Abstract
We describe a technology, the NanoString nCounter gene expression system, which captures and counts individual mRNA transcripts. Advantages over existing platforms include direct measurement of mRNA expression levels without enzymatic reactions or bias, sensitivity coupled with high multiplex capability, and digital readout. Experiments performed on 509 human genes yielded a replicate correlation coefficient of 0.999, a detection limit between 0.1 fM and 0.5 fM, and a linear dynamic range of over 500-fold. Comparison of the NanoString nCounter gene expression system with microarrays and TaqMan PCR demonstrated that the nCounter system is more sensitive than microarrays and similar in sensitivity to real-time PCR. Finally, a comparison of transcript levels for 21 genes across seven samples measured by the nCounter system and SYBR Green real-time PCR demonstrated similar patterns of gene expression at all transcript levels.
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Change history
16 May 2008
The list of authors for this paper omitted the final author, Krassen Dimitrov, and should have read as follows: Gary K Geiss1, Roger E Bumgarner2, Brian Birditt1, Timothy Dahl1, Naeem Dowidar1, Dwayne L Dunaway1, H Perry Fell1, Sean Ferree1, Renee D George1,5, Tammy Grogan1, Jeffrey J James1, Malini Maysuria1, Jeffrey D Mitton1, Paola Oliveri3,5, Jennifer L Osborn1,5, Tao Peng2, Amber L Ratcliffe1, Philippa J Webster1, Eric H Davidson3, Leroy Hood4 & Krassen Dimitrov4,5 Affiliation number five should have included his present address and thus read: 5Present addresses: Department of Genome Sciences, Box 355065, University of Washington, Seattle, Washington 98195, USA (R.D.G.), Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK (P.O.), Department of Bioengineering, Box 355061, University of Washington, Seattle, Washington 98195, USA (J.L.O.) and Australian Institute for Bioengineering and Nanotechnology, Building 75—Cnr of College and Cooper Road, The University of Queensland, Brisbane QLD 4072 Australia (K.D.).
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Acknowledgements
We would like to acknowledge Edward Kelly, at the Center for DNA Sequencing and Gene Analysis, UW School of Pharmacy, Department of Pharmaceutics for TaqMan analysis and the University of Washington's Center for Array Technologies for processing of Affymetrix arrays. Poliovirus (PV) stocks were the kind gift of Kurt Gustin's laboratory (University of Idaho).
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Contributions
G.K.G. designed the experiments, analyzed data and prepared the manuscript. D.L.D., S.F., P.J.W. and G.K.G. designed and developed the NanoString system described. T.D. and J.D.M. developed probe selection and image analysis software, respectively. N.D. performed all nCounter assays described. B.B., R.D.G., T.G., J.J.J., M.M., J.L.O. and A.L.R. provided ideas and technical support. T.P. and P.O. provided microarray and real-time PCR data and samples. R.E.B. contributed to experimental design, scientific direction and manuscript preparation. H.P.F., E.H.D. and L.H. provided scientific direction and experimental concepts. K.D. provided the ideas and design of this technology and participated in the initial research.
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The following authors are current or past employees of and/or have an equity stake in NanoString technologies: G.K.G., B.B., T.D., N.D., D.L.D., H.P.F., S.F., R.D.G., T.G., J.J.J., M.M., J.D.M., J.L.O., A.L.R., P.J.W., E.H.D., L.H. and K.D.
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Supplementary Figures 1, 2; Table 1, Data (PDF 360 kb)
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Geiss, G., Bumgarner, R., Birditt, B. et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 26, 317–325 (2008). https://doi.org/10.1038/nbt1385
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