Figure 1.

Gene Expression Profiling in 84 Directed Differentiations Highlights Broad Transcriptional Similarity and Specific Differences in Expression of Regional Brain Genes

(A) Protocol used to differentiate cortical cultures from PSCs. The early and late stages analyzed are highlighted.

(B) Hierarchical clustering of gene expression from 84 early-stage differentiations profiled with Codeset1. Clusters are named early cluster 1 (EC1)–EC5. Highly expressed cortical development genes are indicated with white arrowheads. Variation was observed in expression of transcripts specific to the telencephalon (FOXG1), the ventral telencephalon (LHX8, LHX6, NKX2-1, DLX1, and DLX5), the hindbrain (HOXA2 and HOXB2), and the dorsal telencephalon (cortex) (EMX1, EMX2, and EOMES), indicated with black arrowheads.

(C) Replicating the patterns observed in (B), genes associated with specific brain regions are highly variable across differentiations in a second independent dataset of 65 early-stage differentiations profiled with Codeset2.

See also Figure S1.