 28 ], Characterisation of the horse transcriptome from immunologically active tissues) [ 27 ] has been re-analysed in this study. Permission to reuse this data was obtained from these authors.…”

Section: Authors’ Contributionsmentioning

confidence: 99%

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RNA expression of TLR10 in normal equine tissues

et al. 2016

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BackgroundToll like receptors are one of the major innate immune system pathogen recognition systems. There is little data on the expression of the TLR10 member of this family in the horse.ResultsThis paper describes the genetic structure of the Equine TLR10 gene and its RNA expression in a range of horse tissues. It describes the phylogenetic analysis of the Equine TLR1,6,10,2 annotations in the horse genome, firmly identifying them in their corresponding gene clades compared to other species and firmly placing the horse gene with other TLR10 genes from odd-toed ungulates. Additional 3’ transcript extensions to that annotated for TLR10 in the horse genome have been identified by analysis of RNAseq data. RNA expression of the equine TLR10 gene was highest in peripheral blood mononucleocytes and lymphoid tissue (lymph nodes and spleen), however some expression was detected in all tissues tested (jejunum, caudal mesenteric lymph nodes, bronchial lymph node, spleen, lung, colon, kidney and liver). Additional data on RNAseq expression of all equine TLR genes (1–4 and 6–10) demonstrate higher expression of TLR4 than other equine TLRs in all tissues.ConclusionThe equine TLR10 gene displays significant homology to other mammalian TLR10 genes and could be reasonably assumed to have similar fuctions. Its RNA level expression is higher in resting state PBMCs in horses than in other tissues.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-016-2161-9) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Authors’ Contributionsmentioning

confidence: 99%

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RNA expression of TLR10 in normal equine tissues

et al. 2016

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“…Several studies have reported the application of RNA‐Seq in horses in an attempt to identify differentially expressed genes 86, 87, 88, 89, 90, 91, 92, 93, 94, 95. To the authors' knowledge, the first report of RNA‐Seq in horses was an effort to characterize the transcriptome and tissue‐specific expression profiles from 8 equine tissues 94.…”

Section: Next Generation Sequencing Techniquesmentioning

confidence: 99%

“…To the authors' knowledge, the first report of RNA‐Seq in horses was an effort to characterize the transcriptome and tissue‐specific expression profiles from 8 equine tissues 94. A subsequent study focused on characterizing gene expression by RNA‐Seq in immunologically active tissues 95. Investigators have used RNA‐Seq to characterize the expression profile of genes critical to the differentiation and regulation of cells during embryogenesis,90 and to characterize the expression and inferred function of RNAs in the equine sperm transcriptome 89.…”

Section: Next Generation Sequencing Techniquesmentioning

confidence: 99%

Genetic Susceptibility to Rhodococcus equi

McQueen

Dindot

2015

Veterinary Internal Medicne

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Rhodococcus equi pneumonia is a major cause of morbidity and mortality in neonatal foals. Much effort has been made to identify preventative measures and new treatments for R. equi with limited success. With a growing focus in the medical community on understanding the genetic basis of disease susceptibility, investigators have begun to evaluate the interaction of the genetics of the foal with R. equi. This review describes past efforts to understand the genetic basis underlying R. equi susceptibility and tolerance. It also highlights the genetic technology available to study horses and describes the use of this technology in investigating R. equi. This review provides readers with a foundational understanding of candidate gene approaches, single nucleotide polymorphism‐based, and copy number variant‐based genome‐wide association studies, and next generation sequencing (both DNA and RNA).

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RNA sequencing as a powerful tool in searching for genes influencing health and performance traits of horses

Stefaniuk‐Szmukier¹,

Ropka‐Molik

2015

J Appl Genetics

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RNA sequencing (RNA-seq) by next-generation technology is a powerful tool which creates new possibilities in whole-transcriptome analysis. In recent years, with the use of the RNA-seq method, several studies expanded transcriptional gene profiles to understand interactions between genotype and phenotype, supremely contributing to the field of equine biology. To date, in horses, massive parallel sequencing of cDNA has been successfully used to identify and quantify mRNA levels in several normal tissues, as well as to annotate genes. Moreover, the RNA-seq method has been applied to identify the genetic basis of several diseases or to investigate organism adaptation processes to the training conditions. The use of the RNA-seq approach has also confirmed that horses can be useful as a large animal model for human disease, especially in the field of immune response. The presented review summarizes the achievements of profiling gene expression in horses (Equus caballus).

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Characterisation of the horse transcriptome from immunologically active tissues

Cited by 6 publications

References 30 publications

RNA expression of TLR10 in normal equine tissues

RNA expression of TLR10 in normal equine tissues

Genetic Susceptibility to Rhodococcus equi

RNA sequencing as a powerful tool in searching for genes influencing health and performance traits of horses

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