Skip to main content
[Preprint]. 2023 Mar 6:2023.03.06.531121. [Version 1] doi: 10.1101/2023.03.06.531121

Figure 3. Neurotransmitter types and their distribution throughout the mouse brain.

Figure 3.

(a-c) UMAP representation of neuronal subclasses containing clusters releasing glutamate-GABA dual transmitters. UMAPs are colored by subclass (a), neurotransmitter type (b), and cluster (c). Glutamate-GABA co-releasing clusters include clusters 559, 560, 563 in subclass 37, cluster 566 in subclass 38, clusters 1249, 1250, 1251 in subclass 80, clusters 1498, 1499 in subclass 93, clusters 1571, 1592, 1593 in subclass 99, clusters 2307, 2308 in subclass129, clusters 2716, 2717, 2721 in subclass 148, clusters 3469, 3480, 3482 in subclass 175, cluster 3609 in subclass 178, cluster 4073 in subclass 201, cluster 4089 in subclass 202, clusters 4496, 4498, 4499, 4501, 4502, 4505, 4506, 4514 in subclass 224, clusters 4526, 4528, 4529 in subclass 225, cluster 4653 in subclass 238, and cluster 5041 in subclass 275. Clusters in italic are shown in MERFISH sections in (j). (d) UMAPs representing the expression of neurotransmitter transporter genes for glutamate, GABA and glycine. (e-g) UMAP representation of neuronal subclasses containing clusters releasing modulatory neurotransmitters and their various combinations of co-releasing with glutamate and/or GABA. UMAPs are colored by subclass (e), neurotransmitter type (f), and cluster (g). Cholinergic neurons include clusters 795 (co-release w/ GABA), 796, 797 (w/ GABA), 798 (w/ GABA), 799 (w/ glut), 800 (w/ GABA), 801, 802, 803–805 (all w/ glut) in subclass 49; cluster 958 (w/ GABA) in subclass 59; clusters 1060–1063, 1070, 1071 and 1075 (all w/ glut) in subclass 63; clusters 3322, 3346, 3347, 3348, 3349, 3350 (all w/ glut except 3349) in subclass 170; cluster 3939 (w/ glut) in subclass 188; clusters 4847–4852 in subclass 248; and cluster 5100 in subclass 282. Dopaminergic neurons include clusters 1221–1224 (all w/ GABA) in subclass 75; clusters 2536 and 2537 (both w/ glut) in subclass 139; clusters 4856 (w/ glut-GABA), 4857 (w/ glut-GABA), 4860 (w/ glut-GABA), 4862 (w/ glut), 4863–4865, 4866 (w/ glut), 4867, 4868 (w/ glut), 4869 (w/ glut), 4870 (w/ GABA), 4871–4875, 4876 (w/ GABA), 4877–4880 (all w/ glut), 4881, 4883–4886 (all w/ glut), 4887–4890, 4891 (w/ glut-GABA), 4892, 4893 in subclass 250; and clusters 5047, 5048, 5050, 5055 (all w/ GABA) in subclass 277. Histaminergic neurons include clusters 1225 (w/ GABA), 1226 (w/ GABA), and 1227–1229 in subclass 76. Noradrenergic neurons include clusters 4823, 4824, 4826–4829, 4832 and 4840 (all w/ glut), as well as 4845 in subclass 247. Serotonergic neurons include clusters 2658, 2659, 2660–2662 (all w/ glut), 2663, 2664, 2665–2667 (all w/ glut), 2674 (w/ glut), 2680, 2681–2685 (all w/ glut), 2688 (w/ glut), and 2689 (w/ glut) in subclass 146. Clusters in italic are shown in MERFISH sections in (j). (h) UMAPs representing the expression of genes for glutamate, GABA and modulatory neurotransmitters. (i-j) Representative MERFISH sections showing the location of neuronal types with glutamate-GABA dual transmitters and those with modulatory neurotransmitters. Cells in (i) are colored and labeled by subclasses. Cells in (j) are colored by neurotransmitter/neuromodulator types and labeled by cluster IDs. See Supplementary Table 7 for detailed neurotransmitter assignment for each cluster.