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Comparative Studies of Large-Scale Single-Cell Sequencing Technologies in Complex Tissues with Integrated On-Chip Imaging

Focus Immune

Project Goal

To compare the performances of single-cell RNA-Seq platforms, particularly microwell- and droplet-based systems, in profiling human tissues and to investigate the utility of merging single-cell imaging and sequencing.

Results & Resources

The Sims lab has continued development of SCOPE-Seq, a technology that allows for linking live cell imaging and single-cell RNA sequencing. They performed several benchmarking experiments to clarify its utility relative to more traditional single-cell RNA-sequencing methods. Resources produced include:

  • Protocol for microwell-based single-cell RNA-sequencing;
  • scPLATE-seq protocol for automated 3’ transcriptome profiling;
  • A single-cell reference map for human blood and tissue T cell activation… Szabo et al., 2019;
  • An optically decoded bead array for linking imaging and sequencing with single-cell resolution, Yuan et al., 2018;
  • Code repository for cluster_diffex: scRNA-seq clustering, visualization, and differential expression pipeline; and
  • Single-cell hierarchical poisson factorization (scHPF) code repository.


Lead Investigator

Peter Sims
Peter Sims