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<p>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 <i>Ciona robusta</i>. Using PBS-M reduces cell death and ambient mRNA, revealing cell states not otherwise detected. We additionally validate PBS-M in a second tunicate species. This simple protocol modification could enable or improve scRNA-seq for many marine organisms.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月1日

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  • Tal D. Scully,
  • Allon M. Klein

摘要

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. We additionally validate PBS-M in a second tunicate species. This simple protocol modification could enable or improve scRNA-seq for many marine organisms.