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A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells

Single-cell RNA sequencing (scRNA-seq) enables discovery of novel cell states by transcriptomic profiling with minimal prior knowledge, making it useful for studying non-model organisms. For most marine organisms, however, cells are viable at a higher salinity than is compatible with scRNA-seq, impa...

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Detalles Bibliográficos
Autores principales: Scully, Tal, Klein, Allon
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10168337/
https://www.ncbi.nlm.nih.gov/pubmed/37163054
http://dx.doi.org/10.1101/2023.04.26.538465
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author Scully, Tal
Klein, Allon
author_facet Scully, Tal
Klein, Allon
author_sort Scully, Tal
collection PubMed
description Single-cell RNA sequencing (scRNA-seq) enables discovery of novel cell states by transcriptomic profiling with minimal prior knowledge, making it useful for studying non-model organisms. For most marine organisms, however, cells are viable at a higher salinity than is compatible with scRNA-seq, impacting data quality and cell representation. We show that a low-salinity phosphate buffer supplemented with D-mannitol (PBS-M) enables higher-quality scRNA-seq of blood cells from the tunicate Ciona robusta. Using PBS-M reduces cell death and ambient mRNA, revealing cell states not otherwise detected. This simple protocol modification could enable or improve scRNA-seq for the majority of marine organisms.
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spelling pubmed-101683372023-05-10 A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells Scully, Tal Klein, Allon bioRxiv Article Single-cell RNA sequencing (scRNA-seq) enables discovery of novel cell states by transcriptomic profiling with minimal prior knowledge, making it useful for studying non-model organisms. For most marine organisms, however, cells are viable at a higher salinity than is compatible with scRNA-seq, impacting data quality and cell representation. We show that a low-salinity phosphate buffer supplemented with D-mannitol (PBS-M) enables higher-quality scRNA-seq of blood cells from the tunicate Ciona robusta. Using PBS-M reduces cell death and ambient mRNA, revealing cell states not otherwise detected. This simple protocol modification could enable or improve scRNA-seq for the majority of marine organisms. Cold Spring Harbor Laboratory 2023-04-28 /pmc/articles/PMC10168337/ /pubmed/37163054 http://dx.doi.org/10.1101/2023.04.26.538465 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
Scully, Tal
Klein, Allon
A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells
title A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells
title_full A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells
title_fullStr A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells
title_full_unstemmed A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells
title_short A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells
title_sort mannitol-based buffer improves single-cell rna sequencing of high-salt marine cells
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10168337/
https://www.ncbi.nlm.nih.gov/pubmed/37163054
http://dx.doi.org/10.1101/2023.04.26.538465
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