PRISM Technology¶
Overview¶
PRISM (Profiling of RNA In-situ through Single-round iMaging) is a high-resolution spatial transcriptomics technology developed by the Huang Lab. It employs color-intensity barcodes and a radius vector encoding strategy to achieve high-plex RNA imaging in a single staining and imaging round with conventional fluorescence microscopes.
Key Features¶
- Single-Round Imaging: No sequential hybridization rounds needed -- all targets are decoded from one imaging session.
- Color-Intensity Barcodes: Expands coding capacity through graded fluorescence intensities across multiple channels, achieving up to 64-plex detection.
- Sub-Micron Resolution: Precise spatial localization of individual RNA molecules.
- 3D Capability: Compatible with both thin sections and thick tissue blocks.
- RCA Amplification: Uses Rolling Circle Amplification to generate bright DNA nanoballs (rolonies) for robust signal detection.
Applications¶
PRISM has been validated across diverse biological contexts, including:
- 3D atlas of mouse embryonic development (E12.5--E14.5)
- Tumor--normal transition landscape in human hepatocellular carcinoma
- 3D cell atlas and subcellular RNA localization in mouse brain
Workflow Summary¶
- Sample Preparation: Tissue sectioning and fixation.
- Probe Hybridization: Target-specific padlock probes hybridize to RNA.
- Ligation: Probes are circularized upon perfect matching.
- RCA Amplification: Generation of DNA nanoballs (rolonies).
- Fluorescent Probe Staining: Detection probes carrying color-intensity barcodes hybridize to rolonies.
- Single-Round Imaging: Multi-channel fluorescence microscopy captures all barcode signals simultaneously.
- Decoding: Radius vector encoding algorithm decodes gene identity from the barcode pattern.