Figure 7

Optimized ATAC-seq libraries return expected cellular markers. ATAC-seq peaks in marker genes for dopaminergic and GABAergic neurons. ATAC-seq reads from dopamine neurons (tyrosine hydroxylase: TH+) are shown in orange and reads from GABA (vesicular GABA transporter: vGAT+) neurons are shown in blue. The genes and gene structures are shown below the ATAC-seq peaks. (a) Peaks in chromatin regions that are more open in dopamine neurons. ple (encoding tyrosine hydroxylase; p = 2.43e−68) and DAT (dopamine transporter; p = 9.64e−7) are classical dopamine neuron markers. hth (homothorax; p = 1.16e−52) is a recently described dopamine neuron marker. ple: p = 3.32e−65 (1) and 5.01e−53 (2); DAT: p = 1.03e−05 (3) and 1.04e−05 (4); hth: p = 0.009 (5), 1.69e−36 (6), and 1.14e−21 (7). (b) Chromatin regions that are more open in GABA neurons. Gad1 (glutamic acid decarboxylase 1; p = 6.64e−8) is a classical GABAergic neuron marker, while Lim3 (Lim3; p < 0.0002) and CG14989 (uncharacterized protein; p = 0.1) are additional GABA neuron markers. Gad1: p = 0.0005 (1), 4.42e−08 (2), 0.04 (3), 0.01 (4), and 6.6e−08 (5); Lim3: p = 1.39e−05 (6) and 0.001 (7). CG14989, Lim3, and hth were described as specific markers using single-cell RNA sequencing⁴¹. The boxes in the gene structures indicate exons and the arrows indicate the transcription direction.