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Nanostring nCounter System

The Nanostring nCounter System

The Koch Institute and the MIT BioMicro Center is hosting a Nanostring nCounter system on a trial basis. The nCounter system is a single molecule visualizer that quantitatively detects RNA and other nucleic acids using a hybridization system in a highly multiplexed manner. The system uses color-coded molecular barcodes to digitally count nucleic acid molecules in solution. The system does not use enzymes for detecting the nucleic acids, allowing direct measurements of mRNA from a variety of input materials including degraded RNA or crude cell lysates, and is amplification free.

The instruments are located in the BioMicro Center and will be available to all members of the MIT community. We will be using the rest of this calendar year, 2010, to gauge the level of interest in the nCounter and whether it would be a viable system to purchase. If you are interested in learning more, please contact Stuart Levine

Code Sets

Binding of an anchor probe and barcode probe to an mRNA

The Nanostring works by hybridizing the nucleic acid to a code set library. The "codes" are two-part oligos with ~50nt of homology each. The first oligo contains an anchoring sequence while the second contains ~7kb of fluorescently labeled nucleotides in a "barcode" that can be read by the imager. Code sets can include 24-500 different oligo pairs. These codesets, purchased from Nanostring, are the most expensive part of the process. Nanostring has created many virtual codesets (e.g. genes involved in angiogenesis or apoptosis)or can create custom code sets.

List of predesigned mouse Nanostring probes

File:Materna et al., 2010.TIF Code sets provide the ability for highly multiplexed experiments with similar results to standard mRNA expression measurements done with qPCR. A study (Materna et al., 2010) on the prevalence of 172 transcription factors and signaling molecules in early sea urchin development was done using the Nanostring nCounter; a subset of these were compared to qPCR. The expression profiles created using nCounter were mostly in agreement with the qPCR results, if a significant difference in prevalence was observed the nCounter usually provided higher prevalence results.


Pricing and Schedules for the Nanostring are forthcoming. We anticipate the price of the run will be minimal ($10-$30 per sample) and your primary cost will be the Code Sets.