Fig. 2

Transcriptome and DHS analysis reveals putative mDA transcriptional regulators. a Pie chart showing the number of genes significantly enriched in HA⁺ mDA neurons compared with VIP, Exc, and PV cortical neuron-expressed genes (FC > 4 and q-value < 0.001, FPKM > 1). b Heatmap showing the 394 genes, respectively, expressed in the HA⁺ mDA neurons, as well as VIP, Exc, and PV cortical neurons. The 107 genes significantly enriched in mDA neurons (top) are termed “mDA-enriched” genes. c Venn diagram showing the overlap between the 28,084 mDA neuron DHS sites (q-value < 0.05) with the ATAC-Seq accessible chromatin regions (q-value < 0.05) in VIP, Exc and PV cortical neurons. The 2374 DHS sites present only in mDA neurons were termed “mDA-enriched DHS”. d List of the motifs identified at the promoter DHS of mDA-enriched genes (q-value < 1e−4). Each base-pair of the motif is proportional to its information content profile⁴⁹. The Atf1 motifs with a * to indicate the low information content along all the positions, thus its motif was instead represented by the relative base frequency. The identifier under the Max motif indicate the motif PWM ID in the CIS-BP database⁵⁰. e List of motifs identified at mDA-enriched distal DHSs of mDA-enriched genes (q-value < 0.01). Each base-pair of the motif is proportional to its information content profile⁴⁹. f Heatmap showing the predicted TF regulatory score (TFRS) associating each TF to the mDA-enriched genes with a promoter DHS