Whole transcriptome analysis of induced serotonergic neurons (iSNs). Whole transcriptome analysis was performed on tryptophan hydroxylase (TPH)-expressing iSNs sorted using the TPH2::GFP lentivirus and compared with control sorted induced neurons (iNs). One-to-one comparison of gene expression levels is shown in (a) scatterplot with normalized counts of upregulated (blue) neuronal genes and downregulated (purple) fibroblast genes in iNs vs fibroblasts. (b) Scatterplot shows normalized expression counts of all genes in iSNs vs iNs. Highlighted are upregulated (green) and downregulated (red) genes in iSNs vs iNs. (c) Scatterplot shows low normalized counts of non-serotonergic monoaminergic genes (pink) in iSNs vs iNs. (d) Venn diagram shows overlapping set of significantly enriched genes between human midbrain raphe (vs human cortex) and iSNs (vs iNs). (d, right) Listed are the 32 overlapping significantly upregulated genes from those shown in the Venn diagram. (e) Listed are selected significantly enriched genes in iSNs vs iNs, previously shown to be expressed in mouse or human raphe. (f) Table shows gene ontology (GO) analysis for genes more than twofold significantly enriched in iSNs vs iNs. Listed are GO categories, genes in sample that fell in the specified category, and (non False Discovery Rate-corrected) P-values for each category. Experiments were run in duplicates, with iSNs and iNs independently generated from fibroblasts derived from two individuals.