Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells

Sci Rep. 2019 Feb 6;9(1):1469. doi: 10.1038/s41598-018-37977-7.


Environmental stimuli often lead to heterogeneous cellular responses and transcriptional output. We developed single-cell RNA and Immunodetection (RAID) to allow combined analysis of the transcriptome and intracellular (phospho-)proteins from fixed single cells. RAID successfully recapitulated differentiation-state changes at the protein and mRNA level in human keratinocytes. Furthermore, we show that differentiated keratinocytes that retain high phosphorylated FAK levels, a feature associated with stem cells, also express a selection of stem cell associated transcripts. Our data demonstrates that RAID allows investigation of heterogeneous cellular responses to environmental signals at the mRNA and phospho-proteome level.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Differentiation
  • Cells, Cultured
  • Focal Adhesion Kinase 1 / genetics*
  • Focal Adhesion Kinase 1 / metabolism*
  • Gene Expression Profiling / methods
  • Gene Expression Regulation
  • Humans
  • Keratinocytes / chemistry
  • Keratinocytes / cytology*
  • Phosphorylation
  • Proteomics / methods
  • Quinazolines / pharmacology
  • Single-Cell Analysis / methods*
  • Tissue Fixation
  • Tyrphostins / pharmacology


  • Quinazolines
  • Tyrphostins
  • RTKI cpd
  • Focal Adhesion Kinase 1
  • PTK2 protein, human