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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
eLife Sciences Publications, Ltd
2020
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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. |
format | Online Article Text |
id | pubmed-7498265 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
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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