MERSCOPE
The Spatial Technologies Unit operates a MERSCOPE (Vizgen), an imaging-based single-cell spatial transcriptomics platform built on MERFISH (Multiplexed Error-Robust Fluorescence in situ Hybridization). Transcripts are assigned combinatorial binary barcodes that are decoded over iterative rounds of imaging, localizing individual RNA molecules at subcellular resolution directly in intact tissue. The assay measures up to 1,000 gene targets, with optional co-detection of up to 6 antibody targets on the same section, and runs on high-quality FFPE and fresh-frozen tissue. Pre-designed and fully custom panels are supported for human and mouse.
Specification
| Vendor | Vizgen |
|---|---|
| Modality | imaging-based spatial transcriptomics |
| Tissue | frozen, high quality FFPE |
| Capture area | approximately 1 cm2 |
| Targets / plex | custom max 1000 targets |
| Resolution | sub-cellular, <=100 nm |
| Species | any, via custom probe design |
Panels
MERSCOPE supports validated pre-designed panels and fully custom panels, both built on MERFISH 2.0 chemistry and compatible with the MERSCOPE.
- MERSCOPE 815 Gene V2.0 pre-designed panels (available in two sizes), with more than 20 panels available across human and mouse.
- Human biology: Brain, Human, Metabolic, Inflammation, Cardiovascular.
- Human oncology: ImmunoOncology, Breast Cancer, Colon Cancer, Lung Cancer, Liver Cancer, Kidney Cancer, Skin Cancer.
- Mouse: Pan Neuro, Pan Mouse, ImmunoOncology, Liver, Kidney, Cardiovascular, Lung, Transcription Factor A, Transcription Factor B.
- Any pre-designed panel can be extended with an add-on of up to 100 custom genes, validated to the same MERFISH 2.0 standard as the base panel.
- Full custom panels are supported up to 1,000 gene targets. (The current Vizgen gene-panel design portal lists custom panels of up to 960 genes;
- The earlier claim of 500 targets in three tiers is stale and is not carried forward.
Multi-omics
Protein can be co-detected alongside RNA on the same tissue section. Up to 6 antibody targets are measured together with the transcriptomic panel using protein co-staining reagents, so RNA and selected protein markers are read from one section in a single run.
What you receive
- raw instrument images and transcript coordinate tables
- cell-by-gene matrix and cell segmentation
- mosaic OME-TIFF images
- H&E where applicable; post-processing QC metrics
- MD5 checksums at transfer
Access and priority
Internal clients (BIDMC, DF/HCC), external academic and non-profit clients, and industry clients all have equal priority. Projects begin upon sample receipt.