Physics / mechanism
Single-cell sequencing resolves genomic, transcriptomic, or epigenomic information at the resolution of individual cells rather than bulk averages. The dominant workflow: cell isolation (microfluidics, droplet-based or combinatorial barcoding), lysis, reverse transcription (for scRNA-seq), library prep, and short- or long-read sequencing. Key parameters — cell capture rate (typically 50–80%), doublet rate (<5% target), UMI sensitivity (~1,000–5,000 genes/cell for 10x Chromium), and throughput (10x Chromium X: ~20k cells/run, Parse Biosciences: ~1M+ cells/run). Long-read single-cell (PacBio MAS-seq, Oxford Nanopore) now resolves full-length isoforms. Cost sits ~$0.01–0.05/cell at scale; sensitivity is the persistent engineering constraint.
Competitive landscape
The primary competitive axis is spatial vs. non-spatial resolution. Bulk RNA-seq loses cell identity; spatial transcriptomics (10x Visium, Vizgen MERFISH, Nanostring CosMx) adds positional context but sacrifices throughput or depth. Proteomics alternatives: mass cytometry (CyTOF) and CITE-seq (protein + RNA co-measurement). Microfluidic competitors include Becton Dickinson Rhapsody and Fluent BioSciences PIP-seq. CRISPR-based perturbation screens (Perturb-seq) extend the modality into functional genomics.
Companies using
Connected ideas
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Frontier (open questions)
- To be added.