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).

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Specialized Center (P50)
Project #
Application #
Study Section
Special Emphasis Panel (ZGM1)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Institute for Systems Biology
United States
Zip Code
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
Mast, Fred D; Herricks, Thurston; Strehler, Kathleen M et al. (2018) ESCRT-III is required for scissioning new peroxisomes from the endoplasmic reticulum. J Cell Biol 217:2087-2102
Pacheco, Derek; Warfield, Linda; Brajcich, Michelle et al. (2018) Transcription Activation Domains of the Yeast Factors Met4 and Ino2: Tandem Activation Domains with Properties Similar to the Yeast Gcn4 Activator. Mol Cell Biol 38:
Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona et al. (2018) Integrative structure and functional anatomy of a nuclear pore complex. Nature 555:475-482
Kearney, Paul; Boniface, J Jay; Price, Nathan D et al. (2018) The building blocks of successful translation of proteomics to the clinic. Curr Opin Biotechnol 51:123-129
Lee, Joon-Yong; Choi, Hyungwon; Colangelo, Christopher M et al. (2018) ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data. J Biomol Tech 29:39-45
Tuttle, Lisa M; Pacheco, Derek; Warfield, Linda et al. (2018) Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex. Cell Rep 22:3251-3264
Maixner, Frank; Turaev, Dmitrij; Cazenave-Gassiot, Amaury et al. (2018) The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals. Curr Biol 28:2348-2355.e9
Holden, Jennifer M; Koreny, Ludek; Obado, Samson et al. (2018) Involvement in surface antigen expression by a moonlighting FG-repeat nucleoporin in trypanosomes. Mol Biol Cell 29:1100-1110

Showing the most recent 10 out of 346 publications