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A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination

ABSTRACT: A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination

PROVIDER: PRJNA1252448 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR33210902_1.fastq.gz	Fastqsanger.gz
	SRR33210902_2.fastq.gz	Fastqsanger.gz
	SRR33210903_1.fastq.gz	Fastqsanger.gz
	SRR33210903_2.fastq.gz	Fastqsanger.gz
	SRR33210904_1.fastq.gz	Fastqsanger.gz

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A transcriptional atlas of early Arabidopsis seed development suggests mechanisms for inter-tissue coordination

Project description:Successful seed development is essential for flowering plant reproduction and requires the coordination of three genetically distinct tissues: the embryo and endosperm, which are the products of fertilization, and the maternal seed coat. Understanding of transcriptional programs that underlie tissue-specific functions and coordination in Arabidopsis seeds is incomplete. To address this, we performed single nucleus RNA-sequencing on seeds at 3, 5, and 7 days after pollination. We characterize all major seed cell types, further refine transcriptional states in the endosperm, and report previously transcriptionally undefined cell types in the seed coat. Among other findings, our analyses reveal the compartmentalization of genes involved in brassinsteroid-responsive transcription factor activation and nutrient transport. Additionally, we identify abundant cell-type specific expression of genes that encode rapidly evolving short, secreted peptides (SSPs) in the micropylar and chalazal endosperm, suggesting that SSP activity is an unexplored but potentially significant contributor to Arabidopsis seed development.

2025-04-28 | GSE295007 | GEO

DBX2 REGULATION IN LIMBS SUGGESTS INTER-TAD SHARING OF ENHANCERS

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A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis

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A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis

Project description:Extensive studies of the model plant Arabidopsis has enabled a deep understanding of organs and tissues throughout plant development. Yet, a fundamental understanding of cell types and states across organs and development is still lacking. Here, we present a single-nucleus transcriptome atlas of Arabidopsis seed-to-seed development encompassing diverse tissues across ten developmental time points. Analysis of over 400,000 nuclei revealed 183 major and 653 subclusters that demarcate cell type and state. Cross-organ analyses revealed that the transcriptional identity of many cell types is conserved across development but influenced by the organ of origin and developmental timing. In addition, groups of transcription factors were enriched and uniquely expressed in individual organs and time points, suggesting developmental gatekeeping of transcription factor activation. Finally, we employed spatial transcriptomics to validate our findings in the highly complex silique organ.

2023-03-25 | GSE226097 | GEO

DBX2 REGULATION IN LIMBS SUGGESTS INTER-TAD SHARING OF ENHANCERS [4C-Seq]

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Individual patient pathway coordination analysis in a cross-species single-cell kidney atlas

Project description:The use of single-cell RNA sequencing in clinical and translational research is limited by cross-species differences and the challenge of identifying cell-type-specific, targetable molecular changes in individual patients. Here, we created an Integrated Single-cell Kidney Atlas including over one million cells from 140 samples, defining more than 70 conserved cell states in human and rodent models. We developed CellSpectra, a computational tool that quantifies changes in gene expression coordination across cellular functions, which we applied to kidney and lung cancer data. This tool powers our Patient-Level Single-Cell Functional Profiling Report, which highlights cell-type-specific changes in pathway gene expression coordination in individuals. Our cross-species atlas facilitates the selection of a rodent model that closely reflects the cellular and pathway-level signatures observed in a patient sample, advancing the application of single-cell methodologies in clinical precision medicine. Finally, by using experimental models, we demonstrate how our informatics approach can be applied for the potential selection of suitable therapeutics.

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SeedMatExplorer: The transcriptome atlas of Arabidopsis seed maturation

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SeedMatExplorer: The transcriptome atlas of Arabidopsis seed maturation

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