Single-Cell Quantification of mRNA Expression in The Human Brain

Sci Rep. 2019 Aug 26;9(1):12353. doi: 10.1038/s41598-019-48787-w.


RNA analysis at the cellular resolution in the human brain is challenging. Here, we describe an optimised approach for detecting single RNA transcripts in a cell-type specific manner in frozen human brain tissue using multiplexed fluorescent RNAscope probes. We developed a new robust analytical approach for RNAscope quantification. Our method shows that low RNA integrity does not significantly affect RNAscope signal, recapitulates bulk RNA analysis and provides spatial context to transcriptomic analysis of human post-mortem brain at single-cell resolution. In summary, our optimised method allows the usage of frozen human samples from brain banks to perform quantitative RNAscope analysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alzheimer Disease / genetics
  • Brain / metabolism*
  • Freezing
  • Gene Expression Regulation*
  • HeLa Cells
  • Hippocampus / metabolism
  • Hippocampus / pathology
  • Humans
  • Membrane Glycoproteins / genetics
  • Membrane Glycoproteins / metabolism
  • Microglia / metabolism
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • Receptors, Immunologic / genetics
  • Receptors, Immunologic / metabolism
  • Single-Cell Analysis*
  • Up-Regulation


  • Membrane Glycoproteins
  • RNA, Messenger
  • Receptors, Immunologic
  • TREM2 protein, human