1. Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization
- Author
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Lisa Kim, Brian Lee, Kimberly A. Smith, Katherine Baker, Aaron Oldre, Ed S. Lein, Rachel A. Dalley, Kristen Hadley, Thomas Braun, Brian E. Kalmbach, Sara Vargas, Jonathan T. Ting, Jim Berg, Ram Rajanbabu, Tae Kyung Kim, Agata Budzillo, Tim Jarsky, Lindsay Ng, Staci A. Sorensen, Jessica Trinh, Bosiljka Tasic, Jeremy A. Miller, Rusty Mann, Gilberto J. Soler-Llavina, Hongkui Zeng, Nathan W. Gouwens, DiJon Hill, and Gabe J. Murphy
- Subjects
Patch-Clamp Techniques ,Mouse ,QH301-705.5 ,Computer science ,Science ,Multimodal data ,Genomics ,Computational biology ,Macaque ,General Biochemistry, Genetics and Molecular Biology ,Mice ,transcriptomics ,High fidelity ,Software ,biology.animal ,Rhesus macaque ,morphology ,Animals ,Humans ,Biology (General) ,Protocol (object-oriented programming) ,Neurons ,General Immunology and Microbiology ,biology ,business.industry ,General Neuroscience ,Brain ,Genetics and Genomics ,General Medicine ,electrophysiology ,Macaca mulatta ,Tools and Resources ,Electrophysiological Phenomena ,Membrane integrity ,Key factors ,Medicine ,patch-seq ,Single-Cell Analysis ,RNA-seq ,Transcriptome ,business ,Neuroscience ,Human - Abstract
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.
- Published
- 2021
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