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

ABSTRACT: 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

SUBMITTER: Morse DB 

PROVIDER: S-EPMC10424188 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature