Sampling time-dependent artifacts in single-cell genomics studies

Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample acquisition can hinder solid, reproducible results, and a systematic benchmarking is requir...

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Autores principales: Massoni-Badosa, Ramon, Iacono, Giovanni, Moutinho, Catia, Kulis, Marta, Palau, Núria, Marchese, Domenica, Rodríguez-Ubreva, Javier, Ballestar, Esteban, Rodriguez-Esteban, Gustavo, Marsal, Sara, Aymerich, Marta, Colomer, Dolors, Campo, Elias, Julià, Antonio, Martín-Subero, José Ignacio, Heyn, Holger
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Short Report
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7212672/
https://www.ncbi.nlm.nih.gov/pubmed/32393363
http://dx.doi.org/10.1186/s13059-020-02032-0
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author Massoni-Badosa, Ramon
Iacono, Giovanni
Moutinho, Catia
Kulis, Marta
Palau, Núria
Marchese, Domenica
Rodríguez-Ubreva, Javier
Ballestar, Esteban
Rodriguez-Esteban, Gustavo
Marsal, Sara
Aymerich, Marta
Colomer, Dolors
Campo, Elias
Julià, Antonio
Martín-Subero, José Ignacio
Heyn, Holger
author_facet Massoni-Badosa, Ramon
Iacono, Giovanni
Moutinho, Catia
Kulis, Marta
Palau, Núria
Marchese, Domenica
Rodríguez-Ubreva, Javier
Ballestar, Esteban
Rodriguez-Esteban, Gustavo
Marsal, Sara
Aymerich, Marta
Colomer, Dolors
Campo, Elias
Julià, Antonio
Martín-Subero, José Ignacio
Heyn, Holger
author_sort Massoni-Badosa, Ramon
collection PubMed
description Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample acquisition can hinder solid, reproducible results, and a systematic benchmarking is required before entering large-scale data production. Here, we report the existence and extent of gene expression and chromatin accessibility artifacts introduced during sampling and identify experimental and computational solutions for their prevention.
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spelling pubmed-72126722020-05-18 Sampling time-dependent artifacts in single-cell genomics studies Massoni-Badosa, Ramon Iacono, Giovanni Moutinho, Catia Kulis, Marta Palau, Núria Marchese, Domenica Rodríguez-Ubreva, Javier Ballestar, Esteban Rodriguez-Esteban, Gustavo Marsal, Sara Aymerich, Marta Colomer, Dolors Campo, Elias Julià, Antonio Martín-Subero, José Ignacio Heyn, Holger Genome Biol Short Report Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample acquisition can hinder solid, reproducible results, and a systematic benchmarking is required before entering large-scale data production. Here, we report the existence and extent of gene expression and chromatin accessibility artifacts introduced during sampling and identify experimental and computational solutions for their prevention. BioMed Central 2020-05-11 /pmc/articles/PMC7212672/ /pubmed/32393363 http://dx.doi.org/10.1186/s13059-020-02032-0 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Short Report
Massoni-Badosa, Ramon
Iacono, Giovanni
Moutinho, Catia
Kulis, Marta
Palau, Núria
Marchese, Domenica
Rodríguez-Ubreva, Javier
Ballestar, Esteban
Rodriguez-Esteban, Gustavo
Marsal, Sara
Aymerich, Marta
Colomer, Dolors
Campo, Elias
Julià, Antonio
Martín-Subero, José Ignacio
Heyn, Holger
Sampling time-dependent artifacts in single-cell genomics studies
title Sampling time-dependent artifacts in single-cell genomics studies
title_full Sampling time-dependent artifacts in single-cell genomics studies
title_fullStr Sampling time-dependent artifacts in single-cell genomics studies
title_full_unstemmed Sampling time-dependent artifacts in single-cell genomics studies
title_short Sampling time-dependent artifacts in single-cell genomics studies
title_sort sampling time-dependent artifacts in single-cell genomics studies
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7212672/
https://www.ncbi.nlm.nih.gov/pubmed/32393363
http://dx.doi.org/10.1186/s13059-020-02032-0
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