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Citations Search

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Invest. Ophthalmol. Vis. Sci. 57(14), 6374-6381.  Molecular Diagnosis of Inherited Retinal Diseases in Indigenous African Populations by Whole-Exome Sequencing. 2016

Roberts, L., Ratnapriya, R., du Plessis, M., Chaitankar, V., Ramesar, R.S. and Swaroop, A..

Notes: The authors quantified purified retinal gDNA samples using the QuantiFluor® dsDNA System prior to whole-exome capture, library preparation and sequencing on an Illumina HiSeq 2500. (4803)

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BMC Genomics 17, 392. A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species. 2016

Torres-Oliva, M., Almudi, I., McGregor, A.P. and Posnien, N.

Notes: The authors quantified TruSeq cDNA libraries with the QuantiFluor® dsDNA System for sequencing on the Illumina HiSeq 2000. (4792)

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Food Microbiol. 54, 60-71. Assessment throughout a whole fishing year of the dominant microbiota of peeled brown shrimp (Crangon crangon) stored for 7 days under modified atmosphere packaging at 4°C without preservatives. 2016

Calliauw, F., De Mulder, T., Broekaert, K., Vlaemynck, G., Michiels, C. and Heyndrickx, M.

Notes: The authors purified DNA and amplified into a library using the Illumina 16S Metagenomic Sequencing Library Preparation protocol. Concentration was determined by the Quantus™ Fluorometer and libraries were normalized, pooled and sequenced on an Illumina MiSeq. (4783)

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Appl. Soil Ecol. 107, 1-12. Biological, physicochemical and plant health responses in lettuce and strawberry in soil or peat amended with biochar.  2016

De Tender, C.A., Debode, J., Vandecasteele, B., D’Hose, T., Cremelie, P., Haegeman, A., Ruttink, T., Dawyndt, P. and Maes, M.

Notes: The authors quantified DNA libraries using the Quantus™ Fluorometer and QuantiFluor® dsDNA System. The DNA libraries were normalized, pooled and sequenced on an Illumina MiSeq. (4784)

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Sci. Rep. 6, 25235. Detection of DNA viruses in prostate cancer. 2016

Smelov, V., Bzhalava, D., Arroyo Mühr, L.S., Eklund, C., Komyakov, B., Gorelov, A., Dillner, J. and Hultin, E.

Notes: The authors purified DNA from expressed prostate secretions (EPS) and quantified using the QuantiFluor® dsDNA System. The purified DNA was made into Illumina libraries, quantified again with the QuantiFluor® dsDNA System, normalized to 10nM and sequenced on an Illumina NextSeq 500. (4802)

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Proc. Biol. Sci. 283(1835), 20160749. Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution. 2016

Vogwill, T., Phillips, R.L., Gifford, D.R. and MacLean, R.C.

Notes: The authors extracted genomic DNA from bacteria using the Wizard® Genomic DNA Purification Kit and quantified using the QuantiFluor® dsDNA System. The DNA was made into libraries and sequenced with an Illumina HiSeq 2000. (4805)

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Sci. Rep. 6, 20582. Genetic regulation of salt stress tolerance revealed by RNA-Seq in cotton diploid wild species, Gossypium davidsonii. 2016

Zhang, F., Zhu, G., Du, L., Shang, X., Cheng, C., Yang, B., Hu, Y., Cai, C. and Guo, W.

Notes: The authors quantified TruSeq cDNA libraries with the QuantiFluor® dsDNA System and then performed RNA-seq using the HiSeq 2000. (4797)

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BMC Genomics 17(1), 982. Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes. 2016

Clawson, M.L., Murray, R.W., Sweeney, M.T., Apley, M.D., DeDonder, K.D., Capik, S.F., Larson, R.L., Lubbers, B.V., White, B.J., Kalbfleisch, T.S., Schuller, G., Dickey, A.M., Harhay, G.P., Heaton, M.P., Chitko-McKown, C.G., Brichta-Harhay, D.M., Bono, J.L. and Smith, T.P.

Notes: The authors purified microbial DNA samples which were quantified with a Quantus™ Fluorometer and QuantiFluor® Dyes prior to using the Nextera™ DNA Library Prep Kit and sequencing on a MiSeq Instrument.  (4785)

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PLos ONE 11(2), e0150361. Metagenomic Characterisation of the Viral Community of Lough Neagh, the Largest Freshwater Lake in Ireland. 2016

Skvortsov, T., de Leeuwe, C., Quinn, J.P., McGrath, J.W., Allen, C.C., McElarney, Y., Watson, C., Arkhipova, K., Lavigne, R. and Kulakov, L.A.

Notes: The authors purified viral DNA from water samples and quantified using a Quantus™ Fluorometer prior to Nextera® DNA library preparation and Illumina MiSeq sequencing. Bacterial 16S rRNA genes were amplified by PCR from the same water samples, purified and then quantified with a Quantus™ Fluorometer prior to amplicon sequencing with a Roche Sequencing 454 GS Junior System. (4787)

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Dent. Mater. 32(1), 93-101. Microbiome of titanium and zirconia dental implants abutments. 2016

Nascimento, C.d., Pita, M.S., Santos Ede, S., Monesi, N., Pedrazzi, V., Albuquerque Jr., R.F. and Ribeiro, R.F..

Notes: The authors quantified 16S rDNA amplicon libraries using the QuantiFluor® dsDNA System and pooled libraries together for sequencing on a Genome Sequencing Junior System (454/Roche). (4793)

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PLos ONE 11(10), e0164964. Morphological and Molecular Characterization of Human Dermal Lymphatic Collectors. 2016

Hasselhof, V., Sperling, A., Buttler, K., Ströbel, P., Becker, J., Aung, T., Felmerer, G. and Wilting, J.

Notes: The authors quantified cDNA libraries with the QuantiFluor® dsDNA System for sequencing on the Illumina HiSeq 2000. (4790)

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Plant Soil 410(1), 193-206. Plant species, temperature, and bedrock affect net methane flux out of grassland and forest soils. 2016

Praeg, N., Wagner, A.O. and Illmer, P.

Notes: The authors quantified purified DNA from rhizopsphere soil samples using the QuantiFluor® dsDNA System prior to library creation and sequencing on an Illumina MiSeq. (4804)

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Hortic. Res. 3, 16043. QTL analysis of soft scald in two apple populations. 2016

McClure, K.A., Gardner, K.M., Toivonen, P.M., Hampson, C.R., Song, J., Forney, C.F., DeLong, J., Rajcan, I. and Myles, S.

Notes: The authors quantified purified apple leaf DNA samples using the QuantiFluor® dsDNA System and the GloMax®-Multi+ Detection System prior to Illumina sequencing. (4798)

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DNA Repair 48, 63-68. Quantification and genome-wide mapping of DNA double-strand breaks. 2016

Grégoire, M.-C., Massonneau, J., Leduc, F., Arguin, M., Brazeau, M.A. and Boissonneault, G.

Notes: The authors quantified cell line DNA using the QuantiFluor® dsDNA System prior to targeted capture, library preparation and Illumina sequencing. (4800)

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Behav. Brain Res. 303, 34-43. Social defeat leads to changes in the endocannabinoid system: An overexpression of calreticulin and motor impairment in mice. 2016

Tomas-Roig, J., Piscitelli, F., Gil, V., Del Río, J.A., Moore, T.P., Agbemenyah, H., Salinas-Riester, G., Pommerenke, C., Lorenzen, S., Beißbarth, T., Hoyer-Fender, S., Di Marzo, V. and Havemann-Reinecke, U.

Notes: The authors quantified TruSeq cDNA libraries with the QuantiFluor® dsDNA System for sequencing on the Illumina HiSeq 2000. (4791)

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Appl. Environ. Microbiol. 82(2), 640-649. Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique. 2016

Ison, S.A., Delannoy, S., Bugarel, M., Nagaraja, T.G., Renter, D.G., den Bakker, H.C., Nightingale, K.K., Fach, P. and Loneragan, G.H.

Notes: Th authors made purified bacterial DNA into amplicon libraries, quantified using the QuantiFluor® dsDNA System and sequenced on an Illumina MiSeq. (4801)

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PLoS Genet. 12(5), e1006005. The Genomic Basis of Evolutionary Innovation in Pseudomonas aeruginosa. 2016

Toll-Riera, M., San Millan, A., Wagner, A. and MacLean, R.C.

Notes: The authors extracted bacterial DNA from 3ml LB broth using the Wizard® Genomic 4 DNA Purification Kit and quantified with the QuantiFluor® dsDNA System prior to sequencing on an Illumina HiSeq 2000. (4796)

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Urology 92, 26-32. The Urinary Microbiome Differs Significantly Between Patients With Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls as Well as Between Patients With Different Clinical Phenotypes. 2016

Shoskes, D.A., Altemus, J., Polackwich, A.S., Tucky, B., Wang, H. and Eng, C.

Notes: The authors quantified 16S rDNA amplicon libraries using the QuantiFluor® dsDNA System and pooled the libraries together for sequencing on an Illumina MiSeq (4794)

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Biol. Reprod. 92(3), 71. Combining RNA and Protein Profiling Data with Network Interactions Identifies Genes Associated with Spermatogenesis in Mouse and Human. 2015

Petit, F.G., Kervarrec, C., Jamin, S.P., Smagulova, F., Hao, C., Becker, E., Jégou, B., Chalmel, F. and Primig, M.

Notes: The authors immunoprecipitated chromatin, purified the DNA and quantified on a Quantus™ Fluorometer with QuantiFluor® dsDNA System. The DNA was made into libraries and sequenced on an Illumina HiSeq2000. (4788)

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J. Craniomaxillofac. Surg. 43(8), 1494-1500. DNA methylation analysis by bisulfite next-generation sequencing for early detection of oral squamous cell carcinoma and high-grade squamous intraepithelial lesion from oral brushing. 2015

Morandi, L., Gissi, D., Tarsitano, A., Asioli, S., Monti, V., Del Corso, G., Marchetti, C., Montebugnoli, L. and Foschini, M.P.

Notes: The authors purified DNA from oral mucosa samples. The DNA was bisulfate treated, made into libraries and quantified with a Quantus™ Fluorometer. The DNA libraries were normalized, pooled and sequenced on a Roche 454 Sequencing GS Junior System. (4789)

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PLos ONE 10(6), e0131918. Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing. 2015

Rocher, S., Jean, M., Castonguay, Y. and Belzile, F.

Notes: The authors quantified amplicon libraries using the QuantiFluor® dsDNA System and the GloMax®-Multi Detection System prior to pooling and sequencing on a 454-GS-FLX Titanium System. (4795)

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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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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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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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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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