Figure 3. Single-cell gene expression of human and mouse progenitors reveals species-specific RGC subpopulations.

a, Multiplexed gene expression profiling of 546 single human RGC reveals distinct transcriptional states defined by the presence or absence of transcripts encoding apical membrane-specific proteins, proneural transcription factors downstream of NEUROG2 such as NEUROD1 and NEUROD4, and additional LG⁺Pr^lo-enriched genes such as TTYH2 and PLCB4. Hierarchical clustering and heatmap representation of single-cell qRT-PCR data (left) indicates the co-expression patterns of these genes, and a schematic representation (right) of the four main subpopulations of RGC identified: “multipotent” RGC (blue) are found as subsets of both the apical (cluster I) and non-apical RGC (cluster IV), as are the “proneural” NEUROG2/TBR2⁺ RGC (clusters II, III, V). In addition, proneural RGC can be further subdivided according to their expression of downstream factors and additional LG⁺Pr^lo-enriched genes (e.g., compare clusters II and V). b, The same genes assayed in 226 RGC from E16-E17 mouse cortex yield only three subpopulations: apical multipotent (i); apical proneural (ii); and non-apical proneural (iii). Schematic representation of these subpopulations (right) highlights the major species differences, namely, the mouse has fewer non-apical cells overall; few if any multipotent (NEUROG2⁻TBR2⁻) non-apical cells, suggesting the absence of a significant subpopulation of proliferative ORG; and very few cells expressing other human subset-enriched genes (e.g., TTYH1, PLCB4). c, Violin plots of gene expression distributions for apical complex, NEUROG2 network, and ORG-enriched genes in human and mouse single RGC. Several ORG-enriched genes appear to be abundantly expressed in subsets of human but not mouse RGC including NEUROD4, GADD45G, PLCB4, TTYH2, SSTR2, RASGRP1.