Rainbow UltraFISH: Rapid Sequential RNA FISH for Single-cell Gene Expression Analysis

SBIR AbstractSingle cell biology is a multi disciplinary study to investigate how large numbers of
molecular species interact with each other in single cellsand how large population of cells work
together as complex systemsCells within a given tissueeven when they are morphologically
similarare heterogeneous in their gene expression patternsDefining gene expression patterns
at the single cell level within the context of the normal tissue architecture is essential to
understanding tissue function and developmentand will ultimately benefit precision and
personalized medicineHowevercurrent tools for single cell gene expression analysissuch as
single cell RNA sequencinglack spatial information and have low cell and RNA detection
efficiencyHencethere is an urgent need for better tools for profiling single cell gene
expression patterns in situi ewithin the context of normal tissue architecture and cell cell
relationshipsRainbow UltraFISH is a technology that integrates spatial and sequence
information together for single cell RNA analysisIt uses rapid sequential fluorescent in situ
hybridizationFISHto achieve multiplex RNA detection at high detection efficiency and singlecell resolutionIn cultured cell linesUltraFISH has been shown to complete each round of
probe target hybridization in andltminwith a detection efficiency ofIn this proposalwe
will expand the UltraFISH technology into primary mouse tissue samplesincluding fresh frozen
tissueAimformaldehyde fixedfrozen tissueAimand formalin fixedparaffin embedded
tissueAimWith the successful outcome of this proposalUltraFISH will be the simplest and
fastest technology for single cell gene expression analysis in situ and ultimately enable more
precision medicine SBIR Project Narrative
Project NarrativeRainbow UltraFISH is a technology that will enable researchers to analyze the expression
patterns of hundreds to thousands of genes within single cells in the context of their normal
tissue environmentWith the coming of the spatial genomics eraUltraFISH will become an
essential research tool for a very broad range of biologists and medical scientists in both
academia and the biotech industryIt will help answer fundamental questions in all aspects of
biologyas well as serve as a powerful tool to unravel the secrets of human disease