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A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast

Current methods for single-cell RNA sequencing (scRNA-seq) of yeast cells do not match the throughput and relative simplicity of the state-of-the-art techniques that are available for mammalian cells. In this study, we report how 10x Genomics’ droplet-based single-cell RNA sequencing technology can...

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Autores principales: Jariani, Abbas, Vermeersch, Lieselotte, Cerulus, Bram, Perez-Samper, Gemma, Voordeckers, Karin, Van Brussel, Thomas, Thienpont, Bernard, Lambrechts, Diether, Verstrepen, Kevin J
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7259953/
https://www.ncbi.nlm.nih.gov/pubmed/32420869
http://dx.doi.org/10.7554/eLife.55320
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author Jariani, Abbas
Vermeersch, Lieselotte
Cerulus, Bram
Perez-Samper, Gemma
Voordeckers, Karin
Van Brussel, Thomas
Thienpont, Bernard
Lambrechts, Diether
Verstrepen, Kevin J
author_facet Jariani, Abbas
Vermeersch, Lieselotte
Cerulus, Bram
Perez-Samper, Gemma
Voordeckers, Karin
Van Brussel, Thomas
Thienpont, Bernard
Lambrechts, Diether
Verstrepen, Kevin J
author_sort Jariani, Abbas
collection PubMed
description Current methods for single-cell RNA sequencing (scRNA-seq) of yeast cells do not match the throughput and relative simplicity of the state-of-the-art techniques that are available for mammalian cells. In this study, we report how 10x Genomics’ droplet-based single-cell RNA sequencing technology can be modified to allow analysis of yeast cells. The protocol, which is based on in-droplet spheroplasting of the cells, yields an order-of-magnitude higher throughput in comparison to existing methods. After extensive validation of the method, we demonstrate its use by studying the dynamics of the response of isogenic yeast populations to a shift in carbon source, revealing the heterogeneity and underlying molecular processes during this shift. The method we describe opens new avenues for studies focusing on yeast cells, as well as other cells with a degradable cell wall.
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spelling pubmed-72599532020-06-02 A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast Jariani, Abbas Vermeersch, Lieselotte Cerulus, Bram Perez-Samper, Gemma Voordeckers, Karin Van Brussel, Thomas Thienpont, Bernard Lambrechts, Diether Verstrepen, Kevin J eLife Chromosomes and Gene Expression Current methods for single-cell RNA sequencing (scRNA-seq) of yeast cells do not match the throughput and relative simplicity of the state-of-the-art techniques that are available for mammalian cells. In this study, we report how 10x Genomics’ droplet-based single-cell RNA sequencing technology can be modified to allow analysis of yeast cells. The protocol, which is based on in-droplet spheroplasting of the cells, yields an order-of-magnitude higher throughput in comparison to existing methods. After extensive validation of the method, we demonstrate its use by studying the dynamics of the response of isogenic yeast populations to a shift in carbon source, revealing the heterogeneity and underlying molecular processes during this shift. The method we describe opens new avenues for studies focusing on yeast cells, as well as other cells with a degradable cell wall. eLife Sciences Publications, Ltd 2020-05-18 /pmc/articles/PMC7259953/ /pubmed/32420869 http://dx.doi.org/10.7554/eLife.55320 Text en © 2020, Jariani et al http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Chromosomes and Gene Expression
Jariani, Abbas
Vermeersch, Lieselotte
Cerulus, Bram
Perez-Samper, Gemma
Voordeckers, Karin
Van Brussel, Thomas
Thienpont, Bernard
Lambrechts, Diether
Verstrepen, Kevin J
A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast
title A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast
title_full A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast
title_fullStr A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast
title_full_unstemmed A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast
title_short A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast
title_sort new protocol for single-cell rna-seq reveals stochastic gene expression during lag phase in budding yeast
topic Chromosomes and Gene Expression
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7259953/
https://www.ncbi.nlm.nih.gov/pubmed/32420869
http://dx.doi.org/10.7554/eLife.55320
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