Literature DB >> 33377040

Protocol for Patch-Seq of Small Interneurons.

Marcela Lipovsek1, Lorcan Browne1, Matthew S Grubb1.   

Abstract

Obtaining electrophysiological recordings and gene expression information from the same neuron (Patch-seq) brings forward a unique opportunity to study the transcriptional correlates of functional properties and vice versa. Here, we provide a detailed Patch-seq protocol tailored to the specialized demands of studying small interneurons. Focusing on the technically demanding process of transitioning between patch recordings and cell extraction, our protocol describes and troubleshoots steps for successfully collecting small interneurons, allowing for multi-modal Patch-seq interrogation of this crucial cell type.
© 2020 The Author(s).

Entities:  

Mesh：

Year:  2020        PMID： 33377040      PMCID： PMC7757288          DOI： 10.1016/j.xpro.2020.100146

Source DB:  PubMed          Journal:  STAR Protoc        ISSN： 2666-1667


  13 in total

1.  Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq.

Authors:  Cathryn R Cadwell; Athanasia Palasantza; Xiaolong Jiang; Philipp Berens; Qiaolin Deng; Marlene Yilmaz; Jacob Reimer; Shan Shen; Matthias Bethge; Kimberley F Tolias; Rickard Sandberg; Andreas S Tolias
Journal:  Nat Biotechnol       Date:  2015-12-21       Impact factor: 54.908

2.  Full-length RNA-seq from single cells using Smart-seq2.

Authors:  Simone Picelli; Omid R Faridani; Asa K Björklund; Gösta Winberg; Sven Sagasser; Rickard Sandberg
Journal:  Nat Protoc       Date:  2014-01-02       Impact factor: 13.491

3.  Synthetic spike-in standards for RNA-seq experiments.

Authors:  Lichun Jiang; Felix Schlesinger; Carrie A Davis; Yu Zhang; Renhua Li; Marc Salit; Thomas R Gingeras; Brian Oliver
Journal:  Genome Res       Date:  2011-08-04       Impact factor: 9.043

4.  Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq.

Authors:  Iain C Macaulay; Mabel J Teng; Wilfried Haerty; Parveen Kumar; Chris P Ponting; Thierry Voet
Journal:  Nat Protoc       Date:  2016-09-29       Impact factor: 13.491

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

Authors:  Cathryn R Cadwell; Federico Scala; Shuang Li; Giulia Livrizzi; Shan Shen; Rickard Sandberg; Xiaolong Jiang; Andreas S Tolias
Journal:  Nat Protoc       Date:  2017-11-16       Impact factor: 13.491

6.  A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

Authors:  Aaron T L Lun; Davis J McCarthy; John C Marioni
Journal:  F1000Res       Date:  2016-08-31

7.  Embryonic and postnatal neurogenesis produce functionally distinct subclasses of dopaminergic neuron.

Authors:  Elisa Galliano; Eleonora Franzoni; Marine Breton; Annisa N Chand; Darren J Byrne; Venkatesh N Murthy; Matthew S Grubb
Journal:  Elife       Date:  2018-04-20       Impact factor: 8.140

8.  Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes.

Authors:  János Fuzik; Amit Zeisel; Zoltán Máté; Daniela Calvigioni; Yuchio Yanagawa; Gábor Szabó; Sten Linnarsson; Tibor Harkany
Journal:  Nat Biotechnol       Date:  2015-12-21       Impact factor: 54.908

9.  A systematic evaluation of single cell RNA-seq analysis pipelines.

Authors:  Beate Vieth; Swati Parekh; Christoph Ziegenhain; Wolfgang Enard; Ines Hellmann
Journal:  Nat Commun       Date:  2019-10-11       Impact factor: 14.919

10.  Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells.

Authors:  Mark van den Hurk; Jennifer A Erwin; Gene W Yeo; Fred H Gage; Cedric Bardy
Journal:  Front Mol Neurosci       Date:  2018-08-10       Impact factor: 5.639
View more
  2 in total

1.  Patch-seq: Past, Present, and Future.

Authors:  Marcela Lipovsek; Cedric Bardy; Cathryn R Cadwell; Kristen Hadley; Dmitry Kobak; Shreejoy J Tripathy
Journal:  J Neurosci       Date:  2021-01-11       Impact factor: 6.167

2.  Protocol for scChaRM-seq: Simultaneous profiling of gene expression, DNA methylation, and chromatin accessibility in single cells.

Authors:  Rui Yan; Xin Cheng; Fan Guo
Journal:  STAR Protoc       Date:  2021-11-20
  2 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.