SCAMPR, a single-cell automated multiplex pipeline for RNA quantification and spatial mapping.

ABSTRACT: Spatial gene expression, achieved classically through in situ hybridization, is a fundamental tool for topographic phenotyping of cell types in the nervous system. Newly developed techniques allow for visualization of multiple mRNAs at single-cell resolution and greatly expand the ability to link gene expression to tissue topography, yet there are challenges in efficient quantification and analysis of these high-dimensional datasets. We have therefore developed the single-cell automated multiplex pipeline for RNA (SCAMPR), facilitating rapid and accurate segmentation of neuronal cell bodies using a dual immunohistochemistry-RNAscope protocol and quantification of low- and high-abundance mRNA signals using open-source image processing and automated segmentation tools. Proof of princi

SUBMITTER: Ali Marandi Ghoddousi R 

PROVIDER: S-EPMC9606134 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature