Extended Data Fig. 9: Correspondence between Cre-dependent retrograde labeling and MERFISH mapping.
From: A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons
a-h, Retrograde labeling was performed with AAVs expressing Cre-dependent GFP in various transgenic mouse lines and compared to MERFISH results. Left panels: representative coronal reconstructions of Cre-dependent retrogradely labelled nuclei various transgenic lines (TH-Cre, Dbh-Cre, Phox2b-Cre, ePet-Cre, ChAT-IRES-Cre, Lhx2-2A-CreER, Gcg-iCre, c-Kit MerCreMer, and Chx10-Cre). Approximate AP position and anatomical regions are annotated. Right panels: representative MERFISH sections showing the spatial ___location of the corresponding SPN type(s). i-k, UMAP plots show expression of marker genes in the SPN transcriptomic dataset, depicted alongside representative coronal reconstructions of Cre-dependent retrogradely labelled in additional transgenic lines without corresponding MERFISH mappings (targeted transgene yields too broad of a distribution to correspond to specific types in MERFISH results). i, PV-Cre, Spp1-Cre, and Kcng4-Cre label rubrospinal neurons and cerebellospinal neurons in Division 1, as well as reticulospinal neurons in Division 2. j,k GlyT2-Cre (j), and Penk-IRES2-Cre (k) lines label reticulospinal neuron populations throughout Division 2. AP, anterior-posterior position (relative to Bregma); RN, red nucleus; DCN, deep cerebellar nuclei; PGRNL, paragigantocellular reticular nucleus lateral part; GRN, gigantocellular reticular nucleus; MARN, magnocellular reticular nucleus; NTS, nucleus of the solitary tract; Amb, nucleus ambiguus; IRN, intermediate reticular nucleus; A11, cell group A11; LC, locus coeruleus; SubCD, subcoeruleus nucleus dorsal part (Paxinos nomenclature54).
