Complex biological questions being addressed using single cell sequencing technologies

Biologists have long desired to understand multi-cellular processes at the resolution of the single cell. Tremendous efforts have been made over more than a century to decipher biology at the single cell level from the advent of immunohistochemistry to high-plex multi-parametric cytometry. More recently, technological developments in extracting and labelling nucleic acids from single cells have boosted single-cell information acquisition to include the genome, transcriptome, epigenome, proteome, and more, even simultaneously collecting data from multiple modalities. Researchers from the National University of Singapore discuss some of the original motivations that have driven the development of new single cell tools, providing perspective on why these new tools were created and which tools we hope to see developed in the future.

Single cell isolation and barcoding strategies

A. Plate-based methods. FACS or limiting dilutions isolate single cells into individual wells (pipette picture by Freepik). Each well contains one unique barcode to label each single cell RNA-seq libraries. B. Droplet-based methods. Water-in-oil droplets are formed in microfluidics. Each droplet contains one hydrogel bead with uniquely barcoded primers and one single cell. C. Nanowell-based methods. Each nanowell is designed to be just enough for one single cell to sit in, and each nanowell contains one unique barcode. D. Combinatorial indexing methods. Cells go through cycles of splitting into individual tubes adding a tube specific barcode and pooling for random distribution to the next splitting. After a few cycles, most cells would receive different combinatorial barcodes indicated by different colors.