Extended Data Figure 6. Single cell gene expression of Dlxi1/2b::eGFP⁺ cells in hSS and hCS (Smart-seq2).

(a) Scheme showing the isolation by dissociation and fluorescence-activated cell sorting (FACS) of Dlxi1/2b::eGFP⁺ cells from hSS or hCS for single cell transcriptional analysis. (b) Violin plots showing expression in Dlxi1/2b::eGFP⁺ cells of selected genes associated with cortical, striatal and olfactory interneurons in hSS (light green, n= 123 cells) or hCS (dark green; n= 106 cells) at 2 weeks after assembly of hSS-hCS. (c) Violin plots showing expression in Dlxi1/2b::eGFP⁺ cells (at 4 weeks after assembly of hSS-hCS) in clusters A, B, and C (likelihood ratio test; GAD1, CELF4: P> 0.05; PBX3: P< e⁻⁷ for A versus B & C; NNAT: P< e⁻¹⁶ for C versus A & B, P< e⁻¹⁶ for B versus A & C; MALAT1: P< e⁻⁹ for C versus A & B; SOX11: P< e⁻¹⁶ for B versus A & C, P< e⁻⁹ for A versus B & C; GRIP2: P< e⁻⁸ for B versus A & C). (d) Scatter plot showing the number of genes detected (≥ 10 reads cutoff) versus the number of reads (n= 410 cells from combined single cell RNA-seq experiments after 2 weeks or 4 weeks of assembly in hSS-hCS). (e) Graph illustrating biologically variable transcripts (red circles) and non-variable transcripts (black circles) along with the technical noise from the ERCC spike in RNAs (blue dots). Green line shows the technical noise fit.