Spatial transcriptomics of fluorescently-tagged cholinergic neuron populations with a versatile LCM-Seq method

Young male ChAT-ZsGreen transgenic mice were killed by transcardiac perfusion with 0.5% formaldehyde, followed by 20% sucrose. Cholinergic neurons were isolated with laser-capture microdissection from the caudate putamen (CPU) and from the medium septum (MS) and subjected to RNA-Sequencing (Illumina). Sequencing results were analyzed in R and presented from 30 or 300 pooled CPU neurons (CPU30 and CPU300 samples; N=4 for each) and from 330 pooled MS neurons (MS330 samples; N=4).