Researchers at UCSF have developed methods for in situ labelling and sequencing to obtain spatial information and multiomics analysis at a single cell level.

Single-cell sequencing has revealed unappreciated cellular diversity in many ostensibly homogeneous systems and led to an ongoing scientific revolution in cell biology. However, droplet microfluidics requires a cell suspension as input material and thus all spatial information, such as the relative position of different cells to each other and the subcellular location of biomolecules, is lost. Recently, methods to capture cellular diversity through in situ sequencing with resolutions of 10-100μm have been developed. However, since a typical mammalian cell is ~10 μm, there remains a need for a method of obtaining spatial information linked with sequence information at single-cell precision.

Stage of Research

The inventors have developed a method of determining the sequence and location of a nucleic acid in a sample at single-cell resolution. The method is a significant improvement to the current in situ sequencing methodologies, enabling spatially-resolved genotyping and ATAC-seq at high resolution. Their methods transform a 2D sample (e.g., a tissue sample) into a spatially-labeled cell suspension compatible with cell sequencing modalities. To validate their methods, the inventors label tissue cryosections with DNA zipcodes (“ZIP-tags”) and correlate the spatial information derived from downstream single cell sequencing analysis with orthogonal microscopy-based analyses.


  • Measuring the same genomic modalities that can be profiled with droplet microfluidics at spatially resolved single cell resolution (e.g., immunophenotype with DNA-tagged antibodies, ATAC-seq, single-cell amplicon sequencing, single-cell RNA-seq)


  • Single-cell resolution using commercially available technologies (e.g., Slide-seq) with minimal changes to the hardware and minimal additional sample handling
  • Feature size of mammalian cells in a tissue sample can be increased using method-compatible gel expansion techniques
  • Barcoded spatial “zipcodes” can be released to diffuse to cellular nucleic acids within a fixed sample, enabling genomic DNA features such as ATAC-seq and chromosomal polymorphisms to be resolved spatially
  • Compatible with many other multiomics sequencing readouts

Stage of Development

Research – in vitro


PCT Publication No. WO2022/132645

Related Web Links



Single cell, Single Cell Analysis, Single Cell Genomics, Single Cell RNA Sequencing, Single-cell transcriptomics

Techology Reference

Chan Zuckerberg Biohub ref. no. CZB-183F

UCSF ref. no. SF2020-292

Patent Information:
For Information, Contact:
Maureen Sheehy
General Counsel
CZ Biohub
Cyrille Delley
Adam Abate
Single Cell
Single Cell Analysis
Single Cell Genomics
Single Cell RNA Sequencing
Single-cell Transcriptomics