Dictionary learning for integrative, multimodal and scalable single-cell analysis

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 42(2), P. 293 - 304

Published: May 25, 2023

Language: Английский

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Single-cell technologies: From research to application

The Innovation, Journal Year: 2022, Volume and Issue: 3(6), P. 100342 - 100342

Published: Oct. 18, 2022

Language: Английский

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Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice

Developmental Cell, Journal Year: 2022, Volume and Issue: 57(9), P. 1177 - 1192.e6

Published: May 1, 2022

Understanding how roots modulate development under varied irrigation or rainfall is crucial for of climate-resilient crops. We established a toolbox tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. used these study in range environments: plates the lab, controlled greenhouse stress recovery conditions, outdoors paddy. Integration mRNA data resolves regulatory networks following: cycle genes proliferating cells that attenuate DNA synthesis submergence; involved auxin signaling, circadian clock, small RNA regulation ground tissue; suberin biosynthesis, iron transporters, nitrogen assimilation endodermal/exodermal modulated with water availability. By applying systems approach, we identify known candidate driver transcription factors water-deficit responses xylem plasticity. Collectively, this resource will facilitate genetic improvements root optimal climate resilience.

Language: Английский

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scPlantDB: a comprehensive database for exploring cell types and markers of plant cell atlases

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D1629 - D1638

Published: Aug. 28, 2023

Abstract Recent advancements in single-cell RNA sequencing (scRNA-seq) technology have enabled the comprehensive profiling of gene expression patterns at level, offering unprecedented insights into cellular diversity and heterogeneity within plant tissues. In this study, we present a systematic approach to construct database, scPlantDB, which is publicly available https://biobigdata.nju.edu.cn/scplantdb. We integrated transcriptomic profiles from 67 high-quality datasets across 17 species, comprising approximately 2.5 million cells. The data underwent rigorous collection, manual curation, strict quality control standardized processing public databases. scPlantDB offers interactive visualization facilitating exploration both single-dataset multiple-dataset analyses. It enables comparison functional annotation markers diverse cell types species while providing tools identify compare based on these markers. summary, serves as database for investigating atlases. valuable resource research community.

Language: Английский

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Spatially resolved transcriptomic analysis of the germinating barley grain

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(15), P. 7798 - 7819

Published: June 23, 2023

Seeds are a vital source of calories for humans and unique stage in the life cycle flowering plants. During seed germination, embryo undergoes major developmental transitions to become seedling. Studying gene expression individual cell types has been challenging due lack spatial information or low throughput existing methods. To overcome these limitations, transcriptomics workflow was developed germinating barley grain. This approach enabled high-throughput analysis expression, revealing specific patterns various functional categories at sub-tissue level. study revealed over 14 000 genes differentially regulated during first 24 h after imbibition. Individual genes, such as aquaporin family, starch degradation, wall modification, transport processes, ribosomal proteins transcription factors, were found have time. Using autocorrelation algorithms, we identified auxin that had increasingly focused within subdomains time, suggesting their role establishing axis. Overall, our provides an unprecedented spatially resolved cellular map germination identifies genomics targets better understand restricted processes germination. The data can be viewed https://spatial.latrobe.edu.au/.

Language: Английский

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The Arabidopsis leaf quantitative atlas: a cellular and subcellular mapping through unified data integration

Quantitative Plant Biology, Journal Year: 2024, Volume and Issue: 5

Published: Jan. 1, 2024

Abstract Quantitative analyses and models are required to connect a plant’s cellular organisation with its metabolism. However, quantitative data often scattered over multiple studies, finding such converting them into useful information is time-consuming. Consequently, there need centralise the available highlight remaining knowledge gaps. Here, we present step-by-step approach manually extract from various sources, unify format. First, Arabidopsis leaf were collated, checked for consistency correctness curated by cross-checking sources. Second, combined applying calculation rules. They then integrated unique comprehensive, referenced, modifiable reusable compendium representing an reference leaf. This atlas contains metrics of 15 cell types found in leaves at subcellular levels.

Language: Английский

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Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology

BioDesign Research, Journal Year: 2024, Volume and Issue: 6, P. 0029 - 0029

Published: Jan. 1, 2024

Plants are complex systems hierarchically organized and composed of various cell types. To understand the molecular underpinnings plant systems, single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for revealing high resolution gene expression patterns at cellular level investigating cell-type heterogeneity. Furthermore, scRNA-seq analysis biosystems great potential generating new knowledge to inform design synthetic biology, which aims modify plants genetically/epigenetically through genome editing, engineering, or re-writing based on rational increasing crop yield quality, promoting bioeconomy enhancing environmental sustainability. In particular, data from studies can be utilized facilitate development high-precision Build-Design-Test-Learn capabilities maximizing targeted performance engineered while minimizing unintended side effects. date, been demonstrated in limited number species, including model (e.g., Arabidopsis thaliana), agricultural crops Oryza sativa), bioenergy Populus spp.). It is expected that future technical advancements will reduce cost consequently accelerate application this emerging technology plants. review, we summarize current scRNA-seq, sample preparation, sequencing, analysis, provide guidance how choose appropriate methods different types samples. We then highlight applications both biology research. Finally, discuss challenges opportunities

Language: Английский

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Single-cell transcriptomics reveals heterogeneity in plant responses to the environment: a focus on biotic and abiotic interactions

Journal of Experimental Botany, Journal Year: 2024, Volume and Issue: 75(17), P. 5188 - 5203

Published: March 11, 2024

Biotic and abiotic environmental cues are major factors influencing plant growth productivity. Interactions with biotic (e.g. symbionts pathogens) changes in temperature, water, or nutrient availability) trigger signaling downstream transcriptome adjustments plants. While bulk RNA-sequencing technologies have traditionally been used to profile these transcriptional changes, tissue homogenization may mask heterogeneity of responses resulting from the cellular complexity organs. Thus, whether different cell types respond equally fluctuations, subsets cell-type specific, long-lasting questions biology. The recent breakthrough single-cell transcriptomics research offers an unprecedented view under changing conditions. In this review, we discuss contribution understanding cell-type-specific interactions. Besides biological findings, present some technical challenges coupled studies plant-environment interactions, proposing possible solutions exciting paths for future research.

Language: Английский

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Unraveling plant–microbe symbioses using single-cell and spatial transcriptomics

Trends in Plant Science, Journal Year: 2024, Volume and Issue: 29(12), P. 1356 - 1367

Published: July 10, 2024

HighlightsBeneficial plant–microbe interactions are critical to plant productivity in both natural and agricultural ecosystems due benefits such as improved nutrition abiotic stress tolerance.The legume–rhizobia symbiosis plant–arbuscular mycorrhizal fungi involve continuous signaling coordination between two organisms.Within symbioses, the development of novel microbial structures is driven by symbiosis-specific gene expression a few specific cell populations.Genetic engineering take better advantage these relies on identification symbiosis-responsive genes that can serve targets for modification.Applying single-cell spatial RNA-seq study endosymbiosis facilitate improve our general understanding complex biology symbiotic interactions.AbstractPlant–microbe symbioses require intense interaction genetic successfully establish types host symbiont. Traditional methodologies lack cellular resolution fully capture complexities, but transcriptomics (ST) now allowing scientists probe at an unprecedented level detail. Here, we discuss advantages transcriptomic technologies provide studying endosymbioses highlight key recent studies. Finally, consider remaining limitations applying approaches research, which mainly related simultaneous transcripts within same cells.

Language: Английский

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Plant synthetic biology innovations for biofuels and bioproducts

Trends in biotechnology, Journal Year: 2022, Volume and Issue: 40(12), P. 1454 - 1468

Published: Oct. 12, 2022

Language: Английский

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