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Welcome to nDesign Gateway

nDesign Gateway enables the selection of fixed-content nCounter Gene Expression Panels and the assembly of custom Gene Expression CodeSets.

Browse Panels Search Genes Browse Genes Manage CodeSets

Designing a custom CodeSet with nDesign Gateway

  • 1

    Select Genes: Genes can be selected by searching based on gene name or browsing based on pathway, gene ontology, disease, or research area. Simply check the boxes next to the genes you would like to include in your CodeSet and select Add to CodeSet.

  • 2

    Select Chemistry: NanoString offers two types of chemistry for custom CodeSets. nCounter Standard chemistry is NanoString’s original chemistry in which the biotin label and molecular barcode are covalently attached to the target specific probe. nCounter Elements are General Purpose Reagents (GPRs) in which the biotin label and molecular barcode are hybridized to target-specific probes (sold separately) via unique tags. nCounter Elements GPRs enable researchers to build their own custom CodeSets by combining Elements GPRs with probes procured from an oligonucleotide vendor. nCounter Elements GPRs offer the option of an Extension CodeSet which can be combined with an existing core CodeSet in order to include additional targets.

  • 3

    Select Alternate Probes: By default, nDesign Gateway will assign an optimal probe for each gene that you select. Optimal probes meet the NanoString standard design criteria and are recommended unless you want to measure a specific exon or region. If you would like to select an alternate probe you can do so by clicking the + to expand the row for the gene of interest. The gene viewer will display the available probes.

Getting a quote through nDesign Gateway

Once a panel is selected or a custom CodeSet design is complete, the order can be submitted for a quote by clicking the button in the lower right corner of the CodeSet view. You will receive an email confirming your quote submission and a NanoString sales representative will follow up with you promptly.

nCounter Elements are for laboratory use

Frequently Asked Questions

What if I don't see my favorite gene on the list?

We can design probes against practically any sequence. For assistance, contact or Someone will be in touch to guide you through the process.

Do you have probes for other species?

Yes, we have large number of predesigned probes from other species that are not listed here at this time. We can design probes for any organism that has an annotated transcript database or set of gene models. For more information, please contact or

How many probes per target do you recommend?

We recommend a single probe per target. However, if you want to include more probes against a single target molecule, it could be possible providing there is no stearic interaction among the multiple probe pairs.

How do I match NanoString probe sequences with other manufacturer’s probe sequences?

Probe sequences are available from in the probe results table. If you don’t see the sequence, click in the row for the probe of interest and the row will expand to show target sequence at the bottom. This can be copied and pasted to BLAST, etc. as desired.

Can I use this site to design my CNV or custom miRNA assays?

Not at this time, but check back soon as the NanoString team will be updating the site frequently to include more products.

I would like to target a different exon/region of my target than I see listed here or I am interested in isoform specific probes. How do I do this?

It is usually possible to design probes to regions other than those listed, and depending on the gene and transcripts, it may be possible to design isoform specific probes. Email or for assistance.

How do I select all probes that were returned from my search?

The probe results table has a check box in the column header that will check all probes returned from a search.

I already have a list of genes selected in Excel or other format, how do I submit this to NanoString? Do I have to search for each gene and add it to my CodeSet?

No, if you have a list of gene names or accession numbers, your list can be submitted via email through your sales person. Please contact or for more information.

Why can’t I find the PAM50 panel in nDesign Gateway?

nDesign Gateway is for NanoString’s Research Use Only products.