RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus)

RNA-seq has emerged as an important technology for measuring gene expression in peripheral blood samples collected from humans and other vertebrate species. In particular, transcriptomics analyses of whole blood can be used to study immunobiology and develop novel biomarkers of infectious disease. H...

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Published in:	Frontiers in genetics Vol. 9; p. 278
Main Authors:	Correia, Carolina N., McLoughlin, Kirsten E., Nalpas, Nicolas C., Magee, David A., Browne, John A., Rue-Albrecht, Kevin, Gordon, Stephen V., MacHugh, David E.
Format:	Journal Article
Language:	English
Published:	Switzerland Frontiers Media S.A 14.08.2018
Subjects:	blood cattle Genetics globin horses pigs reticulocyte pigs RNA-seq globin reticulocyte transcriptome cattle blood horses
ISSN:	1664-8021, 1664-8021
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Abstract	RNA-seq has emerged as an important technology for measuring gene expression in peripheral blood samples collected from humans and other vertebrate species. In particular, transcriptomics analyses of whole blood can be used to study immunobiology and develop novel biomarkers of infectious disease. However, an obstacle to these methods in many mammalian species is the presence of reticulocyte-derived globin mRNAs in large quantities, which can complicate RNA-seq library sequencing and impede detection of other mRNA transcripts. A range of supplementary procedures for targeted depletion of globin transcripts have, therefore, been developed to alleviate this problem. Here, we use comparative analyses of RNA-seq data sets generated from human, porcine, equine, and bovine peripheral blood to systematically assess the impact of globin mRNA on routine transcriptome profiling of whole blood in cattle and horses. The results of these analyses demonstrate that total RNA isolated from equine and bovine peripheral blood contains very low levels of globin mRNA transcripts, thereby negating the need for globin depletion and greatly simplifying blood-based transcriptomic studies in these two domestic species.
AbstractList	RNA-seq has emerged as an important technology for measuring gene expression in peripheral blood samples collected from humans and other vertebrate species. In particular, transcriptomics analyses of whole blood can be used to study immunobiology and develop novel biomarkers of infectious disease. However, an obstacle to these methods in many mammalian species is the presence of reticulocyte-derived globin mRNAs in large quantities, which can complicate RNA-seq library sequencing and impede detection of other mRNA transcripts. A range of supplementary procedures for targeted depletion of globin transcripts have, therefore, been developed to alleviate this problem. Here, we use comparative analyses of RNA-seq data sets generated from human, porcine, equine, and bovine peripheral blood to systematically assess the impact of globin mRNA on routine transcriptome profiling of whole blood in cattle and horses. The results of these analyses demonstrate that total RNA isolated from equine and bovine peripheral blood contains very low levels of globin mRNA transcripts, thereby negating the need for globin depletion and greatly simplifying blood-based transcriptomic studies in these two domestic species. RNA-seq has emerged as an important technology for measuring gene expression in peripheral blood samples collected from humans and other vertebrate species. In particular, transcriptomics analyses of whole blood can be used to study immunobiology and develop novel biomarkers of infectious disease. However, an obstacle to these methods in many mammalian species is the presence of reticulocyte-derived globin mRNAs in large quantities, which can complicate RNA-seq library sequencing and impede detection of other mRNA transcripts. A range of supplementary procedures for targeted depletion of globin transcripts have, therefore, been developed to alleviate this problem. Here, we use comparative analyses of RNA-seq data sets generated from human, porcine, equine, and bovine peripheral blood to systematically assess the impact of globin mRNA on routine transcriptome profiling of whole blood in cattle and horses. The results of these analyses demonstrate that total RNA isolated from equine and bovine peripheral blood contains very low levels of globin mRNA transcripts, thereby negating the need for globin depletion and greatly simplifying blood-based transcriptomic studies in these two domestic species.RNA-seq has emerged as an important technology for measuring gene expression in peripheral blood samples collected from humans and other vertebrate species. In particular, transcriptomics analyses of whole blood can be used to study immunobiology and develop novel biomarkers of infectious disease. However, an obstacle to these methods in many mammalian species is the presence of reticulocyte-derived globin mRNAs in large quantities, which can complicate RNA-seq library sequencing and impede detection of other mRNA transcripts. A range of supplementary procedures for targeted depletion of globin transcripts have, therefore, been developed to alleviate this problem. Here, we use comparative analyses of RNA-seq data sets generated from human, porcine, equine, and bovine peripheral blood to systematically assess the impact of globin mRNA on routine transcriptome profiling of whole blood in cattle and horses. The results of these analyses demonstrate that total RNA isolated from equine and bovine peripheral blood contains very low levels of globin mRNA transcripts, thereby negating the need for globin depletion and greatly simplifying blood-based transcriptomic studies in these two domestic species.
Author	McLoughlin, Kirsten E. MacHugh, David E. Correia, Carolina N. Gordon, Stephen V. Rue-Albrecht, Kevin Magee, David A. Nalpas, Nicolas C. Browne, John A.
AuthorAffiliation	2 UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland 1 Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland 3 UCD Conway Institute of Biomolecular and Biomedical Research University College Dublin, Dublin, Ireland
AuthorAffiliation_xml	– name: 3 UCD Conway Institute of Biomolecular and Biomedical Research University College Dublin, Dublin, Ireland – name: 1 Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland – name: 2 UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
Author_xml	– sequence: 1 givenname: Carolina N. surname: Correia fullname: Correia, Carolina N. – sequence: 2 givenname: Kirsten E. surname: McLoughlin fullname: McLoughlin, Kirsten E. – sequence: 3 givenname: Nicolas C. surname: Nalpas fullname: Nalpas, Nicolas C. – sequence: 4 givenname: David A. surname: Magee fullname: Magee, David A. – sequence: 5 givenname: John A. surname: Browne fullname: Browne, John A. – sequence: 6 givenname: Kevin surname: Rue-Albrecht fullname: Rue-Albrecht, Kevin – sequence: 7 givenname: Stephen V. surname: Gordon fullname: Gordon, Stephen V. – sequence: 8 givenname: David E. surname: MacHugh fullname: MacHugh, David E.
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ContentType	Journal Article
Copyright	Copyright © 2018 Correia, McLoughlin, Nalpas, Magee, Browne, Rue-Albrecht, Gordon and MacHugh. 2018 Correia, McLoughlin, Nalpas, Magee, Browne, Rue-Albrecht, Gordon and MacHugh
Copyright_xml	– notice: Copyright © 2018 Correia, McLoughlin, Nalpas, Magee, Browne, Rue-Albrecht, Gordon and MacHugh. 2018 Correia, McLoughlin, Nalpas, Magee, Browne, Rue-Albrecht, Gordon and MacHugh
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Keywords	pigs RNA-seq globin reticulocyte transcriptome cattle blood horses
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Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Edited by: John Anthony Hammond, Pirbright Institute (BBSRC), United Kingdom Kevin Rue-Albrecht, Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom Reviewed by: Chuanju Dong, Henan Normal University, China; Luiz Lehmann Coutinho, Universidade de São Paulo, Brazil This article was submitted to Livestock Genomics, a section of the journal Frontiers in Genetics Present Address: Nicolas C. Nalpas, Quantitative Proteomics and Proteome Centre Tübingen, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
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Snippet	RNA-seq has emerged as an important technology for measuring gene expression in peripheral blood samples collected from humans and other vertebrate species. In...
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Title	RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus)
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