Solid-phase capture and profiling of open chromatin by spatial ATAC

Nature Biotechnology, Год журнала: 2023, Номер 41(8), С. 1085 - 1088

Опубликована: Янв. 5, 2023

Current methods for epigenomic profiling are limited in their ability to obtain genome-wide information with spatial resolution. We introduce ATAC, a method that integrates transposase-accessible chromatin tissue sections barcoded solid-phase capture perform spatially resolved epigenomics. show ATAC enables the discovery of regulatory programs underlying gene expression during mouse organogenesis, lineage differentiation and human pathology.

Язык: Английский

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Mapping cells through time and space with moscot

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Май 11, 2023

Abstract Single-cell genomics technologies enable multimodal profiling of millions cells across temporal and spatial dimensions. Experimental limitations prevent the measurement all-encompassing cellular states in their native dynamics or tissue niche. Optimal transport theory has emerged as a powerful tool to overcome such constraints, enabling recovery original context. However, most algorithmic implementations currently available have not kept up pace with increasing dataset complexity, so that current methods are unable incorporate information scale single-cell atlases. Here, we introduce multi-omics optimal (moscot), general scalable framework for applications genomics, supporting multimodality all applications. We demonstrate moscot’s ability efficiently reconstruct developmental trajectories 1.7 million mouse embryos 20 time points identify driver genes first heart field formation. The moscot formulation can be used dimensions well: To this, enrich transcriptomics datasets by mapping from profiles liver sample, align multiple coronal sections brain. then present moscot.spatiotemporal, new approach leverages gene expression uncover spatiotemporal embryogenesis. Finally, disentangle lineage relationships novel murine, time-resolved pancreas development using paired measurements chromatin accessibility, finding evidence shared ancestry between delta epsilon cells. Moscot is an easy-to-use, open-source python package extensive documentation at https://moscot-tools.org .

Язык: Английский

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The diversification of methods for studying cell–cell interactions and communication

Nature Reviews Genetics, Год журнала: 2024, Номер 25(6), С. 381 - 400

Опубликована: Янв. 18, 2024

Язык: Английский

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SpatialData: an open and universal data framework for spatial omics

Nature Methods, Год журнала: 2024, Номер unknown

Опубликована: Март 20, 2024

Abstract Spatially resolved omics technologies are transforming our understanding of biological tissues. However, the handling uni- and multimodal spatial datasets remains a challenge owing to large data volumes, heterogeneity types lack flexible, spatially aware structures. Here we introduce SpatialData, framework that establishes unified extensible multiplatform file-format, lazy representation larger-than-memory data, transformations alignment common coordinate systems. SpatialData facilitates annotations cross-modal aggregation analysis, utility which is illustrated in context multiple vignettes, including integrative analysis on Xenium Visium breast cancer study.

Язык: Английский

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Benchmarking spatial clustering methods with spatially resolved transcriptomics data

Nature Methods, Год журнала: 2024, Номер 21(4), С. 712 - 722

Опубликована: Март 15, 2024

Язык: Английский

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