Development of a versatile LCM-Seq method for spatial transcriptomics of fluorescently tagged cholinergic neuron populations.

ABSTRACT: Single-cell transcriptomics are powerful tools to define neuronal cell types based on co-expressed gene clusters. Limited RNA input in these technologies necessarily compromises transcriptome coverage and accuracy of differential expression analysis. We propose that bulk RNA-Seq of neuronal pools defined by spatial position offers an alternative strategy to overcome these technical limitations. We report a laser-capture microdissection (LCM)-Seq method which allows deep transcriptome profiling of fluorescently tagged neuron populations isolated with LCM from histological sections of transgenic mice. Mild formaldehyde fixation of ZsGreen marker protein, LCM sampling of ∼300 pooled neurons, followed by RNA isolation, library preparation and RNA-Seq with methods optimized for nanogram amounts

SUBMITTER: Rumpler E 

PROVIDER: S-EPMC10477691 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature