Transcription factors (TFs) are the key players controlling transcriptional activity during cell-type specification. In recent years, reprogramming, direct programming, and transdifferentiation experiments have taken advantage of this principle to impose cell type-specific gene regulatory programs. This study examined the contribution of a series of TFs to specific neuronal regulatory programs using direct neuronal programming of embryonic stem cells. To determine how TF combinations induce neuronal and serotoninergic differentiation, they constructed a series of mouse isogenic inducible embryonic stem cell lines: Ascl1 (iA), Ascl1 + Lmx1b (iAL), Ascl1 + Lmx1b + Foxa2 (iALF), Ascl1 + Lmx1b + Pet1 (iALP), and Ascl1 + Lmx1b + Foxa2 + Pet1 (iALFP). The dataset contains high throughput sequencing data. In addition, the publication includes supplementary data on raw scoring, genes names for clusters, and gene ontology terms associated with clusters.