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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. and El-Kassaby, Y.A.

Notes: The authors extracted DNA from dormant vegetative buds and quantitated DNA using the QuantiFluor® dsDNA System on a SpectraFluor Plus plate-format fluorometer prior to NGS (4917)

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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, 119–130. 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 VI, R. and Li, C.J.

Notes: The authors performed ChIP and quantitated immunoprecipitated DNA with the QuantiFluor® dsDNA System prior to NGS on an Illumina Instrument. (4918)

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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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