Targeted Gene Expression Analysis

The BD Rhapsody™ targeted gene expression assays are an efficient way to screen hundreds of genes at once that provides cost-effective, sensitive detection of low abundant transcripts.

Start here for a filtered table containing only targeted gene expression analysis FAQ from the master document. Easily searchable with CMD+F on a Mac or CTRL+F on a PC.

If I used two panels on one sample, how can I run the pipeline analysis?

There are two options: you can either use a combined reference file with duplicated reference sequences removed or specify both references in the pipeline run.

What is the minimum and maximum distance that the primer can be from the polyA site in the custom panel design?

150 bp and 1,000 bp for N1. 150 bp and 400 bp for N2. If there is no good priming site found within these ranges, contact us at

Do you have options for species other than human and mouse for targeted mRNA sequencing?

We currently do not have off-the-shelf panel options for species other than human and mouse. However, it is possible to use the BD Rhapsody™ WTA Assay and BD® AbSeq Custom Antibodies on other species. If your species is one of the following, you can perform the WTA assay first and send the WTA data to the BD Rhapsody™ System support team at

We can generate a custom panel for these species based on your WTA data:

  • Human (Homo sapiens)
  • Mouse (Mus musculus)
  • C. elegans (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)
  • Fruit fly (Drosophila melanogaster)
  • Chicken (Gallus gallus)
  • Crab-eating macaque (Macaca fascicularis)
  • Rabbit (Oryctolagus cuniculus)
  • Chimpanzee (Pan troglodytes)
  • Rat (Rattus norvegicus)
  • Pig (Sus scrofa)
  • Frog (Xenopus tropicalis)
  • Mouseear cress (Arabidopsis thaliana)
  • Dog (Canis familiaris)
  • Cow (Bos taurus)

Can I detect gene variants using the BD Rhapsody™ WTA or targeted assays?

It is difficult to detect gene variants using WTA or targeted assays. The BD Rhapsody™ WTA and targeted assays use 3'-end capture technology and sequence a short fragment on the 3'-end of the transcript, which is mostly a non-coding region.

How do we address the amplification efficiency difference between primers?

When designing primers for a panel, our primer design software utilizes important parameters such as secondary structure, GC content and Tm to improve the uniformity of amplification efficiency across primers.

Our molecular indexing technology uses the number of molecules captured before amplification instead of the number of reads (after amplification) for gene-expression measurement. This also reduces the difference in amplification efficiency between primers on gene expression profiling.

What is a supplemental panel?

Users have a choice to add up to 100 primers to any of the predesigned panels.

What is the minimum and the maximum number of primers for a supplemental panel?

Min = 1, Max = 100

What is the minimum and the maximum number of genes required in a custom panel?

Min = 2, Max = 500

For Research Use Only. Not for use in diagnostic or therapeutic procedures.


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