RNA-seq of progenitors and neurons sorted from brain organoids

During development of the human cerebral cortex, multipotent neural progenitors generate excitatory neurons and glial cells. This process is faithfully recapitulated in brain organoids. By using telencephalic brain organoids grown using a dual reporter cell line to isolate neural progenitors and neurons we generated a cell type and developmental stage-specific transcriptome dataset.. Overall design: To investigate progenitor and neuron-specific gene regulatory programs, we generated a dual reporter H9 hESC line that enables sorting of neural progenitors and neurons. To label neural progenitors, we replaced the stop codon of one allele of the pan-neural progenitor marker gene SOX2 with P2A-EGFP. On the other hand, to label neurons, we inserted dTomato driven by human Synapsin1 (hSYN1) promoter in the AAVS1 safe harbor locus. Using this reporter line, we generated telencephalon brain organoids enriched in dorsal telencephalon tissue and isolated EGFP+, dTomato+ and double positive cells across different stages of organoid development (Days 40, 60, 90 and 120) . We isolated RNA from the sorted populations and performed RNA-seq.