Extended Data Figure 6 (related to Figure 3). Novel expression pattern of selected genes and NMF gene modules.
a-d Novel expression patterns emerging from the inferred tree. Expression levels overlaid on the tree (left), UMAP of full scRNA-seq developmental data (middle), and Slide-seq counts on an E15.5 or P1 section of cortex (right) for each gene. Rorb is expressed in developing CFuPN, astrocytes and layer 4 stellate neurons and present in the deep cortical plate (CP) (a). Pcp4 is expressed in migrating and immature neurons that contribute to both CPN and CFuPN, as well as in SCPN, layer 6b, NP and Cajal-Retzius cells (CR), and is found in the intermediate zone (IZ) and CP (b). Npy is expressed in CFuPN and highly in CPN of layers 5&6. Positive Npy signal is evident in the deep CP through Slide-seq (c). Cck was also detected in CFuPN and at higher levels in CPN of layers 5&6. Low levels of expression in the CP were detected via Slide-seq (d). VZ: ventricular zone. e Validation of expression of novel cell type-specific genes emerging from the cascade analysis. Expression levels overlaid on the tree (left), time course expression on purified subtypes of PN from DeCoN transcriptomic resource24,52 (middle), and in situ hybridization from the Allen Developing Mouse Brain Atlas23,53 (right, age indicated in figure).
f Complete set of gene programs of connected modules found by NMF. Each circular node represents a module. Modules are horizontally aligned to the developmental stage the module was computed from, and colored by the annotated function (see also Supplementary Information Table 3). g Scaled expression overlaid on branching tree of modules corresponding to broad neuronal differentiation programs, colored according to program identity. h Selected NMF modules expression from scRNA-seq data mapped onto time-matched Slide-seq section using tangram (Methods).