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| Main Authors: | , |
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| Format: | Artículo científico |
| Language: | en |
| Published: |
BMC genomics
2025
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| Subjects: | |
| Online Access: | https://pubmed.ncbi.nlm.nih.gov/41326993/ |
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| _version_ | 1868266117075566592 |
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| author | Scully, Tal D Klein, Allon M |
| author_facet | Scully, Tal D Klein, Allon M Scully, Tal D Klein, Allon M |
| collection | PubMed - marine biology |
| contents | A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells. Scully, Tal D Klein, Allon M Animals Single-Cell Analysis Mannitol Sequence Analysis, RNA Buffers Ciona intestinalis Salinity Gene Expression Profiling RNA-Seq Transcriptome 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. |
| format | Artículo científico |
| id | pubmed_41326993 |
| institution | PubMed |
| language | en |
| publishDate | 2025 |
| publisher | BMC genomics |
| record_format | pubmed |
| spellingShingle | A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells. Scully, Tal D Klein, Allon M Animals Single-Cell Analysis Mannitol Sequence Analysis, RNA Buffers Ciona intestinalis Salinity Gene Expression Profiling RNA-Seq Transcriptome A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells. Scully, Tal D Klein, Allon M Animals Single-Cell Analysis Mannitol Sequence Analysis, RNA Buffers Ciona intestinalis Salinity Gene Expression Profiling RNA-Seq Transcriptome 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. |
| title | A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells. |
| topic | Animals Single-Cell Analysis Mannitol Sequence Analysis, RNA Buffers Ciona intestinalis Salinity Gene Expression Profiling RNA-Seq Transcriptome |
| url | https://pubmed.ncbi.nlm.nih.gov/41326993/ |