Research Tools

The Storey Lab conducts many types of experiments  in the molecular arena. From enzyme purification to metabolite/antioxidant analysis right through to PCR, transcriptomics and multiplex analyses of cell functions. This is a list of the Topic Areas and Technical Bulletins to give you an idea of the types of projects we can do and the range of molecules we can quantitate. Members of the lab have access to detailed step-by-step instructions of every functional protocol below. Each tested and updated for our current equipment. In almost all cases there is a member of the current lab who is familiar with any particular assay or method. Below is a list of some of the main techniques currently used in the lab, follow the links to our papers for more information about the technique:

 

New Techniques and programs developed in the Storey Lab

DSF to analyze protein stability  (Real-time protein unfolding: a method for determining the kinetics of native protein denaturation using a quantitative real-time thermocycler. BioTechniques 53, 231-238. 2012. PMID: 23046506)

Novel species-specific microRNA prediction software. When using this program please cite: Peace RJ, Biggar KK, Storey KB, and Green JR. (2015) A framework for improving microRNA prediction in non-human genomes. Nucl. Acids Res. Epub. PMID: 26163062

RBioplot – An R package for statistics and graphing for molecular biology and biochemistry. Please visit our RBioPlot page for  more information on installation and usage. When using this program please cite: Zhang J and Storey KB. (2016) RBioplot: an easy-to-use R pipeline for automated statistical analysis and data visualization in molecular biology and biochemistry. PeerJ 4:e2436. PMID:27703842.

RBioMIR – An R package for differential expression (DE) analysis of small RNA-Seq based miRNA profiling experiments. When using this program please cite: Zhang J, Hadj-Moussa H, and Storey KB. (2016). Current progress of high-throughput microRNA differential expression analysis and random forest gene selection for model and non-model systems: an R implementation. Journal of Integrative Bioinformatics, 13(5), 306.  PMID:28187420

RBioFS – A machine learning R package for random forest-based gene selection. This bioinformatic tool can confidently select miRNAs relevant to differentiating physiological phenotypes of interest. When using this program please cite: Zhang J, Hadj-Moussa H, and Storey KB. (2016). Current progress of high-throughput microRNA differential expression analysis and random forest gene selection for model and non-model systems: an R implementation. Journal of Integrative Bioinformatics, 13(5), 306.  PMID:28187420

 

Techniques used in the Storey Lab

Cell signalling studies  (Regulation of the mTOR signaling network in hibernating ground thirteen-lined ground squirrels. J. Exp. Biol. 215, 1720-1727. 2012. PMID: 22539739)

Transcription factor ELISA  (FoxO3a mediated activation of stress responsive genes during early torpor in a mammalian hibernator. Mol. Cell Biochem. 390, 185-195. 2014. PMID 24493314)

qRT-PCR  (Modulation of gene expression in key survival pathways during torpor in the gray mouse lemur, Microcebus murinus. Genom. Proteom. Bioinform. 13,111–118. 2015. PMID 26093281)

MicroRNA qRT-PCR  (Dehydration triggers differential microRNA expression in Xenopus laevis brain. Gene. 2015. PMID 26169019)

Immunoblotting  (Characterization of the SIRT family of NAD+-dependent protein deacetylases in the context of a mammalian model of hibernation, the thirteen-lined ground squirrel. Cryobiology. 2015. PMID: 26277038)

Enzymology  (Free-radical first responders: The characterization of CuZnSOD and MnSOD regulation during freezing of the freeze-tolerant North American wood frog, Rana sylvatica. Biochem. Biophys. Acta 1850(1), 97-106. 2015. PMID 25316288)

Protein purification and structure  (Purification and properties of glyceraldehyde-3-phosphate Dehydrogenase from the skeletal muscle of the hibernating ground squirrel, Ictidomys tridecemlineatus. PeerJ. 2:e634. 2014. PMID 25374779)

Epigenetics (Regulation of hypometabolism: insights into epigenetic controls. J. Exp. Biol. 218, 150-159. 2015.PMID 25568462)

Luminex X-MAP multiplex technology  (Regulation ofthe PI3K/AKT pathway and fuel utilization during primate torpor in the gray mouse lemur, Microcebus murinus. Genom. Proteom. Bioinform. 13, 91–102. 2015. PMID: 26092184)

Bioinformatics – Protein folding  (Expression and characterization of the novel gene fr47 during freezing in the wood frog, Rana sylvatica. Biochem. Res. Intl. 2015, Article ID 363912, 8 pp. 2015. PMID: 26101667)

Immunoprecipitation and Co-Immunoprecipitation  (Akt signaling and freezing survival in the wood frog, Rana sylvatica. Biochem. Biophys. Acta 1830 (10), 4828-4837. 2013. PMID: 23811346)