Identification of reference genes for real-time polymerase chain reaction gene expression studies in Nile rats fed Water-Soluble Palm Fruit Extract.

Molecular Biology Reports
Soon-Sen LeowK C Hayes

Abstract

The Nile rat (Arvicanthis niloticus) is a novel diurnal carbohydrate-sensitive rodent useful for studies on type 2 diabetes mellitus (T2DM) and the metabolic syndrome. Hepatic responses to T2DM and any interventions thereof can be evaluated via transcriptomic gene expression analysis. However, the study of gene expression via real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) requires identification of stably expressed reference genes for accurate normalisation. This study describes the evaluation and identification of stable reference genes in the livers from Control Nile rats as well as those supplemented with Water-Soluble Palm Fruit Extract, which has been previously shown to attenuate T2DM in this animal model. Seven genes identified as having stable expression in RNA-Sequencing transcriptome analysis were chosen for verification using real-time RT-qPCR. Six commonly used reference genes from previous literature and two genes from a previous microarray gene expression study in Nile rats were also evaluated. The expression data of these 15 candidate reference genes were analysed using the RefFinder software which incorporated analyses performed by various algorithms. The Hpd, Pnpla6 and Vpp2 ge...Continue Reading

References

Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Jan 7, 2004·Biochemical and Biophysical Research Communications·Aleksandar RadonićAndreas Nitsche
Dec 8, 2004·Archives of Biochemistry and Biophysics·Graham R Moran
Apr 5, 2007·Nature Protocols·Tania NolanStephen A Bustin
Apr 25, 2007·Nucleic Acids Research·Warren A Kibbe
Jul 8, 2008·Biochemical and Biophysical Research Communications·Kohei TatsumiMidori Shima
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Mar 26, 2010·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Kousuke NodaAli Hafezi-Moghadam
Oct 26, 2010·Nucleic Acids Research·Rasko LeinonenGuy Cochrane
Jul 9, 2011·The British Journal of Nutrition·Ravigadevi SambanthamurthiMohd Basri Wahid
Jul 9, 2011·The British Journal of Nutrition·Ravigadevi SambanthamurthiMohd Basri Wahid
Aug 26, 2011·BMC Genomics·Soon-Sen LeowRavigadevi Sambanthamurthi
Feb 1, 2012·Plant Molecular Biology·Fuliang XieBaohong Zhang
Jun 26, 2012·Nucleic Acids Research·Andreas UntergasserSteven G Rozen
Apr 20, 2013·Nucleic Acids Research·Jaina MistryMarco Punta
Sep 28, 2013·The Journal of Nutritional Biochemistry·Julia BolsingerK C Hayes
Oct 1, 2013·Journal of Applied Genetics·Bartłomiej Kozera, Marcin Rapacz
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Sep 6, 2014·Journal of Nutritional Science·Julia BolsingerK C Hayes
Jun 11, 2015·Bioinformatics·Felipe A SimãoEvgeny M Zdobnov
Jun 12, 2016·The Journal of Endocrinology·Xuemei TangLixia Gan
Dec 18, 2016·Clinical Chemistry and Laboratory Medicine : CCLM·Andreas Kappel, Andreas Keller
Feb 12, 2017·The Journal of Nutritional Biochemistry·Julia BolsingerK C Hayes
Jun 14, 2019·Proceedings of the Japan Academy. Series B, Physical and Biological Sciences·Masamitsu FutaiMayumi Nakanishi-Matsui

❮ Previous
Next ❯

Datasets Mentioned

BETA
PRJEB30590

Methods Mentioned

BETA
Chip
Assay

Software Mentioned

ePCR
NormFinder
BLASTX
BUSCO
RefFinder
BioEdit
ClustalW
HMMER
Trinity
BLASTP

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.