Population transcriptomics with single-cell resolution: a new field made possible by microfluidics: a technology for high throughput transcript counting and data-driven definition of cell types

Bioessays. 2013 Feb;35(2):131-40. doi: 10.1002/bies.201200093. Epub 2012 Dec 27.


Tissues contain complex populations of cells. Like countries, which are comprised of mixed populations of people, tissues are not homogeneous. Gene expression studies that analyze entire populations of cells from tissues as a mixture are blind to this diversity. Thus, critical information is lost when studying samples rich in specialized but diverse cells such as tumors, iPS colonies, or brain tissue. High throughput methods are needed to address, model and understand the constitutive and stochastic differences between individual cells. Here, we describe microfluidics technologies that utilize a combination of molecular biology and miniaturized labs on chips to study gene expression at the single cell level. We discuss how the characterization of the transcriptome of each cell in a sample will open a new field in gene expression analysis, population transcriptomics, that will change the academic and biomedical analysis of complex samples by defining them as quantified populations of single cells.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Eukaryotic Cells / classification*
  • Eukaryotic Cells / cytology
  • Gene Expression Profiling / instrumentation
  • Gene Expression Profiling / methods
  • High-Throughput Screening Assays / instrumentation
  • Humans
  • Lab-On-A-Chip Devices
  • Microfluidics / instrumentation
  • Microfluidics / methods*
  • RNA, Messenger / analysis*
  • RNA, Messenger / genetics
  • Single-Cell Analysis / instrumentation
  • Single-Cell Analysis / methods*
  • Transcriptome*


  • RNA, Messenger