A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells.
Tal ScullyAllon M KleinPublished in: bioRxiv : the preprint server for biology (2023)
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.
Keyphrases
- single cell
- rna seq
- high throughput
- cell death
- cell cycle arrest
- induced apoptosis
- healthcare
- microbial community
- randomized controlled trial
- gram negative
- stem cells
- small molecule
- air pollution
- machine learning
- bone marrow
- gene expression
- big data
- electronic health record
- mesenchymal stem cells
- cell proliferation
- multidrug resistant