Nucleic Acids Core (Rowen and Hood) Overview. Increased dynamic range and potential for novel discoveries resulting from next-gen, sequencing has led to its routine use in Center research for enumeration applications such as genome resequencing, gene expression and DNA-protein interactions. Microarrays continue to provide a cost-effective approach for multisample time-course experiments, and hence they have remained in wide use. Over the past five years, the average cost per array has decreased by 65% due to improvements in feature density, multiplexing and sample preparation. Sample management for microarray and sequencing experiments has been improved by the development of a database system for sample submission and tracking (SlimSuite). The facility has acquired a NanoString nCounter platform and a Fluidigm Biomark, which have enhanced our ability to perform analyses at multiple levels of scale and complexity (see Resources). For example, we can provide high-throughput, high-sensitivity (sub-femtomolar) transcriptomic analysis at low-detail (1 to 96 genes) using the Applied Biosystems and Fluidigm Biomark qPCR platforms, high-detail (24 to 1000 genes) using the Nanostring Technologies nCounter platform, and global profiling by lllumina and SOLiD RNA sequencing. The Fluidigm instrument, which is compatible with Taqman assays, uses microfluidic plates arrayed in either a 48 x 48 or 96 x 96 grid. In this setup, up to 96 assays can be run against 96 samples simultaneously, for a total of 9216 amplifications at once. The nCounter profiles the expression levels of up to 800 genes at a dynamic range of 500-fold. In addition to its role in transcriptomics, the NanoString nCounter provides economical microRNA and genomic DNA copy number variation analysis. The microRNA kit measures more than 700 human (or mouse) and associated viral microRNAs quickly (1 day) and economically ($220/sample).
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| Hoopmann, Michael R; Winget, Jason M; Mendoza, Luis et al. (2018) StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline. J Proteome Res 17:1314-1320 |
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| Jabbari, Neda; Glusman, Gustavo; Joesch-Cohen, Lena M et al. (2018) Whole genome sequence and comparative analysis of Borrelia burgdorferi MM1. PLoS One 13:e0198135 |
| Trachana, Kalliopi; Bargaje, Rhishikesh; Glusman, Gustavo et al. (2018) Taking Systems Medicine to Heart. Circ Res 122:1276-1289 |
| Shao, Wenguang; Pedrioli, Patrick G A; Wolski, Witold et al. (2018) The SysteMHC Atlas project. Nucleic Acids Res 46:D1237-D1247 |
| Kazantsev, Fedor; Akberdin, Ilya; Lashin, Sergey et al. (2018) MAMMOTh: A new database for curated mathematical models of biomolecular systems. J Bioinform Comput Biol 16:1740010 |
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