Extended Data figure 2: Annotation of the developing optic lobe UMAP plot.

(a) UMAP plots showing the expression of different cell type markers that allows for the annotation of the different clusters. Shotgun/DE-Cad (shg) is expressed in the neuroepithelium (NE) and young neuroblasts (NBs). Deadpan (dpn) is expressed in neuroepithelium and neuroblasts. Asense (ase) is expressed in the neuroblasts and GMCs. Elav is mostly expressed in the neurons, although the transcript can already be seen in the GMCs. Finally, repo is expressed in glial cells.

(b) UMAP plot of single-cells coming from larval (L3) and pupal (P15) developing optic lobes. Using cell type annotation, we identify cell types that belong to the four optic lobe neuropils (lamina, medulla, lobula, and lobula plate), as well as central brain cells that were not removed during the dissections, and glial cells.

(c) Expression of markers for the lamina and the lobula plate. Lamina is marked by the expression of gcm, eya, sim, tll, and dac, while lobula plate expresses strongly acj6, faintly dac, and the progenitors (neuroblasts and GMCs) express tll.

(d) (Top) UMAP: Spatial transcription factors (Vsx, Optix, and Rx) are not expressed in medulla neuroblasts (NBs), while only Vsx is expressed in some neuronal types (it is unknown whether this expression reflects their origin from the Vsx spatial domain). (Inset) sTFs are only expressed in the neuroepithelium (NE) in largely non-overlapping domains. (Bottom). UMAP plots with the expression of individual sTFs in the neuroepithelium.

(e) UMAP plot of the neuroepithelial cells. Top: Expression of the spatial transcription factors (Vsx1, Optix, and Rx) can be seen in largely non-overlapping clusters. Bottom: Semi-supervised clustering of the neuroepithelial cells and identification of the three spatial clusters (Vsx, Optix, and Rx).