Fluorescence-Activated Cell Sorting and NanoString Profiling of Single Neural Crest Cells and Pigment Cells

  • Tatiana Subkhankulova
  • Robert Neil KelshEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1976)


Neural crest cells are an important class of multipotent stem cells, generating highly diverse derivatives. Understanding the gene regulatory networks underlying this process is of great interest, but the highly migratory and thus widely dispersed nature of the differentiating cells makes isolation of cells difficult. Fluorescence-activated cell sorting (FACS) of transgenically labelled neural crest-derived cells after disaggregation of embryos is well-suited to purifying these cells. However, their diverse differentiation means that transcriptional analysis at single cell resolution is necessary to dissect the gene regulatory networks at play. NanoString technology provides a method for highly sensitive, quantitative transcriptional profiling for a pre-defined set of genes of interest. Here we provide a detailed protocol for FACS purification of neural crest-derived cells, sorted as single cells into a multi-well plate, and their subsequent NanoString profiling, using a predetermined gene set focused on pigment cells.

Key words

Neural crest Pigment cells Zebrafish NanoString nCounter Single cell expression 



This work was supported by the grant from the BBSRC, reference number BB/L00769X/1.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Biology and BiochemistryUniversity of BathBathUK

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