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10 March 2015 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 Fast and Convenient 5-hydroxymethylcytosine Enrichment Workflow for Next-Generation Sequencing  www.thermofisher.com > The Scientific™ EpiJET™ 5-hmC Enrichment Kit is highly specific for different DNA samples containing 5-hydroxymethylcytosine (5-hmC), an extensively studied DNA epigenetic modification. This tool, when combined with next-generation sequencing, offers new ways of analyzing 5-hmC at the genomic level. The data show that this tool can be used for both locus-specific and whole genome–specific analysis, yielding 5-hmC distribution patterns across different genomes.  PDF

		QuantSeq 3′ mRNA sequencing for RNA quantification  www.lexogen.com > QuantSeq provides an easy protocol to generate highly strand-specific next-generation sequencing (NGS) libraries close to the 3′ end of polyadenylated RNAs within 4.5 h. Only one fragment per transcript is generated, directly linking the number of reads mapping to a gene to its expression. QuantSeq reduces data analysis time and enables a higher level of multiplexing per run. QuantSeq is the RNA sample preparation method for accurate and affordable gene expression measurement.  PDF

		Reporter Assays and More: Applications of NanoLuc® Luciferase  www.promega.com > NanoLuc® Luciferase brings exciting new possibilities and improvements to luminescence applications, including protein stability monitoring, detection of protein interactions using BRET, and in vivoimaging. This article highlights several recent papers that illustrate the use of NanoLuc® Technology as a sensitive reporter for challenging applications beyond those of classic bioluminescence reporter assays.  PDF

		Exploring Protein Phosphorylation with RayBio® Antibody Arrays and ELISAs  www.raybiotech.com > Phosphorylation is arguably the most important regulatory mechanism in biological systems, directing both the activity and subcellular localization of many key signaling proteins. Phosphorylation is often detected by isotope labeling or by 2D gel and mass spectrometry analyses. Both methods are highly sensitive. However, because of the high equipment cost and labor required for mass spectrometry, and the special isotope handling and disposal required for radiolabeling, phospho-specific antibodies are generally the more preferred tool for detection of protein phosphorylation. ELISAs can be designed to rapidly and inexpensively detect phosphorylation-induced conformational changes in a specific protein, allowing many samples to be tested in parallel. Alternatively, phospho-specific antibodies can be multiplexed into an array format, allowing the simultaneous detection of multiple target phospho-proteins. Using these powerful tools, researchers can accomplish either high throughput detection of a specific activated protein in multiple samples, or detect phosphorylation signatures through parallel detection of many related phospho-proteins.  PDF

		Chromatrap® 96: a new solid-state platform for high-throughput ChIP  www.chromatrap.com > Chromatrap® 96 (C96) is a high-throughput analysis platform that profiles up to 96 transcription factors and epigenetic modifications simultaneously in less than 1 d. It enables sensitive, selective and reproducible target amplification with excellent signal-to-noise ratios, even from samples as small as 0.1 μg. Compatible with automated handling, C96 allows simultaneous investigation of parallel epigenetic landscapes, offering unprecedented assay flexibility and speed.  PDF

		Optimized Library Prep for Cell-Free DNA from Human Plasma  www.biooscientific.com > Researchers and clinicians are increasingly interested in using Next Generation Sequencing (NGS) analysis of cell-free DNA (cfDNA) found in plasma (the cell-free fraction of anticoagulated blood) for biomarker discovery and diagnostic applications. Two areas of specific interest are non-invasive prenatal diagnostics (1-6) and monitoring efficacy of treatment in cancer patients (7-20). Many recent studies have shown the feasibility of detecting fetal aneuploidies such as Chromosome 21 trisomy (the cause of Down's Syndrome) by shotgun sequencing of DNA-Seq libraries produced from cell-free DNA isolated from maternal blood. Other aneuploidies including trisomies of Chromosomes 13 and 18 have also been detected (3). This approach is attractive since it avoids the risk of miscarriage associated with invasive tests (amniocentesis and chorionic villi sampling) and may offer cost benefits for prenatal diagnosis.  PDF

		Approaching Single-Cell Sequencing by Understanding NGS Library Complexity and Bias  www.swiftbiosci.com > Demands are growing on genomics to deliver higher quality sequencing data from samples with less input quantity. As the number of genomic equivalents decreases at lower input amounts, library bias and library complexity increasingly affect data quality. Less biased, more complex libraries result in more even and complete coverage, resulting in better sequencing efficiency and reduced costs. This application note describes the sequence coverage performance and preservation of molecular complexity of next generation sequencing (NGS) libraries generated from human and microbial genomic DNA using the Accel-NGS™ 2S DNA Library Kit for whole-genome sequencing (WGS) on the Illumina® platform.  PDF