Fig. 3

Single-cell quantitative RT-PCR analysis. a Hierarchical clustering analysis of the relative mRNA levels (expressed as z-Score) in FACS-sorted induced cortical (iCtx) cells after 4 weeks of induction. The red color indicates higher expression and white indicates lower expression of a given gene for the various samples. All cells group into three main clusters. iCtx and human fetal primary cortical (hCtx) cells spread in two clusters (1 and 3) while a third one mainly contains human fetal lung fibroblast (HEFL) cells (cluster 2). b Three-dimensional principal component analysis (PCA) density plot demonstrating subpopulations of iCtx (red), hCtx (green), and HEFL (blue) cells. A subpopulation of iCtx cells (P1) is proximal to hCtx cells, indicating a high degree of similarity in overall gene expression patterns. HEFL and hCtx cells are the most distant populations. The majority of iCtx cells group away from HEFL cells (P2); only a small fraction of iCtx cells shares gene expression profile with HEFL cells (P3). c Relative gene expression levels in iCtx (red dots) and hCtx (green dots) cells for selected neuronal and cortical genes represented as Ct values. Each dot represents a single cell (cluster 3)