Nature Methods Application Notes e-UPDATE: 14 June 2016

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14 June 2016  Application Notes bring you the latest information about innovative tools and technologies and their applications in the lab. We hope that you will find this service useful and informative and encourage you to sign up for future Updates to ensure that you never miss one!

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FEATURED APPLICATION NOTE A SMARTer Approach to T-Cell Receptor Profiling www.clontech.com/ > Next-generation sequencing (NGS) of T-cell receptors (TCRs) is a powerful method for examining the adaptive immune response. Here we show how the Clontech SMARTer® Human TCR a/b Profiling Kit enables the construction of high quality TCR sequencing libraries from as little as 10 ng of total RNA. By employing a 5&prime RACE-like approach, the Clontech® kit generates full-length sequence data for TCR variable regions and allows for the detection of low abundance TCR clonotypes while avoiding multiplex PCR amplification strategies. PDF

		Standardizing the quality control of any DNA isolation to safequard the success of genetic testing www.trinean.com > Genetic tests become ever more powerful, yet also more complex and costly, which is why it is prudent to include quality control steps throughout the preparation process to ensure the quality of the downstream data obtained. To make an informed go/no go decision and avoid analytical failures, a good assessment of the yield and purity of DNA/RNA isolations is essential, including the detection of carry-over constituents that may interfere with downstream tests. Here, we validate a novel approach for DNA quality assessment using a large DNA sample set derived from a variety of human and other mammalian tissues combined with a wide scale of extraction methods. This new QC tool employs the micro-volume spectroscopy on the DropSense™ 16 'Touch & Go' reader by Trinean combined with its cDrop™ software to specifically quantify the isolated DNA as well as identify each contaminating constituent in the sample contributing to the measured UV/VIS spectra. PDF

		Performing efficient sample preparation with hard tumor tissue: Precellys® bead-beating homogenizer solution www.bertin-technologies.com/ > The Precellys® Evolution is the most efficient homogenizer based on bead-beating technology. It combines high flexibility and high efficiency for either routine or R&D projects. The instrument's unique figure-eight multidirectional motion provides the same high level of energy and homogenization efficiency to all the tubes. PDF

		Variation of homogenization time to optimize yield and quality of DNA extraction from S. cerevisiae suspension www.bio.analytik-jena.com > Analytik Jena's SpeedMill PLUS in combination with innuSPEED Bacteria/Fungi DNA Kit provides a complete system for homogenization of starting material and extraction of DNA. PDF

		HyVolution—the smart path to confocal super-resolution www.leica-microsystems.com/ > Super-resolution refers to any device or method that can resolve better than the classical Abbe limit. Apart from infinite super-resolution techniques such as STED (stimulated emission depletion) and SMLM (single-molecule localization methods) that can theoretically resolve to any detail, there are also methods for limited super-resolution. Here we present HyVolution by Leica, which merges optical super-resolution and computational super-resolution. The optical part is provided by confocal microscopy, and the computational part by deconvolution. Lateral resolution of 140 nm is demonstrated. HyVolution offers multiple fluorescence recording in truly simultaneous mode. PDF

		The Tip of the Iceberg: How Pipette Tips Influence Results www.eppendorf.com/ > Pipettes are tools widely used in the lab and usually purchased with care. However, as pipette tips are only consumables, they are not usually selected with quality in mind. The standard ISO 8655:2002 recommends using pipette and tips from the same supplier. This study including tips from 15 different manufacturers proves that a pipetting system working perfectly with a certain tip exceeds the permissible error tolerances when a tip from a different manufacturer is used. Furthermore, we found that the calibration method influences the performance of the pipetting system: It is significant whether the calibration is done with or without tip change for each measured volume. Autoclaving impacts the tip dimension as well as the calibration result especially with small volumes. Eppendorf standard tips have been shown to perform within permissible error tolerances regardless of the calibration method or autoclaving. Here, the user is free to choose the method most suitable for his application. PDF

		Diagenode® Premium RRBS technology: cost-effective DNA methylation mapping with superior coverage www.diagenode.com/categories/rrbs-service > Reduced representation bisulfite sequencing (RRBS) enables genome-scale DNA methylation analysis in any vertebrate species. The assay benefits from the practical advantages of bisulfite sequencing while avoiding the cost of whole-genome sequencing. The Diagenode Premium RRBS kit makes this technology widely available and provides high coverage (up to 4 million CpGs in human samples). Multiplexing prior to bisulfite conversion allows processing of 96 samples per experiment, enabling studies of large cohorts. PDF

 

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