Citations Search

Notes: This study investigated the effect of nitrate on nitrogenase activity in root nodules of Medicago truncatula . The authors monitored the decline in nitrogenase activity after nitrate exposure, then extracted and sequenced RNA from nodules at two time points: 1) When adequate nitrate to meet the plants needs was taken up; and 2) When nodule nitrogenase activity showed significant decline. Total RNA purified from nodules at these time points was used to construct cDNA libraries. The cDNA was quantified using the Quantifluor® dsDNA System prior to sequencing using the Illumina HiSeq 2000 Instrument. (4500)

Notes: The authors of this study set out to compare five automated systems for purification of DNA from FFPE tissue samples and five DNA quantification methods to determine the systems and methods most favorable to successful downstream massively parallel sequencing (next generation sequencing) analysis. Tissues were processed using commercially available DNA purification kits available for each platform. The authors concluded that the DNA extracted using the Maxwell® 16 systems and platform was of the highest quality in this study and gave the best results in downstream applications. (4512)

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In this paper, the Quantifluor® dsDNA dye was used to quantify cDNA during construction of an RNA sequencing library and prior to sequencing on an Illumina HiSeq 2500 instrument. To understand how the gene activation landscape changes as abundance of the regulatory protein CodY decreases, the authors performed genome-wide transcript profiling of wild type B. subtilis strains and a series of mutants that had varying levels of CodY expression. Comparison of the activation profiles provided insights into how the genes regulated by CodY are controlled depending on the level of activation of CodY by its ligands.

Notes: The authors of this study piloted use of uncomplicated analysis of the full chloroplast genome to study factors that affect the distribution of plant species. They looked at rainforest tree species in two distinct biogeographical areas in New South Wales, Australia. They extracted total genomic DNA from leaf samples, and quantified the DNA with the QuantiFluor™ dsDNA System on the SpectraMax Gemimi XPS detector before next generation sequencing. (4506)

Notes: The authors of this study used next generation sequencing technology to assemble chloroplast genome and detect single nucleotide polymorphisms for a rainforest tree species. Genomic DNA was extracted from leaf samples, and 2-3 extractions per individual tree were pooled. Genomic DNA was quantitated using the QuantiFluor® dsDNA System on the SpectraMAX Gemini XPS detector prior to next generation sequencing. (4509)

Notes: The authors of this study sought to apply a genotyping-by-sequencing approach to genotype cattle from the US and Africa. They collected blood samples from 47 unrelated animals slaughtered in the US and Nigeria. Genomic DNA was extracted and then quantitated using the QuantiFluor® dsDNA System on a SpectraFluor Plus plate-format fluorometer before being used for next-generation sequencing. (4508)

Notes: In this study, the authors evaluated “genotyping-by-sequencing” for the economically important lodgepole pine and white spruce conifer species. DNA samples extracted from dormant vegetative buds and DNA was quantitated using Quantifluor® ds DNA System on a SpectraFluor Plus plate-format fluorometer. (4507)

Notes: The authors studied the effect of butyrate treatment on histone acetylation and characterized how H3 acetylation affects DNA sequence binding specificity. To examine sequence specificity, they performed chromatin immunoprecipitation with butyrate-treated and untreated bovine kidney epithelial cells, quantified the recovered DNA, then sequenced the DNA by Illumina next-generation sequencing. DNA was quantitifed using the QuantiFluor® dsDNA System. (4240)

Notes: The authors of this study sought to determine how a diet enriched with low bush blueberries would affect the metabolic potential of gut microbes. For this study, they fed rats either a control diet or the control diet plus 8% weight/volume powder derived from low bush blueberries. After six weeks, rats were sacrificed and DNA was extracted from stool. Genomic DNA concentration was determined using the Quantus™ Fluorometer prior to being subjected to next generation sequencing (NGS). (4502)