Fig. 1: An anatomically informed transcriptomic atlas of brain-wide spinal projecting neurons.
From: A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons
a, SPNs were labelled via spinal cord injections of a retrograde AAV construct that localizes fluorescent protein expression to the nucleus for parallel anatomical and transcriptomic profiling. Test tubes were drawn using templates from Servier Medical Art (Creative Commons Attribution 3.0 Unported Licence https://creativecommons.org/licences/by/3.0/). The sagittal atlas outline was adapted from the Allen Mouse Brain Atlas (https://atlas.brain-map.org/)53; ©2017 Allen Institute for Brain Science. b, WB reconstructions of segmented and registered SPN nuclei imaged with STPT revealed that SPNs are present across the CTX (RFA, M1M2S1 and S2), HY, MB, CB, PONS and MED. c, Multilevel iterative clustering revealed 76 SPN transcriptomic ‘types’ organized into a taxonomy across 13 ‘subclasses’ and 3 ‘divisions’ (n = 61,484 10x; n = 3,518 SSv4). The colour blocks shading the taxonomy tree indicate division. The nodes at the end of the dendrogram indicate type, with type numbers and names on the far right. From left to right, the bar plots indicate subclass, fractions of nuclei profiled from brain region-enriching dissections and NT-type across each type. The heatmap shows expression of neurotransmitter marker genes. The bar plot below the division legend indicates percentage of total nuclei belonging to each division. d–f, Clustering of SPNs and visualization in UMAP space coloured by brain ROI-enriching dissections (d), division (e) and subclass (f). ROI, division, and subclass colours in c apply to d,e and f, respectively. Percentage labels in d and e indicate percentage of total nuclei belonging to each ROI-enriching dissection or division. NT-type, neurotransmitter type.
