Combining whole-cell patch clamp and dye loading in acute brain slices with bulk RNA sequencing in embryonic to aged mice

Yasmine Kamen*, Ragnhildur Þóra Káradóttir

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Single-cell electrophysiological recordings combined with dye loading and immunohistochemistry provide unparalleled single-cell resolution of cell physiology, morphology, location, and protein expression. When correlated with bulk RNA sequencing, these data can define cell identity and function. Here, we describe a protocol to prepare acute brain slices from embryonic and postnatal mice for whole-cell patch clamp, dye loading and post-hoc immunohistochemistry, and cell isolation for bulk RNA sequencing. While we focus on oligodendrocyte precursor cells, this protocol is applicable to other brain cells. For complete details on the use and execution of this protocol, please refer to Spitzer et al. (2019).

Original languageEnglish
Article number100439
Pages (from-to)100439
JournalSTAR Protocols
Issue number2
Publication statusPublished - 18 Jun 2021

Bibliographical note

We would like to thank Dr. Maike Paramor for comments on the protocol, Kimberley Evans for comments on the protocol and assistance with the graphics, Dr Omar de Faria Jr for assistance with the figures, and our following funders: the European Research Council (ERC: the European Union’s Horizon 2020 research and innovation programme grant agreement No 771411; R.T.K.); the Wellcome (Studentship award 102160/Z/13/Z; Y.K.); the Fonds de recherche du Québec-Santé (a scholarship, Y.K.); The Cambridge Commonwealth European & International Trust (a scholarship, Y.K.); and the Lister Institute of Preventive Medicine (a research prize, R.T.K.). The funders had no role in decision to publish or preparation of the manuscript.

Publisher Copyright:
© 2021 The Author(s)

Other keywords

  • Cell isolation
  • Microscopy
  • Molecular Biology
  • Neuroscience
  • RNA-seq
  • Stem Cells


Dive into the research topics of 'Combining whole-cell patch clamp and dye loading in acute brain slices with bulk RNA sequencing in embryonic to aged mice'. Together they form a unique fingerprint.

Cite this