Detecting Stem Cell Marker Expression Using the NanoString nCounter System

Methods Mol Biol. 2019;1869:57-67. doi: 10.1007/978-1-4939-8805-1_5.


The use of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) has become commonplace in the study of neuronal development, physiology, disease modelling, and therapy development. Due to the transient nature of working with these cells, it is important to regularly confirm the cell status as a naive stem cell versus a more defined neural progenitor cell (NPC). Classically, this has been done using a panel of specific antibodies to test for the expression of transcription factors known to be observed in ESCs, but not NPCs. However, this method is both time consuming and expensive. Here, we describe the use of the NanoString nCounter system for determining the levels of expression of key transcription factors that will effectively aid in determining the state of your stem cell cultures.

Keywords: Embryonic stem cells (ESCs); Expression; Induced-pluripotent stem cells (iPSCs); NanoString nCounter; Neural; Neural progenitor; Transcription factor.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Biomarkers / metabolism
  • DNA Probes / metabolism
  • Data Analysis
  • Embryonic Stem Cells / cytology
  • Embryonic Stem Cells / metabolism
  • Gene Expression Regulation
  • Humans
  • Induced Pluripotent Stem Cells / cytology
  • Induced Pluripotent Stem Cells / metabolism
  • Nanotechnology / methods*
  • Neural Stem Cells / cytology
  • Neural Stem Cells / metabolism
  • Stem Cells / metabolism*


  • Biomarkers
  • DNA Probes

Grant support