Nature Methods Application Notes e-UPDATE: 15 January 2013

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15 JANUARY 2013  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 SENSE: a fast RNA-seq library preparation protocol with superior strand specificity www.lexogen.com > The SENSE mRNA-seq library preparation kit generates ready-to-sequence libraries from low amounts of total RNA within 4 h. SENSE libraries are significantly more strand specific (>99.9%) than leading alternatives and are virtually free of rRNA contamination. The protocol does not rely on RNA or cDNA fragmentation or additional kits for rRNA depletion, library amplification or size selection. PDF

		Targeted Mutation Profiling of Non-Small Cell Lung Cancer Samples using the Sequenom Lungcarta™ Panel* for Clinical Research www.sequenom.com > Sequenom's MassARRAY® System* enables sensitive and rapid somatic mutation profiling in non-small cell lung carcinoma (NSCLC) samples. A new research use only LungCarta Panel offers highly valuable content with 214 mutations in 26 tumor suppressors and oncogenes. We evaluated the LungCarta Panel against known standards, NCI-60 cell line DNA, and formalin-fixed paraffin embedded lung adenocarcinoma samples, and demonstrate that the panel provides a robust method for confirmation of known mutations. PDF

		A novel RNA detection reagent enables gene expression analysis and sorting of living cells www.millipore.com > Detecting gene expression has traditionally been limited to technologies that examine expression in lysed or fixed cell populations. The ability to detect RNAs in individual, live cells can enable an unequivocal assessment of gene expression changes that occur in direct response to specified perturbations. Determining which genes are up- or down-regulated in these perturbed cells provides insight into the relationships between gene expression networks and cell functions. To meet this challenge, we developed SmartFlare™ RNA Detection Probes, capable of detecting specific mRNAs and miRNAs in live, intact cells (Figure 1). This technology allows for carrier-free cellular endocytosis of the reagent, followed by detection and relative quantitative analysis of RNA levels. PDF

		Rapid and Non-Phenol Extraction of Circulating and Exosomal RNA from Bodily Fluids www.norgenbiotek.com > Norgen Biotek has developed various products (Plasma/Serum Circulating RNA Purification Kits and Exosome RNA Purification Kits) that are specifically optimized for purifying circulating or exosomal RNA (large RNA and microRNA) from plasma/serum or urine with the following advantages: Simple and Fast Procedure with no lengthy phenol:chloroform extraction, filtration or precipitation Scalable Purification of RNA from 50 µL to 5 mL of plasma/serum and 1 mL to 10 mL of urine High Yield, High Quality and Inhibitor-Free RNA isolated from all types of plasma, serum or urine PDF

		Understanding the impact of cancer cells' metabolic phenotype and intervention strategies www.seahorsebio.com > Cancer cells exhibit high rates of glycolysis, even in the presence of oxygen, a phenomenon known as the Warburg effect. While normal cells generate most of their ATP via oxidative phosphorylation, cancer cells are more reliant on glycolysis to generate ATP. Energy production through glycolysis results in a net production of protons; as glycolysis occurs, protons are extruded into the extracellular environment, acidifying the medium surrounding the cells or tissue. PDF

		Long-span, mate-pair scaffolding and other methods for faster next-generation sequencing library creation www.lucigen.com > The NxSeq™ 40 kb Mate-Pair Cloning Kit facilitates the creation of scaffolds for de novo genome assembly. Supporting either Illumina or 454 sequencing, the kit produces long-span, mate-pair sequences with greater efficiency than existing protocols. In addition, NxSeq DNA Sample Prep Kits can be used to streamline workflow and speed up DNA library preparation for next-generation sequencing. PDF

		High-content analysis of biomarker intensity and distribution in 3D microtissues www.perkinelmer.com > Three-dimensional (3D) cell culture methods are widely accepted as more physiologically relevant than conventional 2D cell culture methods and are believed to improve the prediction of drug candidates at an early stage of the drug development process. Here we describe the analysis of a spherical colon cancer microtissue model using the Operetta® High Content Imaging System. In vivo near-infrared (NIR) agents allowed visualization and quantification of cancer-associated biomarker intensity and distribution in microtissues. PDF

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