The MERSCOPE® Platform Reagents and Consumables

User-friendly MERSCOPE reagent kits and consumables provide researchers with sample and tissue type flexibility for high-quality MERFISH spatial genomics experiments performed with the MERSCOPE® Platform.

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Predesigned Panels

Spatial transcriptomics provides powerful insights into complex biology but can require significant resources to build meaningful gene panels. Vizgen’s new Predesigned Panels for the MERSCOPE® Platform provide researchers with curated lists of genes focused on neuroscience and oncology research, making MERFISH experiments even easier for your lab.

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MERSCOPE PanNeuro Cell Type Panel- 500 Genes

  • Identify all major cell types
  • Subtype neurons across the mouse brain
  • Probe neuronal signaling, activity, and interactions at cellular and sub-cellular levels
Learn more
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MERSCOPE PanCancer Pathways Panel- 500 Genes

  • Explore canonical signaling pathways of cancer
  • Characterize tumor behavior
  • Investigate interactions between tumor, immune, and stromal cells across human cancers
Learn more
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MERSCOPE Immuno-Oncology Panel-500 Genes

  • Identify major immune cell types, subtypes, and immune checkpoint molecules.
  • Target key genes involved in the immune response to cancer and explore cytokine signaling
  • Study human breast, lung, liver, prostate, colon, melanoma, ovarian, brain, and uterine cancers.
Learn More

How the reagents work

Vizgen’s reagents enable researchers to prepare samples for downstream MERFISH spatial imaging on the MERSCOPE® Platform. We developed specific sample processing protocols and reagents for fresh frozen (FF), fixed frozen, cell culture (CC), and FFPE sample types that are easy to adopt in labs of all sizes.   Samples can be prepared in batches to maximize efficiency.

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Featured Workflows

Fresh Frozen, Fixed Frozen, Cell Culture

FFPE

1

Preparation

Sectioned tissues are adhered to a MERSCOPE slide, fixed if needed, and permeabilized to allow encoding probe access. Alternatively, for cell culture samples adherent cells are cultured on the MERSCOPE slide or suspension cells are spun down onto the slide. Optional secondary staining is performed to mark cell boundaries and/or detect proteins of interest.

Fresh and Fixed Frozen Tissue Sample Preparation

Cultured Cells Sample Preparation

1

Preparation

Sectioned FFPE tissues are adhered to a MERSCOPE FFPE Slide. Deparaffinization, decrosslinking, and RNA anchoring steps prepare the sample for embedding and encoding probe access. Optional secondary staining is performed to mark cell boundaries and/or detect proteins of interest.

 

MERSCOPE FFPE Tissue Sample Preparation

2

Hybridization

Custom encoding MERFISH probes are added to the sample and hybridize to the targeted transcripts.

2

Embedding

Gel embedding provides an anchor point to immobilize transcripts and secondary staining probes to prevent loss during tissue clearing.

3

Embedding

Gel embedding provides an anchor point to immobilize transcripts and secondary staining probes to prevent loss during tissue clearing.

3

Clearing

Clearing removes all tissue components other than RNA and secondary probes anchored in the gel, minimizing tissue autofluorescence background.

4

Clearing

Clearing removes all tissue components other than RNA and secondary probes anchored in the gel minimizing tissue autofluorescence background.

4

Hybridization

Custom encoding MERFISH probes are added to the sample and hybridize to the targeted transcripts.

Fresh Frozen, Fixed Frozen, Cell Culture

1

Preparation

Sectioned tissues are adhered to a MERSCOPE slide, fixed if needed, and permeabilized to allow encoding probe access. Alternatively, for cell culture samples adherent cells are cultured on the MERSCOPE slide or suspension cells are spun down onto the slide. Optional secondary staining is performed to mark cell boundaries and/or detect proteins of interest.

Fresh and Fixed Frozen Tissue Sample Preparation

Cultured Cells Sample Preparation

2

Hybridization

Custom encoding MERFISH probes are added to the sample and hybridize to the targeted transcripts.

3

Embedding

Gel embedding provides an anchor point to immobilize transcripts and secondary staining probes to prevent loss during tissue clearing.

4

Clearing

Clearing removes all tissue components other than RNA and secondary probes anchored in the gel minimizing tissue autofluorescence background.

FFPE

1

Preparation

Sectioned FFPE tissues are adhered to a MERSCOPE FFPE Slide. Deparaffinization, decrosslinking, and RNA anchoring steps prepare the sample for embedding and encoding probe access. Optional secondary staining is performed to mark cell boundaries and/or detect proteins of interest.

 

MERSCOPE FFPE Tissue Sample Preparation

2

Embedding

Gel embedding provides an anchor point to immobilize transcripts and secondary staining probes to prevent loss during tissue clearing.

3

Clearing

Clearing removes all tissue components other than RNA and secondary probes anchored in the gel, minimizing tissue autofluorescence background.

4

Hybridization

Custom encoding MERFISH probes are added to the sample and hybridize to the targeted transcripts.

5

MERSCOPE Spatial Imaging

Prepared tissue sections are pre-stained with DAPI/PolyT and loaded into the flow chamber which is placed in the MERSCOPE Instrument. The MERSCOPE® Platform automates the MERFISH experiment.

Available MERSCOPE Reagents and Consumables

Vizgen provides the specialized reagent kits and consumables your lab needs for performing MERFISH spatial genomics and multiomics experiments on your MERSCOPE® Platform. We have successfully demonstrated MERSCOPE reagent workflows on over 40 different tissue types including human breast, prostate, and ovarian tumors as well as, murine brain, small intestine, and liver.

Product
Size
Description
MERSCOPE Slides
Package of 20

Sample slides for MERSCOPE instrument that are functionalized for tissue samples to enable Vizgen sample preparation protocols.

MERSCOPE Non-Beaded Slides
Package of 20

Sample slides for MERSCOPE instrument that do not have fiducial beads to enable adherent cells to adhere to slide.

MERSCOPE FFPE Slides
Package of 10

Sample slides for MERSCOPE instrument functionalized for FFPE tissues to enable Vizgen FFPE sample preparation protocols.

MERSCOPE Gene Panels
20 samples

Custom gene panels comprised of encoding probes. Currently available in four sizes; up 140 genes, up to 300 genes, up to 500 genes and up to 1000 genes.

Available Sizes
up to 140 genes
up to 300 genes
up to 500 genes
up to 1000 genes
MERSCOPE Gene Imaging Kits
1 Kit

Imaging reagent kits containing the reagents and cartridge for running a measurement on the MERSCOPE platform. Currently available in four sizes; up 140 genes, up to 300 genes, up to 500 genes and up to 1000 genes.

Available Sizes
up to 140 genes
up to 300 genes
up to 500 genes
up to 1000 genes
MERSCOPE Cell Boundary Staining Kit
20 Samples

Kit containing a 3-protein staining reagent for cell segmentation in dense tissues. Compatible with human and mouse samples.

MERSCOPE Sample Prep Kit
20 Samples

Kit containing sample preparation reagents for 20 samples. Compatible with fixed, fresh frozen tissue, and cultured cells.

MERSCOPE FFPE Sample Prep Kit
10 Samples

Kit containing sample preparation reagents for 10 FFPE samples. Compatible with FFPE tissues only.

MERSCOPE Protein Stain Kit
20 Samples

Kits containing oligo-conjugated secondary antibodies and reagents for co-detecting proteins during a MERFISH experiment.

MERSCOPE Protein Verification Kit
5 samples

Kit containing reagents to verify protein co-detection using MERSCOPE Protein Stain Kits.

MERSCOPE Sample Verification Kit
5 Samples

Kit containing smFISH probes and imaging reagents to do a single imaging run. Currently available for human and mouse.

MERSCOPE PanCancer Pathways Panel 500 Gene, (Human) Small
 4 Fresh Frozen / Fixed Frozen  or 2 FFPE samples

MERSCOPE 500 gene predesigned panel targeting canonical signaling pathways in human cancer tissue samples

MERSCOPE PanCancer Pathways Panel 500 Gene, (Human) Large
12 Fresh Frozen / Fixed Frozen or 6 FFPE samples.

MERSCOPE 500 gene predesigned panel targeting canonical signaling pathways in human cancer tissue samples.

MERSCOPE PanNeuro Cell Type Panel 500 Gene, (Mouse) Small
4 Fresh Frozen / Fixed Frozen or 2 FFPE samples

MERSCOPE 500 gene predesigned panel providing ability to cell type major cells in mouse brain tissue samples.

MERSCOPE PanNeuro Cell Type Panel 500 Gene, (Mouse) Large
12 Fresh Frozen / Fixed Frozen or 6 FFPE samples.

MERSCOPE 500 gene predesigned panel providing ability to cell type major cells in mouse brain tissue samples.

MERSCOPE Immuno-Oncology Panel 500 Gene, (Human) Small
4 Fresh Frozen / Fixed Frozen  or 2 FFPE samples

MERSCOPE 500 gene predesigned panel allows characterization of tumor and immune behavior at cellular and subcellular levels across multiple different types of cancers.

MERSCOPE Immuno-Oncology Panel 500 Gene, (Human) Large
12 Fresh Frozen / Fixed Frozen  or 6 FFPE samples

MERSCOPE 500 gene predesigned panel allows characterization of tumor and immune behavior at cellular and subcellular levels across multiple different types of cancers.

Resources

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Your guide to single-cell spatial genomics

Explore new dimensions with MERSCOPE, the first high resolution in situ platform to combine single-cell and spatial genomics analysis powered by MERFISH technology.

Download Brochure
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Vizgen MERSCOPE FFPE Solution

Vizgen’s MERSCOPE FFPE solution is the first to bring high multiplexing, high resolution single-cell and spatial genomics analysis to FFPE samples.

Download Brochure
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Application and Technical Notes FFPE Sample Preparation with MERSCOPE

A protocol that provides unmatched accuracy and sensitivity and ensures successful, impactful spatial data generation with FFPE samples..

Download application note
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Application and Technical Notes Protein Co-detection with MERSCOPE

Cell types and states are not only affected by the transcriptome, but also by the proteome. A tool to analyze both is needed to understand complex biology.

Download application note
View All Resources
If you are interested in using MERSCOPE for your research, contact us today.
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