Extended Data Fig. 3: UMAP analysis of scRNA-seq data.
From: A transcriptomic axis predicts state modulation of cortical interneurons
Each dot represents a V1 inhibitory cell, from the Tasic et al.3 data, with glyph representing its assigned subtype. UMAP analysis was performed separately for MGE and CGE derived interneuron subtypes, using 150 log-transformed genes selected by the ProMMT algorithm10. This analysis reveals both highly discrete subtypes such as Pvalb-Vipr2 (putative chandelier cells) and smoothly varying continua where boundaries between subtypes appear arbitrary, such as Lamp5-Ntn-Npy2r, Lamp5-Plch2-Dock5, and Lamp5-Lsp1 (putative neurogliaform subtypes). Also note the smooth transition between Sst-Calb2 (putative Martinotti subtypes), Sst-Tac1 (putative Sst non-Martinotti), and Pvalb-Tpbg (putative superficial basket cell subtypes). Text on main plots indicates location of in vivo imaged subtypes.
