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Science  24 Jul 2015:
Vol. 349, Issue 6246, pp. 441
DOI: 10.1126/science.349.6246.441-a

Real-Time PCR Systems

New real-time polymerase chain reaction (PCR) systems that fully integrate with cloud computing technology mark a new era in data sharing and global research collaboration. Designed for low to mid throughput laboratories conducting real-time PCR experiments, QuantStudio 3 and 5 are the first to connect to the Thermo Fisher Cloud computing platform, allowing researchers to learn, analyze, share, collaborate, and obtain support within a single platform. Researchers worldwide can now collaborate online in real-time, and access their data wherever and whenever necessary. Laboratories can also share experimental conditions and results with their partners, while providing a uniform experience for every user, and helping minimize training and errors. With the Applied Biosystems QuantStudio 3 and QuantStudio 5 Real-Time PCR systems hosted on Amazon Web Services (AWS), these PCR systems benefit from the inherent security of the AWS Cloud. The new instruments seamlessly integrate with existing analysis workflows, syncing with next generation sequencing, capillary electrophoresis, and qPCR applications to create a customized data ecosystem.

Multiplexing PCR Amplicons

Direct polymerase chain reaction (PCR) amplification of a specific region is a powerful technique to perform targeted sequencing. When combined with multiplexing capability, PCR amplification is an efficient manner to study many samples. PacBio offers two barcoding strategies for multiplexing up to ninety-six 10 kb amplicons. In the first approach, barcodes are added to the end of the amplicon during PCR and the standard SMRTbell adapter is subsequently ligated onto the barcoded amplicon. In the second approach, the barcode is added to the SMRTbell adapter and the amplicon is ligated to the SMRTbell barcoded adapter. The second approach is recommended for validated PCR systems since the amplicon is generated with the unmodified primers. The first approach provides researchers more cost savings because the barcode is added to the amplicon and samples can be pooled prior to the SMRTbell template preparation steps.

ChIRP RNA Interactome Kits

Magna ChIRP RNA Interactome Kits allow researchers to more easily identify, recover, and analyze regions of chromatin that interact with chromatin-associated RNAs such as long noncoding RNA (lncRNA). The highly effective multiprobe-based capture strategy uses cross-linked chromatin to provide reliable detection and discovery of RNA-associated genomic DNA sequences, RNA sequences, and proteins. The new kits use the ChIRP method (Chromatin Isolation by RNA Purification) to isolate chromatin complexes using RNA as the target, allowing researchers to pinpoint specific sites of genomic interaction for chromatin-associated RNAs. The kits simplify the ChIRP method, providing all necessary buffers, enzymes, and reagents in one validated kit as well as a negative control probe set and detailed protocol with capture probe design guidelines. In addition, first-time users can opt for the EZ-Magna ChIRP kit, which includes a positive control capture probe set and detection primers that make it easier to validate an experiment's success.

GeneChip Whole-Transcriptome Arrays

The GeneChip WT Pico Kit is designed for gene expression array target preparation from as little as 100 pg of total RNA input. Working with as few as 10 cells, the new kit offers a high degree of flexibility and precision, enabling analyses of samples too small for other methods as well as the interrogation of small subpopulations of cells within larger samples. For use with Affymetrix' GeneChip Whole-Transcriptome Arrays, the new WT Pico Kit is compatible with small sample isolation techniques, including flow cytometry, laser capture microdissection, and fine needle aspiration. The kit prepares targets from multiple sample types, including fresh and fresh frozen tissues, cultured cells, FFPE specimens, and whole blood samples without a globin mRNA reduction step. The use of a single kit for multiple sample types improves the ability to better compare data from different samples, especially important for translational research.

NGS Software Analysis Templates

Customized analysis workflow templates have been incorporated into the NextGENe NGS software providing users of the ThunderBolts Cancer and Myeloid Panels with predefined settings for detecting minor allele frequencies at different sensitivity settings (1% and 5%). Use of the predefined NextGENe settings for the ThunderBolts panels provides a simple, automated, accurate, and rapid NGS bioinformatics workflow solution on the analysis of important oncogenes of clinical relevance to cancer diseases, with important results visualization provided by NextGENe software. Through the NextGENe AutoRun, a template for the ThunderBolts Cancer or Myeloid Panel can now be selected. With a single click of the template, our users will have configured a project to automatically trim the adapters and primer sequences from the ends of reads, set the appropriate read alignment settings, chosen an appropriate variant detection sensitivity and selected useful quality and variant reports to be generated.

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