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-sequencing of neuronal pools defined by spatial position
offers an alternative strategy to overcome these technical limitations. We report
an LCM-Seq method which allows deep transcriptome profiling of fluorescently-tagged
neuron populations isolated with laser-capture microdissection (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-sequencing with methods optimized for nanogram amounts of moderately degraded
RNA enabled us to detect ∼15,000 different transcripts in fluorescently-labeled cholinergic
neuron populations. The LCM-Seq approach showed excellent accuracy in quantitative
studies, allowing us to detect 2,891 transcripts expressed differentially between
the spatially defined and clinically relevant cholinergic neuron populations of the
dorsal caudate-putamen and medial septum. In summary, the LCM-Seq method we report
in this study is a versatile, sensitive and accurate bulk sequencing approach to study
the transcriptome profile and differential gene expression of fluorescently tagged
neuronal populations isolated from transgenic mice with high spatial precision.
