qPCR NEWS - May 2011- focus on single-cell qPCR ------------------------------------------------------------------
Dear researcher, dear Gene Quantification page reader, Our newsletter informs about the latest news in quantitative real-time PCR (qPCR and qRT-PCR), which are compiled and summarised on the Gene Quantification homepage. The focus of this newsletter issue is: - UPDATE - new papers and applications for single-cell qPCR - http://singlecell.gene-quantification.info - MIQE qPCR APP for iPhone, iPad and iPod - iOS Universal - http://MIQE.gene-quantification.info - TATAA Biocenter qPCR Symposium ”Developments in Real-time PCR - >From Preanalytics to Molecular Diagnostics” ----------------------------------------------------------------------------- Nature Methods - Summary of the supplement on single-cell analysis Supplement issue: April 2011 Volume 8, No 4 Read the supplement http://www.nature.com/nmeth/journal/v8/n4s/index.html http://singlecell.gene-quantification.info Foreword In a series of commissioned pieces, authors discuss methods for the analysis of single cells and consider technical developments still needed. Three Reviews describe methods to study single-cell gene expression, peptide, and small-molecule metabolite profiles. Two Perspectives describe live-cell imaging and clonal analysis applied to single stem cells. A Commentary provides an overview of the technological developments underlying single-cell analysis and discusses applications of genome analysis in single cells. Single-cell analysis - Methods to study single cell genomics Since the beginning of research on cell biology, say Stephen Quake and Tomer Kalisky in a Commentary, technological advances have driven biological understanding of the single cell. Early microscopes that permitted biologists to observe single cells have led, via molecular marking techniques and flow cytometry, to the ability to rapidly monitor dozens of markers on thousands of individual cells. But the scale of single-cell analysis has not stopped there. The authors discuss methodologies, such as microfluidics, that are enabling highly parallel genome-scale analysis at single-cell resolution. They consider new applications—including haplotyping of human cells and the analysis of complex bacterial populations—for whole-genome sequencing of single cells. (Nat. Methods 8, 311–314, 2011) Transcriptomes - Methods for single-cell transcriptome profiling Strategies for single-cell transcriptome analysis Cells, even when derived from a common tissue source or progenitor, vary in their gene expression, and this in turn influences their behavior and fate. It is thus important to analyze transcriptomes at single-cell resolution. In a Review, Azim Surani and colleagues take the reader through the steps of single-cell transcriptome analysis, from the isolation of single cells to the release and reverse transcription of mRNA and the amplification of the resulting cDNA, followed by DNA microarray analysis or high-throughput sequencing. The authors present available software tools for bioinformatic analysis of sequence data and discuss current limitations of single-cell transcriptome analyses such as the lack of discrimination between sense and antisense strands and the exclusion of non-polyadenylated transcripts. Finally, they describe up-and-coming areas such as single- molecule sequencing for full-length RNAs and the ability to sequence RNA that is actively being translated. (Nat. Methods 8, S6–S11, 2011) Transcript imaging - Validating transcripts in single cells Schematic of a branched probe for transcript imaging High-throughput sequencing of transcripts in a single cell yields bulk information on what is being transcribed; to follow up on single transcripts in more detail, one needs to visualize the transcripts. In a Review, Alexander van Oudenaarden and Shalev Itzkovitz discuss methods for single-molecule transcript imaging in living and fixed cells. For transcript imaging in fixed cells, they describe fluorescence in situ hybridization (FISH) and derivative approaches based on labeled probes. For live cells, the authors compare methods based on gene fusion to the MS2 bacteriophage coat protein and molecular beacons. They discuss imaging technology and data analysis needed to extract information from single-molecule FISH experiments. In an outlook section they provide a glimpse into what is still required to make these methods more sensitive and to combine them with quantitative measurements of DNA and protein for a more complete picture of the expression networks that underlie tissue function. (Nat. Methods 8, S12–S19, 2011) -------------------------------------------------------------------------------- single-cell qPCR publications updated in May 2011 http://singlecell.gene-quantification.info Relevance of circulating tumor cells, extracellular nucleic acids, and exosomes in breast cancer Visualizing high error levels during gene expression in living bacterial cells An improved one-tube RT-PCR protocol for analyzing single-cell gene expression in individual mammalian cells Defining cell populations with single-cell gene expression profiling: correlations and identification of astrocyte subpopulations Single-cell qPCR on dispersed primary pituitary cells - an optimized protocol RT-qPCR based quantitative analysis of gene expression in single bacterial cells Real-time PCR of single bacterial cells on an array of adhering droplets Paired analysis of TCRa and TCRß chains at the single-cell level in mice Single Cell RT-PCR on Mouse Embryos: A General Approach for Developmental Biology ... ... and much more here ... ... -------------------------------------------------------------------------------- MIQE_qPCR APP for iPhone, iPad and iPod - iOS Universal http://MIQE-press.gene-quantification.info Get help from a special team of experts in qPCR while on the move. MIQE - qPCR helps you in reviewing scientific works and checking your own experiments, when qPCR is involved. Check your project's compliance to MIQE in minutes, have all required references to hand, and follow qPCR events and news. http://itunes.apple.com/app/miqe-qpcr/id423650002?mt=8 -------------------------------------------------------------------------------- qPCR SYMPOSIUM IN PRAGUE Welcome to the TATAA Biocenter qPCR Symposium ”Developments in Real- time PCR - From Preanalytics to Molecular Diagnostics” This event will be held in the beautiful city of Prague, Czech Republic, June 13-17, 2011 http://www.qPCRsymposium.eu The symposium will consist of two days of scientific sessions and industrial exhibition and both pre- and post symposium workshops. Besides interesting talks about the new developments in real-time qPCR research, special focus in this symposium will be on preanalytics and standardization, as well as molecular diagnostics with a separate track on Circulating Tumor Cells (CTCs). Symposium Topics: - Preanalytics - Sample preparation, extraction and purification - Standardization and quality control; MIQE guidelines - Experimental design and data analysis - Molecular diagnostics of complex diseases, detection and profiling of circulating tumor cells, CTCs - High throughput expression profiling - Digital PCR and copy number variations - Epigenetics and mutation analysis - Single cell expression profiling - MicroRNAs and non-coding RNAs Scientific Board: - Mikael Kubista, Institute of Biotechnology, CAS, and founder of TATAA Biocenter - Klaus Pantel, Director, Institute of Tumorbiology, University Medical Center Hamburg-Eppendorf, Germany - Michael W. Pfaffl, Professor of Molecular Physiology, TUM, Weihenstephan, Germany - Tomas Zima, Head Institute of Clinical Chemistry and Laboratory Medicine of the First Faculty of Medicine and General Teaching Hospital, Prague, Czech Republic -Mario Pazzagli, Professor of Clinical Biochemistry and Clinical Molecular Biology, University of Florence, Italy - Uwe Oelmueller, Vice president R&D Diagnostic Sample Preparation & Stabilization, QIAGEN GmbH, Hilden, Germany qPCR Workshops: In conjunction with the symposium several interesting courses will be given. Course program: - Introduction to real-time qPCR, 1 day, 13th of June - SPIDIA: Towards the standardization of the pre-analytical phase, 1 day, 13th of June - Hands-on qPCR workshop, 2 days, 16th-17th of June - Experimental design and statistical data analysis for qPCR workshop, 2 days, 16th-17th of June - Sample preparation and quality control of nucleic acids workshop, 2 days, 16th-17th of June - Invited speakers course, 1 day, 16th of June News: - Symposium schedule is available. - Join the Evening cruise with sightseeing. - Sponsorships and exhibition opportunities are available. - Students purchasing a post symposium workshop spot attend the symposium free of charge. - REGISTRATION FORM => http://www.qpcrsymposium.eu/content/view/6/9/ -------------------------------------------------------------------------------- Advanced qPCR Techniques for Publication Success: Following MIQE Recommendation http://www.embl.de/training/events/2011/MIQ11-01/index.html Overview -The real-time reverse transcription (RT) polymerase chain reaction (PCR) (RT-qPCR) and real time PCR methods address the evident requirement for quantitative data analysis in molecular medicine, biotechnology, microbiology, diagnostics and other areas and have become the methods of choice for the quantification of nucleic acid targets and identification of sequence specific variations. Although often described as a “gold” standard, these are far from being routine assays. Date: July 11–15, 2011 Location: EMBL, Heidelberg, Germany Register: http://www.embl.de/training/events/2011/MIQ11-01/index.html -------------------------------------------------------------------------------- Forward Please send the qPCR NEWS to further scientists and friends who are interested in qPCR ! Best regards, Michael W. Pfaffl responsible Editor of the Gene Quantification Pages http://www.gene-quantification.info -------------------------------------------------------------------------------- If this newsletter is not displayed correctly by your email client, please use following link: http://qPCRnews.gene-quantification.info/ The qPCR NEWS and the Gene Quantification Pages are educational sites with the only purpose of facilitating access to qPCR related information on the internet. The qPCR NEWS and the Gene Quantification Pages are edited by Michael W. Pfaffl. 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