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Coverage-dependent bias creates the appearance of binary splicing in single cells

Single-cell RNA sequencing provides powerful insight into the factors that determine each cell’s unique identity. Previous studies led to the surprising observation that alternative splicing among single cells is highly variable and follows a bimodal pattern: a given cell consistently produces eithe...

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Autores principales: Buen Abad Najar, Carlos F, Yosef, Nir, Lareau, Liana F
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7498265/
https://www.ncbi.nlm.nih.gov/pubmed/32597758
http://dx.doi.org/10.7554/eLife.54603
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author Buen Abad Najar, Carlos F
Yosef, Nir
Lareau, Liana F
author_facet Buen Abad Najar, Carlos F
Yosef, Nir
Lareau, Liana F
author_sort Buen Abad Najar, Carlos F
collection PubMed
description Single-cell RNA sequencing provides powerful insight into the factors that determine each cell’s unique identity. Previous studies led to the surprising observation that alternative splicing among single cells is highly variable and follows a bimodal pattern: a given cell consistently produces either one or the other isoform for a particular splicing choice, with few cells producing both isoforms. Here, we show that this pattern arises almost entirely from technical limitations. We analyze alternative splicing in human and mouse single-cell RNA-seq datasets, and model them with a probabilistic simulator. Our simulations show that low gene expression and low capture efficiency distort the observed distribution of isoforms. This gives the appearance of binary splicing outcomes, even when the underlying reality is consistent with more than one isoform per cell. We show that accounting for the true amount of information recovered can produce biologically meaningful measurements of splicing in single cells.
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spelling pubmed-74982652020-09-21 Coverage-dependent bias creates the appearance of binary splicing in single cells Buen Abad Najar, Carlos F Yosef, Nir Lareau, Liana F eLife Chromosomes and Gene Expression Single-cell RNA sequencing provides powerful insight into the factors that determine each cell’s unique identity. Previous studies led to the surprising observation that alternative splicing among single cells is highly variable and follows a bimodal pattern: a given cell consistently produces either one or the other isoform for a particular splicing choice, with few cells producing both isoforms. Here, we show that this pattern arises almost entirely from technical limitations. We analyze alternative splicing in human and mouse single-cell RNA-seq datasets, and model them with a probabilistic simulator. Our simulations show that low gene expression and low capture efficiency distort the observed distribution of isoforms. This gives the appearance of binary splicing outcomes, even when the underlying reality is consistent with more than one isoform per cell. We show that accounting for the true amount of information recovered can produce biologically meaningful measurements of splicing in single cells. eLife Sciences Publications, Ltd 2020-06-29 /pmc/articles/PMC7498265/ /pubmed/32597758 http://dx.doi.org/10.7554/eLife.54603 Text en © 2020, Buen Abad Najar 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
Buen Abad Najar, Carlos F
Yosef, Nir
Lareau, Liana F
Coverage-dependent bias creates the appearance of binary splicing in single cells
title Coverage-dependent bias creates the appearance of binary splicing in single cells
title_full Coverage-dependent bias creates the appearance of binary splicing in single cells
title_fullStr Coverage-dependent bias creates the appearance of binary splicing in single cells
title_full_unstemmed Coverage-dependent bias creates the appearance of binary splicing in single cells
title_short Coverage-dependent bias creates the appearance of binary splicing in single cells
title_sort coverage-dependent bias creates the appearance of binary splicing in single cells
topic Chromosomes and Gene Expression
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7498265/
https://www.ncbi.nlm.nih.gov/pubmed/32597758
http://dx.doi.org/10.7554/eLife.54603
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