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 )

Frontiers in Genetics
Carolina N CorreiaDavid E MacHugh

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.

References

Oct 1, 1985·The Anatomical Record·F Tablin, L Weiss
Jul 1, 1994·ASAIO Journal : a Peer-reviewed Journal of the American Society for Artificial Internal Organs·S B HarperC M Lang
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Mar 26, 2003·The Journal of Veterinary Medical Science·Mohammad Alamgir HossainYoshimitsu Maede
Dec 19, 2003·Nucleic Acids Research·Donna KarolchikW James Kent
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Feb 22, 2005·Current Molecular Medicine·Hongtao Fan, Priti S Hegde
Aug 17, 2005·Journal of Applied Physiology·C CooperD Bienzle
Oct 27, 2006·The Journal of Molecular Diagnostics : JMD·Jinny LiuDzung Thach
Sep 15, 2009·Cell Host & Microbe·Octavio Ramilo, Asunción Mejías
May 18, 2010·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Mary E WinnNicholas J Schork
Aug 18, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Philip K Thornton
Dec 12, 2012·PloS One·Alexander Churbanov, Brook Milligan
Mar 14, 2013·Animal Science Journal = Nihon Chikusan Gakkaihō·Ki-Duk SongSung Woo Kim
Aug 21, 2013·PLoS Computational Biology·Michael LawrenceVincent J Carey
Oct 22, 2013·The Journal of Infection·Asuncion Mejias, Octavio Ramilo
May 14, 2014·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Simon BlankleyAnne O'Garra
Jun 24, 2014·Source Code for Biology and Medicine·Chuming ChenCathy H Wu
Sep 11, 2014·Frontiers in Immunology·Kirsten E McLoughlinDavid E MacHugh
Sep 28, 2014·Bioinformatics·Simon AndersWolfgang Huber
Jul 7, 2015·Expert Review of Molecular Diagnostics·Emily R KoEphraim L Tsalik
Dec 17, 2015·Experimental and Therapeutic Medicine·Yafen ChengHsiang-Jung Tsai
Mar 24, 2016·BMC Medicine·Carolin T HaasMahdad Noursadeghi
Aug 16, 2016·Scientific Reports·Kaarel KrjutškovJuha Kere

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE53655
GSE83404

Methods Mentioned

BETA
RNA-seq
antisense oligonucleotides
PCR
Assay

Software Mentioned

Python
tidyverse
Bioconductor
Ubuntu Linux OS
Linux Compute Server
tximport
Salmon
Ensembl Table Browser
TopHat
skimr

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.