A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1241883 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32858063.fastq.gz | Fastqsanger.gz | |||
| SRR32858064.fastq.gz | Fastqsanger.gz |
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Project 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.
2025-04-02 | GSE292926 | GEO
Project description:Mannitol is a putative osmoprotectant contributing to salt tolerance in several species. Arabidopsis plants transformed with the mannose-6-phosphate reductase (M6PR) gene from celery were dramatically more salt tolerant (at 100 mM NaCl) as exhibited by reduced salt injury, less inhibition of vegetative growth, and increased seed production relative to the wild type (WT). When treated with 200 mM NaCl, transformants produced no seeds, but did bolt, and exhibited less chlorosis/necrosis and greater survival and dry weights than the WT. Without salt there were no M6PR effects on growth or phenotype, but expression levels of 2272 genes were altered. Many fewer differences (1039) were observed between M6PR and WT plants in the presence of salt, suggesting that M6PR pre-conditioned the plants to stress. Previous work suggested that mannitol is an osmoprotectant, but mannitol levels are invariably quite low, perhaps inadequate for osmoprotectant effects. In this study, transcriptome analysis reveals that the M6PR transgene activated the downstream abscisic acid (ABA) pathway by up-regulation of ABA receptor genes (PYL4, PYL5, and PYL6) and down-regulation of protein phosphatase 2C genes (ABI1 and ABI2). In the M6PR transgenic lines there were also increases in transcripts related to redox and cell wall-strengthening pathways. These data indicate that mannitol-enhanced stress tolerance is due at least in part to increased expression of a variety of stress-inducible genes.
2010-03-01 | GSE18217 | GEO
Project description:Saccharomyces cerevisiae normally cannot assimilate mannitol, a promising brown macroalgal carbon source for bioethanol production. To date, the molecular mechanisms underlying this inability remain unknown. Here, we found that cells acquiring mannitol-assimilating ability appeared from wild-type S. cerevisiae strain during prolonged culture in mannitol medium. Our microarray analysis revealed that genes for putative mannitol dehydrogenase and hexose transporters were up-regulated in cells acquiring mannitol-assimilating ability. Take account of our other results including complementation analysis and cell growth data, we demonstrated that this acquisition of mannitol-assimilating ability was due to the spontaneous mutation in the gene encoding Tup1 or Cyc8. Tup1-Cyc8 is the general corepressor complex involved in the repression of many kinds of genes. Thus, it is suggested that the inability of wild-type S. cerevisiae to assimilate mannitol can be attributed to the transcriptional repression of a set of genes involved in mannitol utilization by Tup1-Cyc8 corepressor. In other words, Tup1-Cyc8 is a key regulator of mannitol metabolism in S. cerevisiae. We also showed that S. cerevisiae strain which carries mutant allele of TUP1 or CYC8 produced ethanol from mannitol efficiently. Especially, strain carrying mutant allele of CYC8 showed high tolerance to salt, which is superior to other ethanologenic microorganisms. This characteristic is highly beneficial to produce bioethanol from marine biomass. Taken together, Tup1-Cyc8 can be an ideal target to develop a yeast-algal bioethanol production system. To figure out how Mtl+ strains (cells acquiring ability to grow in mannitol medium) had acquired the ability to assimilate mannitol, we performed genome-wide analysis by using Nimblegen microarrays.
2014-12-04 | GSE55755 | GEO
Project description:Mannitol is a sugar alcohol that serves as a compatible solute contributing to exceptional salt tolerance in several plant species. Arabidopsis plants transformed with the mannose-6-phosphate reductase (M6PR) gene from celery were dramatically more salt tolerant. Following treatment with 100mM NaCl, transgenic plants, relative to wild type (WT), were more successful in bolting, flowering, and production of viable seed, were less chlorotic/necrotic, and with less inhibition of growth (leaf number, rosette diameter, plant height, stalk number, and dry weight). When irrigated with 200 mM NaCl, both transformants and WT plants died without producing seeds, but M6PR transformants bolted and showed significantly less chlorosis and necrosis and had higher survival rates and dry weights than those of WT. Under normal growth conditions there were no negative effects of the M6PR transgene on overall growth (leaf number, rosette diameter, plant height, stalk number, and dry weight), or time to bolting/flowering or seed production compared to wild type (WT). Despite the lack of effects on phenotype in the absence of salt stress, genome wide expression analyses indicated that expression levels of more than 2000 genes were altered by presence of the M6PR transgene: however, there were many fewer differences observed between the M6PR and non-transgenic plants in the presence of salt stress (459), suggesting that M6PR pre-conditioned the plants for exposure to salinity. Gene categories most affected in the M6PR transgenic plants were involved in DNA binding, signal transduction, metabolism/energy, cell structure, membrane transport, defense response, and transcription. Notably, a large number of known stress genes were induced, including those related to cell walls, biotic stress, and ABA- and ethylene-responses. Our work and that in other labs has suggested that mannitol acts as an osmoprotectant, but mannitol levels are invariably quite low, and perhaps inadequate to explain its effects as an osmoprotectant. The gene expression data here indicate that stress tolerance of mannitol-producing Arabidopsis is also due, at least in part, to enhanced expression of a number of stress inducible genes related to both biotic and abiotic stress tolerance. Both M6PR transgenic and Col WT plants were grown in the growth chamber in the absence and presence of salt stress. Plants from 20 days after sowing (6 days after salt treatment) were used for RNA extraction and hybridization on Affymetrix microarrays. There were two biological replicates for each genotype and salt treatment combination.
2010-03-07 | E-GEOD-18217 | biostudies-arrayexpress
Project description:Buffer microcosmic sample Raw sequence reads
| PRJNA531098 | ENA
Project description:Saccharomyces cerevisiae normally cannot assimilate mannitol, a promising brown macroalgal carbon source for bioethanol production. To date, the molecular mechanisms underlying this inability remain unknown. Here, we found that cells acquiring mannitol-assimilating ability appeared from wild-type S. cerevisiae strain during prolonged culture in mannitol medium. Our microarray analysis revealed that genes for putative mannitol dehydrogenase and hexose transporters were up-regulated in cells acquiring mannitol-assimilating ability. Take account of our other results including complementation analysis and cell growth data, we demonstrated that this acquisition of mannitol-assimilating ability was due to the spontaneous mutation in the gene encoding Tup1 or Cyc8. Tup1-Cyc8 is the general corepressor complex involved in the repression of many kinds of genes. Thus, it is suggested that the inability of wild-type S. cerevisiae to assimilate mannitol can be attributed to the transcriptional repression of a set of genes involved in mannitol utilization by Tup1-Cyc8 corepressor. In other words, Tup1-Cyc8 is a key regulator of mannitol metabolism in S. cerevisiae. We also showed that S. cerevisiae strain which carries mutant allele of TUP1 or CYC8 produced ethanol from mannitol efficiently. Especially, strain carrying mutant allele of CYC8 showed high tolerance to salt, which is superior to other ethanologenic microorganisms. This characteristic is highly beneficial to produce bioethanol from marine biomass. Taken together, Tup1-Cyc8 can be an ideal target to develop a yeast-algal bioethanol production system. To figure out how Mtl+ strains (cells acquiring ability to grow in mannitol medium) had acquired the ability to assimilate mannitol, we performed genome-wide analysis by using Nimblegen microarrays. Yeast Saccharomyces cerevisiae cells (wild-type BY4742 strain and two Mtl+ strains, MK3619 and MK3683) were grown at 30°C to the logarithmic phase in SC or SM media. Total RNA was purified and the 4 RNA samples (BY4742 cells in SC as control, MK3619 cells in SM, MK3683 cells in both SC and SM) were analyzed with Nimblegen microarrays.
2014-12-04 | E-GEOD-55755 | biostudies-arrayexpress
Project description:Burkholderia multivorans was grown on agar plates containing mannitol as substrate and compared to growth on control plates containing mannose
2014-03-02 | E-MEXP-3971 | biostudies-arrayexpress
Project description:We report the comparison of low salt vs high salt diet fed Dahl rat kidney glomeruli by sequencing analysis
2023-09-01 | GSE237521 | GEO
Project description:RNA-seq of 14 day old wild type and ppdnmt2 protonemata exposed to 24 hour mannitol stress
2024-08-06 | GSE181719 | GEO
Project description:Interventions: Group A:20%Mannitol, 0.9% saline;Group B:20%Mannitol, 0.9% saline?simethicone;Group C:20%Mannitol, 0.9% saline?simethicone
Primary outcome(s): The level of small bowel cleaning
Study Design: Randomized parallel controlled trial
| 2662332 | ecrin-mdr-crc