Visually guided aspiration of fluorescently labelled single neurons from acute midbrain slices followed by Smart-seq2 v1

To link the expression of ion channels, receptors, and molecular effectors to specific brain areas and their subdivisions, it is necessary to perform single-cell RNA-sequencing while preserving the anatomical origin of each neuron. Here we describe a protocol to perform visually guided aspiration of fluorescently labelled single neurons from acute midbrain slices of transgenic mice, followed by Smart-seq2 and deep sequencing. This protocol enables researchers to obtain detailed transcriptomic profiles from any cell-type labelled using transgenic lines - and potentially other methods like viral injections - located in a brain area of interest.