MERSCOPE Frequently Asked Questions

• What is included with the MERSCOPE platform solution?

  The MERSCOPE Platform is an end-to-end solution and includes the custom targeted gene panel built using an interactive platform, reagents and consumables for sample preparation and the imaging run, the MERSCOPE instrument itself, an analysis computer, and the visualization and analysis software.

• When will MERSCOPE be available?

  Vizgen is supporting a limited commercial release in the US this summer, with a full commercial release towards the end of the year. We will be expanding to select international markets in 2022.

• What applications can MERSCOPE be used for? What are the biological questions MERSCOPE can answer?

  Neuroscience, Human Brain Atlas, Cancer Research, Infectious Disease, Developmental Biology, Drug Development, Cell & Gene Therapy and more. There is important information encoded on spatial locations within cells as much as there is spatial information between cells; with MERSCOPE we can investigate individual cells and see how different transcripts are expressed to learn about development and disease.

• What types of samples are compatible?

  Fresh or fixed frozen, PBMCs, adherent or suspended cells

• How does the custom gene panel design work?

  Vizgen has developed a custom Gene Panel Design software application for building the panels. The intuitive MERSCOPE gene panel design software enables automatic and immediate feedback to the end user about the suitability of the genes selected for a MERFISH measurement.

• What is a standard number of targets?

  We offer three different target sizes of our Encoding Probe and Imaging Kits at this time; 18 bit for up to 140 genes, 21 bit for up to 300 genes, and 27 bit for up to 500 genes.

• Are the MERSCOPE reads getting sequenced?

  No, MERFISH is not a sequencing technology and does not require any downstream sequencing. The chemistry is based on single molecule FISH which has been established as the gold standard for quantifying gene expression. For single molecule FISH, multiple fluorescently labelled probes are designed to bind to the desired RNA target with high specificity. By directly counting the number of RNA targets that fluoresce, we achieve incredibly high detection efficiency for determining RNA expression. This is true quantitation of RNA, even for low expressing genes which have been very challenging to detect by traditional technologies such as single cell sequencing.

• What is the recommended sample size for a MERSCOPE run?

  Imageable area up to 1 cm²

• What does the sample workflow look like?

  The sample preparation workflow for MERSCOPE is similar to the sample preparation workflow for standard tissue pathology procedures. To prepare a sample with the MERSCOPE workflow the sample is sliced, loaded onto a MERSCOPE slide, stained with the custom gene panel, embedded into a polyacrylamide to digest away the proteins to reduce the auto fluorescent background, and finally the sample is imaged.

• What does the data output from a MERSCOPE measurement look like?

  The data output from a MERSCOPE measurement includes the list of all detected transcripts and their spatial locations in three dimensions (CSV), the mosaic images (TIFF), output from the cell segmentation analysis: the transcripts per cell matrix (CSV), the cell metadata (CSV) and the cell boundaries (HDF5).