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Citations Search

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Plant Physiol. 164, 400-11. An RNA sequencing transcriptome analysis reveals novel insights into molecular aspects of the nitrate impact on the nodule activity of Medicago truncatula. 2014

Cabeza, R., Koester, B., Liese, R., Lingner, A., Baumgarten, V., Dirks, J., Salinas-Riester, G., Pommerenke, C., Dittert, K., and Schulze, J.

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)

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PLos ONE 9, e104566. Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics 2014

Heydt, C., Fassunke, J., Künstlinger, H., Ihle, M.A., König, K., Heukamp, L.C., Schidhaus, H-U., Odenthal, M., Büttner, R. and Merkelbach-Bruse, S.

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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Proc. Natl. Acad. Sci. USA 111, 8227–8232. Hierarchical expression of genes controlled by the Bacillus subtilis global regulatory protein CodY. 2014

Brinsmade S.R., Alexander, E.L., Livny, J., Stettner, A.I., Segrè, D., Rhee, K.Y., and Sonenshein, A.L.

Notes:

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.


(4449)

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Mol. Ecol. Resour. 14, 199–208. Next-Gen phyogeography of rainforest trees: Exploring landscape-level cpDNA variation from whole-genome sequencing 2014

Van der Merwe, M., McPherson, H., Siow, J. and Rossetto, M.

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)

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BMC Ecol. 13. Capturing chloroplast variation for molecular ecology studies: A simple next generation sequencing approach applied to a rainforest tree 2013

McPherson, H., van der Merwe, M., Delaney, S.K., Edwards, M.A., Henry, R.J., McInstosh, E., Rymer, P.D., Milner, M.L., Siow, J. and Rossetto, M.

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)

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PLos ONE 8, e62137. Genotyping-by-Sequencing (GBS): A novel, efficient and cost-effective genotyping method for cattle using next-generation sequencing 2013

De Donato, M., Peters, S.O., Mitchell, S.E., Hussain, T. and Imumorin, I.G.

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)

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Tree Genetics and Genomes 9, 1537–1544. Mining conifers’ mega-genome using rapid and efficient multiplexed high-throughput genotyping-by-sequencing (GBS) SNP discovery platform 2013

Chen, C., Mitchell, S.E., Elshire, R.J., Buckler, E.S., El-Kassably, Y.A.

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)

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Funt. Integr. Genomics 12, 119–30. Genome-wide ChIP-seq mapping and analysis reveal butyrate-induced acetylation of H3K9 and H3K27 correlated with transcription activity in bovine cells. 2012

Shin, J.H., Li, R.W., Gao, Y., Baldwin, R. 6th and Li, C.J.

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)

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Funct. Food Health Disease 2, 228–241. Lowbush blueberries, Vaccinium angustifolium, modulate the functional potential of nutrient utilization and DNA maintenance mechanisms in the rat proximal colon microbiota 2012

Lacombe, A., Li, R.W., Klimis-Zacas, D., Kristo, A.S., Tadepalli, S., Krauss, E., Young, R. and Wu, V.C.H.

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)

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