Extended Data Fig. 10: Developmental trajectories of visual cortex CGE GABA cell types.
From: Continuous cell-type diversification in mouse visual cortex development
(a-c) UMAPs for CGE cells colored by subclass (a), cluster (b) and synchronized age (c). (d) Transcriptomic trajectory tree for CGE clusters starting from the common CGE GABA antecedent, with corresponding MET types labeled. Nodes are clusters subdivided by synchronized age, and edges represent antecedent-descendant relationship between adjacent nodes, with thicker end at the antecedent node and thinner end at the descendant node. Nodes are grouped by subclass, and adult clusters are labeled. Each MET type is enclosed within a dashed outline among the CGE cell clusters. BP/BTC, bipolar/bitufted cells. (e) Cluster composition of all CGE cells at each age. (f) Clusters are grouped together based on similar trajectories. Within each cluster group, all cells along their trajectories, including all antecedent nodes, are shown and are colored by cluster membership. (g) Spatial distribution of CGE subclasses and clusters within each subclass in P56 MERFISH data, based on the ABC-WMB Atlas14. (h) Marker genes illustrating cell type diversification along trajectories. Specifically, in the Vip subclass, group 1 (Crispld2 and Mybpc1) contains clusters 645, 646, 648 and 629 that are split from 645 around P21. Group 2 (Rspo2 and Rspo4) contains cluster 627. Group 3 (Chat and Npy2r) contains the root cluster 641, plus 643 and 663 emerging at P11, 633 at P19, 638 at P23, and 640 at P56. Group 4 (Sntb1) contains clusters 662, 661, 660 and 639, with 639 emerging at P2, 662 at P9, 661 at P15, and 660 at P21. Group 5 (Grin3a and Igfbp6) contains two clusters, with 623 split from 624 at P23. The Sncg subclass has one main trajectory marked by Plcxd3, Frem1, Egln3 and Sncg, with Sncg expressed the latest. Among the 3 Sncg clusters, cluster 676 gives rise to 682 and 673 at P11 and P20, respectively. In the Lamp5 subclass, group 1 (Egln3, Col14a1 and Fbn2) contains clusters 719 (emerging at P2), 720 (P12) and 722 (P21). Group 2 (clusters 716, 717 and 718, split from 718 at P25) and group 3 (clusters 706 and 708, split at P28) are very similar, marked by shared expression of Dock5 and Ndnf, with 708 as the root cluster and 718 split from 708 at P11. Group 4, containing cluster 709 and enriched in Lsp1 and Cemip, shares expression of Tox2 and Sv2c with groups 2 and 3 and emerges at P1 along with cluster 708.
