RNA-seq analysis dataset: FACS-sorted Ptf1a-lineage cells from E14.5 hypothalamus Hetero vs Homo (Table S2)

RNA-seq analysis on hypothalamic Ptf1a-lineage cells Because Ptf1a is a transcription factor, this protein should regulate transcription of various genes in Ptf1a-expressing cells of the hypothalamus. To detect those downstream genes, we purified cells in the Ptf1a-lineage from the hypothalamus at E14.5 by FACS sorting, subsequently performed RNA-seq analysis and obtained 706 differentially expressed genes. 386 genes had lower and 320 had higher expression in Ptf1a-lineage cells from homozygous Ptf1a deficient mice. The down-regulated genes included Prdm13, Corl2 and Lhx5 that were known downstream targets of Ptf1a, in addition, Sox3 and Nkx2-1, which are known to be required for hypothalamic development. Interestingly, among those affected genes, we detected several genes encoding transmembrane and/or secreted proteins, such as Jag2 (ligand for Notch receptors), Sema6b, Sema4g (ligands for Plexin family proteins). These genes may have a non-cell autonomous role in the sexual differentiation of hypothalamic cells adjacent to Ptf1a-lineage cells. Kiss1 expression was not altered, as was expected by the finding that most Kiss1-expressing cells were not in the Ptf1a lineage.