Scalable microfluidics for single-cell RNA printing and sequencing

Genome Biol. 2015 Jun 6;16(1):120. doi: 10.1186/s13059-015-0684-3.


Many important biological questions demand single-cell transcriptomics on a large scale. Hence, new tools are urgently needed for efficient, inexpensive manipulation of RNA from individual cells. We report a simple platform for trapping single-cell lysates in sealed, picoliter microwells capable of printing RNA on glass or capturing RNA on beads. We then develop a scalable technology for genome-wide, single-cell RNA-Seq. Our device generates pooled libraries from hundreds of individual cells with consumable costs of $0.10-$0.20 per cell and includes five lanes for simultaneous experiments. We anticipate that this system will serve as a general platform for single-cell imaging and sequencing.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Dimethylpolysiloxanes
  • Gene Expression Profiling / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Microfluidic Analytical Techniques / methods*
  • Optical Imaging
  • RNA / isolation & purification
  • Sequence Analysis, RNA / methods*
  • Single-Cell Analysis / methods


  • Dimethylpolysiloxanes
  • baysilon
  • RNA

Associated data

  • GEO/GSE66357