Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization

Elife. 2021 Aug 13:10:e65482. doi: 10.7554/eLife.65482.


The Patch-seq approach is a powerful variation of the patch-clamp technique that allows for the combined electrophysiological, morphological, and transcriptomic characterization of individual neurons. To generate Patch-seq datasets at scale, we identified and refined key factors that contribute to the efficient collection of high-quality data. We developed patch-clamp electrophysiology software with analysis functions specifically designed to automate acquisition with online quality control. We recognized the importance of extracting the nucleus for transcriptomic success and maximizing membrane integrity during nucleus extraction for morphology success. The protocol is generalizable to different species and brain regions, as demonstrated by capturing multimodal data from human and macaque brain slices. The protocol, analysis and acquisition software are compiled at https://githubcom/AllenInstitute/patchseqtools. This resource can be used by individual labs to generate data across diverse mammalian species and that is compatible with large publicly available Patch-seq datasets.

Keywords: RNA-seq; electrophysiology; genetics; genomics; human; morphology; mouse; neuroscience; patch-seq; rhesus macaque; transcriptomics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Brain
  • Electrophysiological Phenomena*
  • Humans
  • Macaca mulatta
  • Mice
  • Neurons / cytology
  • Neurons / physiology
  • Patch-Clamp Techniques
  • Single-Cell Analysis / methods*
  • Software
  • Transcriptome*