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Nat Protoc. 2017 Dec;12(12):2531-2553. doi: 10.1038/nprot.2017.120. Epub 2017 Nov 16.

Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq.

Author information

1
Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA.
2
Ludwig Institute for Cancer Research, Stockholm, Sweden.
3
Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
4
Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.
5
Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, Texas, USA.
6
Department of Electrical and Computer Engineering, Rice University, Houston, Texas, USA.

Abstract

Neurons exhibit a rich diversity of morphological phenotypes, electrophysiological properties, and gene-expression patterns. Understanding how these different characteristics are interrelated at the single-cell level has been difficult because of the lack of techniques for multimodal profiling of individual cells. We recently developed Patch-seq, a technique that combines whole-cell patch-clamp recording, immunohistochemistry, and single-cell RNA-sequencing (scRNA-seq) to comprehensively profile single neurons from mouse brain slices. Here, we present a detailed step-by-step protocol, including modifications to the patching mechanics and recording procedure, reagents and recipes, procedures for immunohistochemistry, and other tips to assist researchers in obtaining high-quality morphological, electrophysiological, and transcriptomic data from single neurons. Successful implementation of Patch-seq allows researchers to explore the multidimensional phenotypic variability among neurons and to correlate gene expression with phenotype at the level of single cells. The entire procedure can be completed in ∼2 weeks through the combined efforts of a skilled electrophysiologist, molecular biologist, and biostatistician.

PMID:
29189773
PMCID:
PMC6422019
DOI:
10.1038/nprot.2017.120
[Indexed for MEDLINE]
Free PMC Article

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