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Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics

ABSTRACT: Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics

PROVIDER: PRJNA660781 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12569300.fastq.gz	Fastqsanger.gz
	SRR12569301.fastq.gz	Fastqsanger.gz
	SRR12569302.fastq.gz	Fastqsanger.gz
	SRR12569303.fastq.gz	Fastqsanger.gz
	SRR12569304.fastq.gz	Fastqsanger.gz

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Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics

Project description:Single-cell RNA-sequencing (scRNA-seq) is a powerful technique for describing cell states. Unfortunately, identifying the spatial arrangement of these states in tissues remains challenging. Here, we describe SEgmentation by Exogenous Perfusion (SEEP), a rapid and integrated method to link positional location to transcriptional identity within three-dimensional (3D) disease models. The method utilizes the steady-state diffusion kinetics of a fluorescent dye to establish a gradient along the radial axis of 3D disease models. Classification of sample layers based on dye accessibility permits dissociated and sorted cells to be retrospectively characterized by transcriptomic and regional identity. Using SEEP, we analyze spheroid, organoid, and in vivo tumor models of high grade serous ovarian cancer (HGSOC). The results validate long-standing beliefs regarding the relationship between cell state and position while also revealing new concepts on how the spatially unique microenvironment of individual cells within tumors influences cell identity.

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Project description:Single-cell RNA sequencing (scRNA-seq) is a powerful technique for describing cell states. Identifying the spatial arrangement of these states in tissues remains challenging, with the existing methods requiring niche methodologies and expertise. Here, we describe segmentation by exogenous perfusion (SEEP), a rapid and integrated method to link surface proximity and environment accessibility to transcriptional identity within three-dimensional (3D) disease models. The method utilizes the steady-state diffusion kinetics of a fluorescent dye to establish a gradient along the radial axis of disease models. Classification of sample layers based on dye accessibility enables dissociated and sorted cells to be characterized by transcriptomic and regional identities. Using SEEP, we analyze spheroid, organoid, and in vivo tumor models of high-grade serous ovarian cancer (HGSOC). The results validate long-standing beliefs about the relationship between cell state and position while revealing new concepts regarding how spatially unique microenvironments influence the identity of individual cells within tumors.

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Maintenance of neural stem cell positional identity by Mixed-lineage leukemia 1

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Maintenance of neural stem cell positional identity by Mixed-lineage leukemia 1

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Project description:The cranial neural crest cells are pluripotent cells that provide head skeletogenic mesenchyme and are crucial for craniofacial patterning. Here, we analyzed the in vivo chromatin landscapes of mouse cranial neural crest subpopulations. Early postmigratory neural crest subpopulations contributing to distinct mouse craniofacial structures displayed similar chromatin accessibility patterns, yet differed transcriptionally. Accessible promoters and enhancers of differentially silenced genes carried H3K27me3/H3K4me2 bivalent chromatin marks embedded in large Ezh2-dependent Polycomb domains, indicating transcriptional poising. These postmigratory bivalent regions were already present in neural crest premigratory progenitors. At Polycomb domains, H3K27me3 antagonized H3K4me2 deposition, which was restricted to accessible sites. Thus, bivalent Polycomb domains provide a chromatin template for the regulation of cranial neural crest cell positional identity in vivo contributing novel insights into the epigenetic regulation of face morphogenesis.

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