KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
snRNA-seq data	This paper	GEO : GSE168156
Software and algorithms
Cell Ranger v3.0.2	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
Seurat v3.2.2	Stuart et al. (2019)	https://satijalab.org/seurat/
MAGMA	de Leeuw et al. (2015)	https://ctg.cncr.nl/software/magma
ImageJ2	Schindelin et al. (2015) & Rueden et al., 2017	https://imagej.net/software/imagej2/
StarDist	Schmidt et al. (2018)	https://imagej.net/plugins/stardist
Other
Rscripts	This paper	https://gitlab.rc.uab.edu/day-lab/rat-vta-snrna-seq, https://doi.org/10.5281/zenodo.6205342
Th RNAscope probe	ACD Bio	Catalog no. 314651-C3
Gch1 RNAscope probe	ACD Bio	Catalog no. 1094971-C4
Slc26a7 RNAscope probe	ABD Bio	Catalog no. 1094961-C1
Chromium NextGem Single Cell Chip	10x Genomics	catalog no. 10000121
Chromium Next GEM single cell 3′ library and gel bead kit, v3.1 single index	10x Genomics	catalog no. 10000121