title: Comparison of quantitative real-time polymerase chain reaction with NanoString® methodology using adipose and liver tissues from rats fed seaweed.
abstract: Experimental methods are constantly being improved by new technology. Recently a new technology, NanoString®, has been introduced to the market for the analysis of gene expression. Our experiments used adipose and liver samples collected from a rat feeding trial to explore gene expression changes resulting from a diet of 7.5% seaweed. Both quantitative real-time polymerase chain reaction (qPCR) and NanoString methods were employed to look at expression of genes related to fat and glucose metabolism and this paper compares results from both methods. We conclude that NanoString offers a valuable alternative to qPCR and our data suggest that results are more accurate because of the reduced sample handling and direct quantification of gene copy number without the need for enzymatic amplification. However, we have highlighted a potential challenge for both methods, which needs to be addressed when designing primers or probes. We suggest a literature search for known splice variants of a particular gene to be completed so that primers or probes can be designed that do not span exons which may be affected by alternative gene sequences.
authors.affiliation: The New Zealand Institute for Plant & Food Research Ltd, Palmerston North 4410, New Zealand. Electronic address: Kerry.Bentley-Hewitt@plantandfood.co.nz.
authors.forename: Kerry L
authors.initials: KL
authors.lastname: Bentley-Hewitt
authors.affiliation: The New Zealand Institute for Plant & Food Research Ltd, Palmerston North 4410, New Zealand.
authors.forename: Duncan I
authors.initials: DI
authors.lastname: Hedderley
authors.affiliation: The New Zealand Institute for Plant & Food Research Ltd, Palmerston North 4410, New Zealand.
authors.forename: John
authors.initials: J
authors.lastname: Monro
authors.affiliation: The New Zealand Institute for Plant & Food Research Ltd, Palmerston North 4410, New Zealand.
authors.forename: Sheridan
authors.initials: S
authors.lastname: Martell
authors.affiliation: The New Zealand Institute for Plant & Food Research Ltd, Palmerston North 4410, New Zealand.
authors.forename: Hannah
authors.initials: H
authors.lastname: Smith
authors.affiliation: The New Zealand Institute for Plant & Food Research Ltd, Palmerston North 4410, New Zealand.
authors.forename: Suman
authors.initials: S
authors.lastname: Mishra
mesh_terms: D000273:Adipose Tissue / Q000378:metabolism*; D017398:Alternative Splicing / Q000235:genetics; D000818:Animals; D006903:Hydroxymethylglutaryl CoA Reductases / Q000235:genetics; D008099:Liver / Q000378:metabolism*; D036103:Nanotechnology / Q000379:methods*; D051381:Rats; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012015:Reference Standards; D012624:Seaweed / Q000378:metabolism*; D018709:Statistics, Nonparametric
chemical_list: D006903:Hydroxymethylglutaryl CoA Reductases