XYZeq – Spatially-Resolved Single Cell Sequencing

Tech ID: 32239 / UC Case 2019-106-0

Brief Description

Researchers at UCSF have developed XYZeq, a method for coupling a cell’s spatial location with single-cell sequencing. Single-cell genomic techniques have emerged as powerful approaches to further our understanding of disease states and cellular heterogeneity. Single-cell imaging methods gain spatial information, but lack throughput and detailed transcriptomic information. Current single-cell sequencing approaches require dissociation of cells during preparation, as a result cannot record a cell’s physical location. UCSF researchers eliminate this step using XYZeq, a new scRNA-seq process that incorporates the benefits of single-cell imaging techniques with single-cell sequencing, without an imaging step. XYZeq simultaneously discerns the location and gene expression of a single cell residing within a complex tissue microenvironment. The technology has been validated in a laboratory setting.


  • Novel technology to provide spatially-resolved single-cell sequencing data 
  • XYZeq adds dimensionality to data from current sequencing approaches
  • The current iteration of the technology can resolve a single cells spatial information to 500 µm
  • The first technique to gain spatial information of single cells without the need for an imaging step
  • XYZeq has potential for increased throughput and decreased cost per data point relative to imaging-based techniques gaining spatial information 
  • XYZeq can perform cell segmentation to discern similar, but distinct cellular clusters in a complex sample. 


Not available at this time

Patent Status

Patent Pending


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