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. 2019 Nov 20;8:e50354. doi: 10.7554/eLife.50354

Figure 2. Identification of neural progenitor cell populations.

(A) Expression-pattern of genes from the temporal cascade distinguish population of cells. Two dimensions UMAP plot labeling genes from the temporal cascade. Grh, grainy head in green and Kr, Kruppel in red. Grh is broadly expressed in the recently born neuroprogenitors, while Kr is expressed in mature cells. (B) Re-analysis of the neurogenic populations by sub-clustering the original NPCs population, plotted in a Seurat UMAP plot, identifies 11 sub-populations of cells. NPCs are further divided into neuroblasts and optic lobe epithelium (OLE). (C) lncRNAs are present in NPCs expression profile. Color coded UMAP plot showing the abundance of long non-coding RNAs (lncRNAs). The scale represents gene expression levels. (D) OLE can be distinguished from the remaining neuroblasts based on the expression of characterized marker genes. Dot size corresponds to the percentage of cells expressing a particular gene, while color intensity represents gene expression levels. (E) Cell-cycle scores can be estimated transcriptionally. UMAP plot showing the different NPCs color coded based on cell-cycle phases. The pie graph illustrates the percentage of NPCs in each phase, G1, G2M and S. (F) EdU incorporation and NPCs proliferation. Immunostaining of the larval brain illustrating Dpn+ proliferating NPCs at 16 hr ALH. Proliferation index (PI) was calculated as the ratio between Dpn+EdU+ NPCs and Dpn+ NPCs. Error bars represent standard error. N = 5. Nuclei were labeled with DAPI. Scale bar: 20 µm.

Figure 2.

Figure 2—figure supplement 1. Marker genes for the identification of neural progenitor cell populations.

Figure 2—figure supplement 1.

(A) Two dimensions UMAP plot labeling neurogenic marker genes: dpn, klu, ase, erm, pnt and pros. Localization of the neurogenic population in the original dataset is outlined with a dash line. (B) The original NPCs were sub-clustering, re-analyzed and represented in UMAP plots, indicating the expression of neurogenic marker genes: dpn, klu, ase, erm, pnt and pros. Gene expression level is color coded.
Figure 2—figure supplement 2. Identifying undifferentiated neurons in the larval brain.

Figure 2—figure supplement 2.

(A) On top, UMAP plot showing the localization of the undifferentiated neurons (UNs) in the original representation. Bottom, zoom into the UNs displaying the expression of neuronal marker genes: elav, Syt1, nrv3, and other upregulated genes: br, hdc, unk, Thor, scyl and hig. Gene expression level is color coded.