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Nanostring Facility

Nanostring


The UCL Nanostring Facility has been established to provide access to the nCounter technology for the research community. The facility owes its origins to a UCL Platform Technologies Initiative Grant and it is managed by the GEE Department.

Nanostring

The nCounter system from Nanostring Technologies is a direct, reliable and highly sensitive multiplexed measurement of nucleic acids (DNA and RNA) based on a novel digital barcode technology.

The nCounter system is fully automated and uses fluorescently labelled reporter probes, called ‘codesets’, and single molecule imaging to detect and count hundreds of molecules in a single reaction. The system is very resistant to poor quality of the RNA samples and it is perfectly suited for critical samples such as FFPE (formalin-fixed, paraffin-embedded) samples.

The nCounter technology has sensitivity and specificity comparable to Real Time PCR (RT-PCR). This technology takes advantage of the well-understood nucleic acid hybridization reaction and no enzymatic reactions are involved, no reverse transcription or DNA amplification is necessary.

Applications

The Nanostring technology is the perfect tool for validation of NGS and microarray data; for quantification of multiple genes from a limited amount of material; for pathway analysis, expression analyses of defined gene sets, for biomarker validation and more.
Gene expression analysis
Custom Codeset of genes or off-the-shelf preassembled panels and on single cell (details on NanoString website)
miRNA Profiling
Ready panel from Human, Mouse, Rat and Fly micro RNA profiling (details on NanoString website).

miRGE™ (miRNA & mRNA) Analysis
mRNA and miRNA simultaneous quantification (details on NanoString website)
Analysis of DNA (CNVs, ChIP, and Gene Fusion) (details on NanoString website)

Contacts

For any enquiry about the nCounter service at UCL please use the following email address nanostring@ucl.ac.uk

Paola Oliveri Head of Facility
Fraser Simpson Technical Staff
Wendy Hart Technical Staff


For Codeset ordering, please make direct contact with the Nanostring rep Aziz Mustafa, amustafa@nanostring.com or europe.sales@nanostring.com

nCounter Service

 The UCL Nanostring facility is open to every University, Research Institute and Private Company and provides the following types of service:

  • Full nConter service: all different steps from sample quality control to initial data analysis are carried out by UCL service staff
  • nCounter machine training: an experienced researcher is trained in using the nCounter machine for the first 12 samples. After he/she will be given access to the machine to run other samples.
  • Data analysis: background correction and normalization are provided in a excel format.
  • Data analysis training: A person is trained in data analysis using excel.
Flowchart

For nCounter Gene Expression Panels, which are off-the-shelf preassembled CodeSets that include nCounter Master Kits with all of the consumables and reagents to perform the assay, please contact Nanostring direct.

For custom projects, probes for a Codeset are designed by nanostring bioinformaticians, on the basis of  RefSeq ID’s or Fasta sequences. This format is available for 48 or 96 samples, or multiples.

An nCounter Codeset contains positive controls (10 RNA spiked in the Codeset) and negative controls (7 probes against alien sequences) that are used for internal QC, calibration and background evaluation.

Similar to RT PCR, probes for normalization genes must be included in the Codeset. These must be selected based on prior knowledge.

How to start the process
If this is the first time using the service please contact the facility in advance by e-mail (nanostring@ucl.ac.uk) regarding your project ideas.  We can answer any questions that you may have, and advise you on what technique would suit your needs.

Once agreed on the type of service, please fill out the Registration Form. You will take care to order the necessary codesets directly from nanostring.


How to prepare the samples

For more details please download the Sample Submission Form

Quality control of RNA samples can be carried out at extra cost using the BioAnalyzer in this case we have to request an amount of at least 300 ng RNA (between 20-100ng/uL). If samples fail to meet incoming quality checks they will be rejected with a given reason.

In case you want to readout a cartridge, please fill in the Cartridge Submission Form

Charges

NOTE: All prices are subject to change without notice.
The customer will have to pay a service fee for all consumables, handling of samples, data generation and processing. Prices vary depending on the type of experiment and service provided by the facility. A general pricing list can be downloaded here Price List.

Citing Us

Please cite our service in the acknowledgements section of your publication in cases where we have just performed the standard service. The following statement may be used: "We thank the UCL Nanostring Facility for providing the nCounter system and related services."


In brief

  •     Multiplex up to 800 hundreds of targets in a single reaction.
  •     Low amount of input material (100 ng of total RNA or 500 ng of gDNA per sample)
  •     Ability to analyze RNA samples directly from lysate or from FFPE samples
  •     No enzymatic reactions involved
  •     Very high dynamic range of quantification
  •     High sensitivity and reproducibility.

The nCounter technology has first been described by Geiss et al., 2008. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nature Biotechnology 26, 317-325.