A total of ten control and ten PD midbrains were imaged and quantified for the following sets of markers: TH/AGTR1/SOX6 and TH/CALB1/TMEM200A. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

Expression of AQP4 was characteristic for astrocytes [EXTERNAL REFERENCES] and FOXJ1 for ependymal cells [EXTERNAL REFERENCES]. [MT]

We utilized a panel of markers to assign nuclei to various CNS cell types, including neurons (SYT1 & SNAP25), astrocytes (AQP4 & SLC1A3), oligodendrocytes (MOBP & MBP), microglia (CD74 & ITGAM), VC (FLT1 & DCN), OPCs (VCAN & PDGFRA) and T cells (THEMIS & CD2). [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

A total of ten control and ten PD midbrains were imaged and quantified for the following sets of markers: TH/AGTR1/SOX6 and TH/CALB1/TMEM200A. [MT]

We utilized a panel of markers to assign nuclei to various CNS cell types, including neurons (SYT1 & SNAP25), astrocytes (AQP4 & SLC1A3), oligodendrocytes (MOBP & MBP), microglia (CD74 & ITGAM), VC (FLT1 & DCN), OPCs (VCAN & PDGFRA) and T cells (THEMIS & CD2). [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

Also, immune and vascular cells displayed a highly specific expression of well-known marker genes; CD74 in microglia [EXTERNAL REFERENCES], CLDN5 in endothelial cells [EXTERNAL REFERENCES] and GFRB in pericytes [EXTERNAL REFERENCES]. [MT]

We utilized a panel of markers to assign nuclei to various CNS cell types, including neurons (SYT1 & SNAP25), astrocytes (AQP4 & SLC1A3), oligodendrocytes (MOBP & MBP), microglia (CD74 & ITGAM), VC (FLT1 & DCN), OPCs (VCAN & PDGFRA) and T cells (THEMIS & CD2). [MT]

Also, immune and vascular cells displayed a highly specific expression of well-known marker genes; CD74 in microglia [EXTERNAL REFERENCES], CLDN5 in endothelial cells [EXTERNAL REFERENCES] and GFRB in pericytes [EXTERNAL REFERENCES]. [MT]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

We utilized a panel of markers to assign nuclei to various CNS cell types, including neurons (SYT1 & SNAP25), astrocytes (AQP4 & SLC1A3), oligodendrocytes (MOBP & MBP), microglia (CD74 & ITGAM), VC (FLT1 & DCN), OPCs (VCAN & PDGFRA) and T cells (THEMIS & CD2). [MT]

Canonical marker genes, Th, Slc6a3 (DAT), Ddc, and Slc18a2 (VMAT2) were strongly enriched in DA neurons, relative to other cell types. [MT]

We utilized a panel of markers to assign nuclei to various CNS cell types, including neurons (SYT1 & SNAP25), astrocytes (AQP4 & SLC1A3), oligodendrocytes (MOBP & MBP), microglia (CD74 & ITGAM), VC (FLT1 & DCN), OPCs (VCAN & PDGFRA) and T cells (THEMIS & CD2). [MT]

Expression of AQP4 was characteristic for astrocytes [EXTERNAL REFERENCES] and FOXJ1 for ependymal cells [EXTERNAL REFERENCES]. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

Regarding neuronal cells, we identified four cell types: excitatory (SLC17A6) [EXTERNAL REFERENCES], inhibitory (GAD2) [EXTERNAL REFERENCES], GABAergic (GAD2/GRIK1) [EXTERNAL REFERENCES] and, dopaminergic neurons (TH) [EXTERNAL REFERENCES]. [MT]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

Regarding neuronal cells, we identified four cell types: excitatory (SLC17A6) [EXTERNAL REFERENCES], inhibitory (GAD2) [EXTERNAL REFERENCES], GABAergic (GAD2/GRIK1) [EXTERNAL REFERENCES] and, dopaminergic neurons (TH) [EXTERNAL REFERENCES]. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

Also, immune and vascular cells displayed a highly specific expression of well-known marker genes; CD74 in microglia [EXTERNAL REFERENCES], CLDN5 in endothelial cells [EXTERNAL REFERENCES] and GFRB in pericytes [EXTERNAL REFERENCES]. [MT]

Regarding neuronal cells, we identified four cell types: excitatory (SLC17A6) [EXTERNAL REFERENCES], inhibitory (GAD2) [EXTERNAL REFERENCES], GABAergic (GAD2/GRIK1) [EXTERNAL REFERENCES] and, dopaminergic neurons (TH) [EXTERNAL REFERENCES]. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

First, we confirmed the increased fraction of microglia in idiopathic Parkinson’s disease midbrains by labelling it with an antibody against the marker protein IBA1. [MT]

We utilized a panel of markers to assign nuclei to various CNS cell types, including neurons (SYT1 & SNAP25), astrocytes (AQP4 & SLC1A3), oligodendrocytes (MOBP & MBP), microglia (CD74 & ITGAM), VC (FLT1 & DCN), OPCs (VCAN & PDGFRA) and T cells (THEMIS & CD2). [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

We utilized a panel of markers to assign nuclei to various CNS cell types, including neurons (SYT1 & SNAP25), astrocytes (AQP4 & SLC1A3), oligodendrocytes (MOBP & MBP), microglia (CD74 & ITGAM), VC (FLT1 & DCN), OPCs (VCAN & PDGFRA) and T cells (THEMIS & CD2). [MT]

Oligodendrocytes, the most abundant cell type in the midbrain, were characterized by the expression of MOBP [EXTERNAL REFERENCES]. [MT]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

We utilized a panel of markers to assign nuclei to various CNS cell types, including neurons (SYT1 & SNAP25), astrocytes (AQP4 & SLC1A3), oligodendrocytes (MOBP & MBP), microglia (CD74 & ITGAM), VC (FLT1 & DCN), OPCs (VCAN & PDGFRA) and T cells (THEMIS & CD2). [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

In a scRNA-seq dataset of mouse midbrain22, we identified the gene Nr4a2 encoding a TF as specific to mammalian midbrain DA neurons. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

We utilized a panel of markers to assign nuclei to various CNS cell types, including neurons (SYT1 & SNAP25), astrocytes (AQP4 & SLC1A3), oligodendrocytes (MOBP & MBP), microglia (CD74 & ITGAM), VC (FLT1 & DCN), OPCs (VCAN & PDGFRA) and T cells (THEMIS & CD2). [MT]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

Regarding neuronal cells, we identified four cell types: excitatory (SLC17A6) [EXTERNAL REFERENCES], inhibitory (GAD2) [EXTERNAL REFERENCES], GABAergic (GAD2/GRIK1) [EXTERNAL REFERENCES] and, dopaminergic neurons (TH) [EXTERNAL REFERENCES]. [MT]

Canonical marker genes, Th, Slc6a3 (DAT), Ddc, and Slc18a2 (VMAT2) were strongly enriched in DA neurons, relative to other cell types. [MT]

To accomplish this, we subsetted our macaque midbrain data to DA neurons only (defined by expression of TH, SLC6A3 and SLC18A2). [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

We utilized a panel of markers to assign nuclei to various CNS cell types, including neurons (SYT1 & SNAP25), astrocytes (AQP4 & SLC1A3), oligodendrocytes (MOBP & MBP), microglia (CD74 & ITGAM), VC (FLT1 & DCN), OPCs (VCAN & PDGFRA) and T cells (THEMIS & CD2). [MT]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

To accomplish this, we subsetted our macaque midbrain data to DA neurons only (defined by expression of TH, SLC6A3 and SLC18A2). [MT]

Canonical marker genes, Th, Slc6a3 (DAT), Ddc, and Slc18a2 (VMAT2) were strongly enriched in DA neurons, relative to other cell types. [MT]

For example, neurons were distinguished from glia by the expression of Snap25 and by patterned localization in regions, such as the hippocampus or thalamus. [MT]

We utilized a panel of markers to assign nuclei to various CNS cell types, including neurons (SYT1 & SNAP25), astrocytes (AQP4 & SLC1A3), oligodendrocytes (MOBP & MBP), microglia (CD74 & ITGAM), VC (FLT1 & DCN), OPCs (VCAN & PDGFRA) and T cells (THEMIS & CD2). [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

A total of ten control and ten PD midbrains were imaged and quantified for the following sets of markers: TH/AGTR1/SOX6 and TH/CALB1/TMEM200A. [MT]

We utilized a panel of markers to assign nuclei to various CNS cell types, including neurons (SYT1 & SNAP25), astrocytes (AQP4 & SLC1A3), oligodendrocytes (MOBP & MBP), microglia (CD74 & ITGAM), VC (FLT1 & DCN), OPCs (VCAN & PDGFRA) and T cells (THEMIS & CD2). [MT]

Canonical marker genes, Th, Slc6a3 (DAT), Ddc, and Slc18a2 (VMAT2) were strongly enriched in DA neurons, relative to other cell types. [MT]

To accomplish this, we subsetted our macaque midbrain data to DA neurons only (defined by expression of TH, SLC6A3 and SLC18A2). [MT]

Regarding neuronal cells, we identified four cell types: excitatory (SLC17A6) [EXTERNAL REFERENCES], inhibitory (GAD2) [EXTERNAL REFERENCES], GABAergic (GAD2/GRIK1) [EXTERNAL REFERENCES] and, dopaminergic neurons (TH) [EXTERNAL REFERENCES]. [MT]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

A total of ten control and ten PD midbrains were imaged and quantified for the following sets of markers: TH/AGTR1/SOX6 and TH/CALB1/TMEM200A. [MT]

A total of ten control and ten PD midbrains were imaged and quantified for the following sets of markers: TH/AGTR1/SOX6 and TH/CALB1/TMEM200A. [MT]

We utilized a panel of markers to assign nuclei to various CNS cell types, including neurons (SYT1 & SNAP25), astrocytes (AQP4 & SLC1A3), oligodendrocytes (MOBP & MBP), microglia (CD74 & ITGAM), VC (FLT1 & DCN), OPCs (VCAN & PDGFRA) and T cells (THEMIS & CD2). [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

A total of ten control and ten PD midbrains were imaged and quantified for the following sets of markers: TH/AGTR1/SOX6 and TH/CALB1/TMEM200A. [MT]

Oligodendrocytes, astrocytes, microglia, and erythrocytes were readily identifiable by marker expression: oligodendrocytes, Olig1, Mbp, Sox10, Mog; astrocytes: Gfap, Slc1a3, Atp1a2, Mt3; microglia, Tyrobp/Dap12, Ftl1, Cts(a/b/d/f/h/l/s/z), Aif1, Tmem119, Cd68; erythrocytes, Hba- and Hbb- genes. [MT]

OPCs highly express VCAN [EXTERNAL REFERENCES]. [MT]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

We utilized a panel of markers to assign nuclei to various CNS cell types, including neurons (SYT1 & SNAP25), astrocytes (AQP4 & SLC1A3), oligodendrocytes (MOBP & MBP), microglia (CD74 & ITGAM), VC (FLT1 & DCN), OPCs (VCAN & PDGFRA) and T cells (THEMIS & CD2). [MT]

This population also expressed members of the heat shock protein family (HSPA and HSP90), as well as genes associated with dopamine secretion/metabolic processes/transport (e.g., SYT11, KCNA2 and ABAT) [MT]

Microglia3 was characterized by expression of ABCA1, MITF and STARD13. [MT]

[SM]

Pathway over-representation analysis, using the specific marker genes identified for this subpopulation, identified pathways predominantly associated with the metabolism of fatty acids (e.g., PTGES3, ABHD3, ADIPOR2 and ABHD2) and the UPR (e.g., BAG3, SERPINH1, DNAJB1 and HSPB1), suggesting a reactive-astrocyte identity [EXTERNAL REFERENCES]. [MT]

Pathway over-representation analysis, using the specific marker genes identified for this subpopulation, identified pathways predominantly associated with the metabolism of fatty acids (e.g., PTGES3, ABHD3, ADIPOR2 and ABHD2) and the UPR (e.g., BAG3, SERPINH1, DNAJB1 and HSPB1), suggesting a reactive-astrocyte identity [EXTERNAL REFERENCES]. [MT]

Similarly, Microglia1 was also positive for markers associated with apoptosis (e.g., FOS and ACTG1). [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

First, we identified five astrocyte subpopulations characterized by high expression of VAV3, LRRC4C, ELMO1, ADGRV1 and CD44. [MT]

Pathway over-representation analysis, using the specific marker genes identified for this subpopulation, identified pathways predominantly associated with the metabolism of fatty acids (e.g., PTGES3, ABHD3, ADIPOR2 and ABHD2) and the UPR (e.g., BAG3, SERPINH1, DNAJB1 and HSPB1), suggesting a reactive-astrocyte identity [EXTERNAL REFERENCES]. [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

The SOX6_AGTR1 population was the most strongly enriched in the ventral tier, consistent with previous marker analyses performed on laser-capture microdissection subsets of A9 DA neurons [EXTERNAL REFERENCES], while the CALB1_GEM and CALB1_TRHR populations were strongly enriched in the dorsal tier [EXTERNAL REFERENCES]. [MT]

smFISH of the human midbrain confirmed localization of the SOX6_AGTR1 subtype to the ventral tier and types CALB1_GEM and CALB1_TRHR to the dorsal tier. [MT]

[SM]

[SM]

A single subtype, marked by the expression of the gene AGTR1 and spatially confined to the ventral tier of SNpc, was highly susceptible to loss in PD and showed the strongest upregulation of targets of TP53 and NR2F2, nominating molecular processes associated with degeneration. [Ab]

We also observed high expression of AGTR1 in this population, which has previously been linked to a subpopulation of DA neurons highly vulnerable to PD [EXTERNAL REFERENCES]. [MT]

Two-hundred and twenty differentially expressed genes were identified between the two subpopulations (FDR-adjusted p < 0.05), including established (VTA, Calb1, Calb2; SN, Kcnj6 [Girk2], Cplx1) and putative markers (SN, Ndnf, Rab3c, Rab6b; VTA, Ahi1, Nnat). [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Spatial representation of region-specific marker expression (Calb1 is VTA; Cplx1, Aldh1a1, Rab3c are SN). [FL]

This revealed a gradient of expression aligning with the SN (e.g., Cplx1, Nrip3) and VTA (e.g., Calb1, Aldh1a1) of the ventral midbrain. [MT]

We found Neurons0 to be characterized by key markers associated with dopaminergic neurons, including TH, SLC6A3, SNCA, and ALDH1A1, highlighting that the primary subpopulation lost in PD samples is DA neurons. [MT]

This population is also enriched in transcripts linked to axon development and synapse organization (e.g., UCHL1, NEFL, MAP1B and NRXN3), transcripts linked to ion transport (e.g., CNTN1 and ANK3) and the synaptic vesicle cycle (e.g., SLC18A2 and CALY). [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Astrocytes4 also has the highest expression of APOE, MT3 and CLU, which are associated with mitochondrial changes, oxidative stress and immune response-related processes. [MT]

Microglia4 was characterized by the high expression of APOE and SPP1. Microglia4 is the only subpopulation of microglia that expressed a high level of APOE. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Furthermore, DOCK8, a neuroinflammation-associated gene, was also highly expressed in Microglia2 (Fig. 4D), which also expressed ARHGAP family transcripts (including ARHGAP22 and ARHGAP15), which are known to be linked to alterations in the microglial activation state upon aging [EXTERNAL REFERENCES]. [MT]

Furthermore, DOCK8, a neuroinflammation-associated gene, was also highly expressed in Microglia2 (Fig. 4D), which also expressed ARHGAP family transcripts (including ARHGAP22 and ARHGAP15), which are known to be linked to alterations in the microglial activation state upon aging [EXTERNAL REFERENCES]. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Pathway analysis of subpopulation marker genes showed over-representation of key cellular processes known to be implicated in PD pathology, such as energy production (e.g., ATP1B1, ENO1 and ENO2), cholesterol metabolism (e.g., DHCR24, CYB5R3 and HDLBP), iron transport (e.g., FTL, FTH1 and SLC22A17), oxidative stress (e.g., CHCHD10, CLU and SOD1) and transcripts linked to the UPR (including chaperones, e.g., HSPA8 and HSP90AA1). [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

Similarly, we investigated the oligodendrocyte diversity and reconstructed its differentiation trajectory. We identified five subpopulations characterized by the expression of ATP6V02, OPALIN, TRPM3, ST6GAL1, and RBFOX1. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Pathway over-representation analysis, using the specific marker genes identified for this subpopulation, identified pathways predominantly associated with the metabolism of fatty acids (e.g., PTGES3, ABHD3, ADIPOR2 and ABHD2) and the UPR (e.g., BAG3, SERPINH1, DNAJB1 and HSPB1), suggesting a reactive-astrocyte identity [EXTERNAL REFERENCES]. [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Microglia4 also appears to represent a population of reactive microglia, expressing genes involved in the complement cascade (e.g., C1QC, C1QB and C1QA), the HLA system (e.g., HLA-DRA and HLA-DRB1), the UPR (e.g., HSP90 and HSPA), and the oxidative stress response (e.g., HSPA1A, TREM2, GSTP1 and HSPB1). [MT]

Microglia4 also appears to represent a population of reactive microglia, expressing genes involved in the complement cascade (e.g., C1QC, C1QB and C1QA), the HLA system (e.g., HLA-DRA and HLA-DRB1), the UPR (e.g., HSP90 and HSPA), and the oxidative stress response (e.g., HSPA1A, TREM2, GSTP1 and HSPB1). [MT]

Microglia4 also appears to represent a population of reactive microglia, expressing genes involved in the complement cascade (e.g., C1QC, C1QB and C1QA), the HLA system (e.g., HLA-DRA and HLA-DRB1), the UPR (e.g., HSP90 and HSPA), and the oxidative stress response (e.g., HSPA1A, TREM2, GSTP1 and HSPB1). [MT]

The well-known markers of reactive astrocytes, C3 and CD44, are more enriched in Astrocytes1, a subpopulation likely to represent another reactive astrocyte state [EXTERNAL REFERENCES]. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Interestingly, we also found a neuronal cluster of 120 cells, which we could not annotate initially based on known marker genes, that was characterized by high expression of CADPS2. [MT]

[SM]

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Spatial representation of region-specific marker expression (Calb1 is VTA; Cplx1, Aldh1a1, Rab3c are SN). [FL]

The SOX6_AGTR1 population was the most strongly enriched in the ventral tier, consistent with previous marker analyses performed on laser-capture microdissection subsets of A9 DA neurons [EXTERNAL REFERENCES], while the CALB1_GEM and CALB1_TRHR populations were strongly enriched in the dorsal tier [EXTERNAL REFERENCES]. [MT]

The SOX6_AGTR1 population was the most strongly enriched in the ventral tier, consistent with previous marker analyses performed on laser-capture microdissection subsets of A9 DA neurons [EXTERNAL REFERENCES], while the CALB1_GEM and CALB1_TRHR populations were strongly enriched in the dorsal tier [EXTERNAL REFERENCES]. [MT]

smFISH of the human midbrain confirmed localization of the SOX6_AGTR1 subtype to the ventral tier and types CALB1_GEM and CALB1_TRHR to the dorsal tier. [MT]

smFISH of the human midbrain confirmed localization of the SOX6_AGTR1 subtype to the ventral tier and types CALB1_GEM and CALB1_TRHR to the dorsal tier. [MT]

Four DA clusters preferentially expressed SOX6 while the other six expressed CALB1, recapitulating a well-defined developmental axis of variation within midbrain DA neurons [MT]

[SM]

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Two-hundred and twenty differentially expressed genes were identified between the two subpopulations (FDR-adjusted p < 0.05), including established (VTA, Calb1, Calb2; SN, Kcnj6 [Girk2], Cplx1) and putative markers (SN, Ndnf, Rab3c, Rab6b; VTA, Ahi1, Nnat). [MT]

[SM]

This population is also enriched in transcripts linked to axon development and synapse organization (e.g., UCHL1, NEFL, MAP1B and NRXN3), transcripts linked to ion transport (e.g., CNTN1 and ANK3) and the synaptic vesicle cycle (e.g., SLC18A2 and CALY). [MT]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

[SM]

[SM]

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Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

We recovered the astrocyte activation trajectory based on the main cell types comprising VAV3high, LRRC4Chigh, and CD44/S100A6high subpopulations. [MT]

First, we identified five astrocyte subpopulations characterized by high expression of VAV3, LRRC4C, ELMO1, ADGRV1 and CD44. [MT]

The well-known markers of reactive astrocytes, C3 and CD44, are more enriched in Astrocytes1, a subpopulation likely to represent another reactive astrocyte state [EXTERNAL REFERENCES]. [MT]

Given that CD44 expression implicates reactive astrogliosis [EXTERNAL REFERENCES], we ordered cells on the activation trajectory by setting the root in the trajectory graph-node that maximizes the distance from the CD44high branch end. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Pathway analysis of subpopulation marker genes showed over-representation of key cellular processes known to be implicated in PD pathology, such as energy production (e.g., ATP1B1, ENO1 and ENO2), cholesterol metabolism (e.g., DHCR24, CYB5R3 and HDLBP), iron transport (e.g., FTL, FTH1 and SLC22A17), oxidative stress (e.g., CHCHD10, CLU and SOD1) and transcripts linked to the UPR (including chaperones, e.g., HSPA8 and HSP90AA1). [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Astrocytes4 also has the highest expression of APOE, MT3 and CLU, which are associated with mitochondrial changes, oxidative stress and immune response-related processes. [MT]

Pathway analysis of subpopulation marker genes showed over-representation of key cellular processes known to be implicated in PD pathology, such as energy production (e.g., ATP1B1, ENO1 and ENO2), cholesterol metabolism (e.g., DHCR24, CYB5R3 and HDLBP), iron transport (e.g., FTL, FTH1 and SLC22A17), oxidative stress (e.g., CHCHD10, CLU and SOD1) and transcripts linked to the UPR (including chaperones, e.g., HSPA8 and HSP90AA1). [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

This population is also enriched in transcripts linked to axon development and synapse organization (e.g., UCHL1, NEFL, MAP1B and NRXN3), transcripts linked to ion transport (e.g., CNTN1 and ANK3) and the synaptic vesicle cycle (e.g., SLC18A2 and CALY). [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Spatial representation of region-specific marker expression (Calb1 is VTA; Cplx1, Aldh1a1, Rab3c are SN). [FL]

By contrasting DA neuron gene expression with other cell types, we identified strongly specific, yet understudied, markers, including Slc10a4 and Cpne7. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Oligos5 highly expresses CRYAB, a small heat shock protein, which is implicated in various protein aggregation-related neurodegenerative diseases, such as PD, AD, ALS and prion disorders [EXTERNAL REFERENCES]. [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

[SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Pathway analysis of subpopulation marker genes showed over-representation of key cellular processes known to be implicated in PD pathology, such as energy production (e.g., ATP1B1, ENO1 and ENO2), cholesterol metabolism (e.g., DHCR24, CYB5R3 and HDLBP), iron transport (e.g., FTL, FTH1 and SLC22A17), oxidative stress (e.g., CHCHD10, CLU and SOD1) and transcripts linked to the UPR (including chaperones, e.g., HSPA8 and HSP90AA1). [MT]

[SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

[SM]

Pathway analysis of subpopulation marker genes showed over-representation of key cellular processes known to be implicated in PD pathology, such as energy production (e.g., ATP1B1, ENO1 and ENO2), cholesterol metabolism (e.g., DHCR24, CYB5R3 and HDLBP), iron transport (e.g., FTL, FTH1 and SLC22A17), oxidative stress (e.g., CHCHD10, CLU and SOD1) and transcripts linked to the UPR (including chaperones, e.g., HSPA8 and HSP90AA1). [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Pathway over-representation analysis, using the specific marker genes identified for this subpopulation, identified pathways predominantly associated with the metabolism of fatty acids (e.g., PTGES3, ABHD3, ADIPOR2 and ABHD2) and the UPR (e.g., BAG3, SERPINH1, DNAJB1 and HSPB1), suggesting a reactive-astrocyte identity [EXTERNAL REFERENCES]. [MT]

Furthermore, DOCK8, a neuroinflammation-associated gene, was also highly expressed in Microglia2 (Fig. 4D), which also expressed ARHGAP family transcripts (including ARHGAP22 and ARHGAP15), which are known to be linked to alterations in the microglial activation state upon aging [EXTERNAL REFERENCES]. [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

First, we identified five astrocyte subpopulations characterized by high expression of VAV3, LRRC4C, ELMO1, ADGRV1 and CD44. [MT]

[SM]

The top TFs ranked by AUC per DA subtype contained many TFs previously implicated in specifying DA identity, including those encoded by the genes SOX6, OTX2, SMAD1, PBX1, LMX1B, NFE2L1 and EN2 [EXTERNAL REFERENCE]. [MT]

Pathway analysis of subpopulation marker genes showed over-representation of key cellular processes known to be implicated in PD pathology, such as energy production (e.g., ATP1B1, ENO1 and ENO2), cholesterol metabolism (e.g., DHCR24, CYB5R3 and HDLBP), iron transport (e.g., FTL, FTH1 and SLC22A17), oxidative stress (e.g., CHCHD10, CLU and SOD1) and transcripts linked to the UPR (including chaperones, e.g., HSPA8 and HSP90AA1). [MT]

Pathway analysis of subpopulation marker genes showed over-representation of key cellular processes known to be implicated in PD pathology, such as energy production (e.g., ATP1B1, ENO1 and ENO2), cholesterol metabolism (e.g., DHCR24, CYB5R3 and HDLBP), iron transport (e.g., FTL, FTH1 and SLC22A17), oxidative stress (e.g., CHCHD10, CLU and SOD1) and transcripts linked to the UPR (including chaperones, e.g., HSPA8 and HSP90AA1). [MT]

[SM]

[SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

We also observed that the Astrocytes2 subpopulation expressed transcripts involved in ubiquitination (e.g., UBB and UBC), as well as transcripts associated with endocytic vesicle trafficking, protein folding (e.g., HSP90AA1, HSP90AB1 and HSPA8), and JUN & FOS signaling, suggesting activation of apoptosis. [MT]

Similarly, Microglia1 was also positive for markers associated with apoptosis (e.g., FOS and ACTG1). [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Pathway analysis of subpopulation marker genes showed over-representation of key cellular processes known to be implicated in PD pathology, such as energy production (e.g., ATP1B1, ENO1 and ENO2), cholesterol metabolism (e.g., DHCR24, CYB5R3 and HDLBP), iron transport (e.g., FTL, FTH1 and SLC22A17), oxidative stress (e.g., CHCHD10, CLU and SOD1) and transcripts linked to the UPR (including chaperones, e.g., HSPA8 and HSP90AA1). [MT]

Like Microglia4, Oligos5 has high expression of FTL and FTH1, genes which encode proteins involved in iron storage. [MT]

Pathway analysis of subpopulation marker genes showed over-representation of key cellular processes known to be implicated in PD pathology, such as energy production (e.g., ATP1B1, ENO1 and ENO2), cholesterol metabolism (e.g., DHCR24, CYB5R3 and HDLBP), iron transport (e.g., FTL, FTH1 and SLC22A17), oxidative stress (e.g., CHCHD10, CLU and SOD1) and transcripts linked to the UPR (including chaperones, e.g., HSPA8 and HSP90AA1). [MT]

Like Microglia4, Oligos5 has high expression of FTL and FTH1, genes which encode proteins involved in iron storage. [MT]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

Neurons3 represents a second neuronal population, which was found to be significantly depleted in PD samples. We found that cells in this population were characterized by the expression of key GABAergic markers, such as GAD1, GAD2, GABRA1 and GABRB2, indicating a putative inhibitory identity (Fig. 2D, Supplementary Table 5). [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

Neurons3 represents a second neuronal population, which was found to be significantly depleted in PD samples. We found that cells in this population were characterized by the expression of key GABAergic markers, such as GAD1, GAD2, GABRA1 and GABRB2, indicating a putative inhibitory identity (Fig. 2D, Supplementary Table 5). [MT]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

Neurons3 represents a second neuronal population, which was found to be significantly depleted in PD samples. We found that cells in this population were characterized by the expression of key GABAergic markers, such as GAD1, GAD2, GABRA1 and GABRB2, indicating a putative inhibitory identity (Fig. 2D, Supplementary Table 5). [MT]

Neurons3 represents a second neuronal population, which was found to be significantly depleted in PD samples. We found that cells in this population were characterized by the expression of key GABAergic markers, such as GAD1, GAD2, GABRA1 and GABRB2, indicating a putative inhibitory identity (Fig. 2D, Supplementary Table 5). [MT]

Top marker genes of DA neurons identified from Stereo-seq and TRAP data, including less commonly recognized Slc10a4, Gap43, and Cpne7. [MT]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

The SOX6_AGTR1 population was the most strongly enriched in the ventral tier, consistent with previous marker analyses performed on laser-capture microdissection subsets of A9 DA neurons [EXTERNAL REFERENCES], while the CALB1_GEM and CALB1_TRHR populations were strongly enriched in the dorsal tier [EXTERNAL REFERENCES]. [MT]

smFISH of the human midbrain confirmed localization of the SOX6_AGTR1 subtype to the ventral tier and types CALB1_GEM and CALB1_TRHR to the dorsal tier. [MT]

[SM]

We labelled astrocytes and oligodendrocytes with antibodies against their marker proteins GFAP and PLP1, respectively [MT]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

This astrocyte subpopulation also highly expresses GFAP, a canonical marker of astrogliosis [EXTERNAL REFERENCES]. [MT]

[SM]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

While P2RY12 is highly abundant in the resting microglia [EXTERNAL REFERENCES], GPNMB [EXTERNAL REFERENCES], HSP90 [EXTERNAL REFERENCES], and IL-1β [EXTERNAL REFERENCES] are involved in the inflammatory response and have previously been linked to neurodegeneration [EXTERNAL REFERENCES] supporting the notion that the idiopathic Parkinson’s disease-specific upregulation of GPNMB and HSP90AA1 are markers of microglial activation. [MT]

While P2RY12 is highly abundant in the resting microglia [EXTERNAL REFERENCES], GPNMB [EXTERNAL REFERENCES], HSP90 [EXTERNAL REFERENCES], and IL-1β [EXTERNAL REFERENCES] are involved in the inflammatory response and have previously been linked to neurodegeneration [EXTERNAL REFERENCES] supporting the notion that the idiopathic Parkinson’s disease-specific upregulation of GPNMB and HSP90AA1 are markers of microglial activation. [MT]

We identified seven microglia subpopulations characterized by the expression of a few marker genes. The three biggest subpopulations are defined by the high expression of P2RY12, GPNMB, and HSP90AA1. [MT]

[SM]

[SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Microglia4 also appears to represent a population of reactive microglia, expressing genes involved in the complement cascade (e.g., C1QC, C1QB and C1QA), the HLA system (e.g., HLA-DRA and HLA-DRB1), the UPR (e.g., HSP90 and HSPA), and the oxidative stress response (e.g., HSPA1A, TREM2, GSTP1 and HSPB1). [MT]

[SM]

Pathway analysis of subpopulation marker genes showed over-representation of key cellular processes known to be implicated in PD pathology, such as energy production (e.g., ATP1B1, ENO1 and ENO2), cholesterol metabolism (e.g., DHCR24, CYB5R3 and HDLBP), iron transport (e.g., FTL, FTH1 and SLC22A17), oxidative stress (e.g., CHCHD10, CLU and SOD1) and transcripts linked to the UPR (including chaperones, e.g., HSPA8 and HSP90AA1). [MT]

Microglia4 also appears to represent a population of reactive microglia, expressing genes involved in the complement cascade (e.g., C1QC, C1QB and C1QA), the HLA system (e.g., HLA-DRA and HLA-DRB1), the UPR (e.g., HSP90 and HSPA), and the oxidative stress response (e.g., HSPA1A, TREM2, GSTP1 and HSPB1). [MT]

Microglia4 also appears to represent a population of reactive microglia, expressing genes involved in the complement cascade (e.g., C1QC, C1QB and C1QA), the HLA system (e.g., HLA-DRA and HLA-DRB1), the UPR (e.g., HSP90 and HSPA), and the oxidative stress response (e.g., HSPA1A, TREM2, GSTP1 and HSPB1). [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

While P2RY12 is highly abundant in the resting microglia [EXTERNAL REFERENCES], GPNMB [EXTERNAL REFERENCES], HSP90 [EXTERNAL REFERENCES], and IL-1β [EXTERNAL REFERENCES] are involved in the inflammatory response and have previously been linked to neurodegeneration [EXTERNAL REFERENCES] supporting the notion that the idiopathic Parkinson’s disease-specific upregulation of GPNMB and HSP90AA1 are markers of microglial activation. [MT]

Microglia4 also appears to represent a population of reactive microglia, expressing genes involved in the complement cascade (e.g., C1QC, C1QB and C1QA), the HLA system (e.g., HLA-DRA and HLA-DRB1), the UPR (e.g., HSP90 and HSPA), and the oxidative stress response (e.g., HSPA1A, TREM2, GSTP1 and HSPB1). [MT]

This population also expressed members of the heat shock protein family (HSPA and HSP90), as well as genes associated with dopamine secretion/metabolic processes/transport (e.g., SYT11, KCNA2 and ABAT). [MT]

We also observed that the Astrocytes2 subpopulation expressed transcripts involved in ubiquitination (e.g., UBB and UBC), as well as transcripts associated with endocytic vesicle trafficking, protein folding (e.g., HSP90AA1, HSP90AB1 and HSPA8), and JUN & FOS signaling, suggesting activation of apoptosis. [MT]

While P2RY12 is highly abundant in the resting microglia [EXTERNAL REFERENCES], GPNMB [EXTERNAL REFERENCES], HSP90 [EXTERNAL REFERENCES], and IL-1β [EXTERNAL REFERENCES] are involved in the inflammatory response and have previously been linked to neurodegeneration [EXTERNAL REFERENCES] supporting the notion that the idiopathic Parkinson’s disease-specific upregulation of GPNMB and HSP90AA1 are markers of microglial activation. [MT]

We identified seven microglia subpopulations characterized by the expression of a few marker genes. The three biggest subpopulations are defined by the high expression of P2RY12, GPNMB, and HSP90AA1. [MT]

Furthermore, this population expresses a high number of transcripts linked to processes involved in the UPR (e.g., HSP90AA1, HSP90AB1 and HSPA8), like we observed for Astrocytes2. [MT]

Pathway analysis of subpopulation marker genes showed over-representation of key cellular processes known to be implicated in PD pathology, such as energy production (e.g., ATP1B1, ENO1 and ENO2), cholesterol metabolism (e.g., DHCR24, CYB5R3 and HDLBP), iron transport (e.g., FTL, FTH1 and SLC22A17), oxidative stress (e.g., CHCHD10, CLU and SOD1) and transcripts linked to the UPR (including chaperones, e.g., HSPA8 and HSP90AA1). [MT]

We also observed that the Astrocytes2 subpopulation expressed transcripts involved in ubiquitination (e.g., UBB and UBC), as well as transcripts associated with endocytic vesicle trafficking, protein folding (e.g., HSP90AA1, HSP90AB1 and HSPA8), and JUN & FOS signaling, suggesting activation of apoptosis. [MT]

Furthermore, this population expresses a high number of transcripts linked to processes involved in the UPR (e.g., HSP90AA1, HSP90AB1 and HSPA8), like we observed for Astrocytes2. [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

Microglia4 also appears to represent a population of reactive microglia, expressing genes involved in the complement cascade (e.g., C1QC, C1QB and C1QA), the HLA system (e.g., HLA-DRA and HLA-DRB1), the UPR (e.g., HSP90 and HSPA), and the oxidative stress response (e.g., HSPA1A, TREM2, GSTP1 and HSPB1). [MT]

This population also expressed members of the heat shock protein family (HSPA and HSP90), as well as genes associated with dopamine secretion/metabolic processes/transport (e.g., SYT11, KCNA2 and ABAT) [MT]

Microglia4 also appears to represent a population of reactive microglia, expressing genes involved in the complement cascade (e.g., C1QC, C1QB and C1QA), the HLA system (e.g., HLA-DRA and HLA-DRB1), the UPR (e.g., HSP90 and HSPA), and the oxidative stress response (e.g., HSPA1A, TREM2, GSTP1 and HSPB1). [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

We also observed that the Astrocytes2 subpopulation expressed transcripts involved in ubiquitination (e.g., UBB and UBC), as well as transcripts associated with endocytic vesicle trafficking, protein folding (e.g., HSP90AA1, HSP90AB1 and HSPA8), and JUN & FOS signaling, suggesting activation of apoptosis. [MT]

Furthermore, this population expresses a high number of transcripts linked to processes involved in the UPR (e.g., HSP90AA1, HSP90AB1 and HSPA8), like we observed for Astrocytes2. [MT]

Pathway analysis of subpopulation marker genes showed over-representation of key cellular processes known to be implicated in PD pathology, such as energy production (e.g., ATP1B1, ENO1 and ENO2), cholesterol metabolism (e.g., DHCR24, CYB5R3 and HDLBP), iron transport (e.g., FTL, FTH1 and SLC22A17), oxidative stress (e.g., CHCHD10, CLU and SOD1) and transcripts linked to the UPR (including chaperones, e.g., HSPA8 and HSP90AA1). [MT]

Pathway over-representation analysis, using the specific marker genes identified for this subpopulation, identified pathways predominantly associated with the metabolism of fatty acids (e.g., PTGES3, ABHD3, ADIPOR2 and ABHD2) and the UPR (e.g., BAG3, SERPINH1, DNAJB1 and HSPB1), suggesting a reactive-astrocyte identity [EXTERNAL REFERENCES]. [MT]

Microglia4 also appears to represent a population of reactive microglia, expressing genes involved in the complement cascade (e.g., C1QC, C1QB and C1QA), the HLA system (e.g., HLA-DRA and HLA-DRB1), the UPR (e.g., HSP90 and HSPA), and the oxidative stress response (e.g., HSPA1A, TREM2, GSTP1 and HSPB1). [MT]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

We observed the strongest expression of SLC44A1, the gene encoding the choline transporter-like protein 1, in Neurons4, whereas Neurons2 had the highest expression of HTR2C. [MT]

[SM]

While P2RY12 is highly abundant in the resting microglia [EXTERNAL REFERENCES], GPNMB [EXTERNAL REFERENCES], HSP90 [EXTERNAL REFERENCES], and IL-1β [EXTERNAL REFERENCES] are involved in the inflammatory response and have previously been linked to neurodegeneration [EXTERNAL REFERENCES] supporting the notion that the idiopathic Parkinson’s disease-specific upregulation of GPNMB and HSP90AA1 are markers of microglial activation. [MT]

[SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

We also observed that the Astrocytes2 subpopulation expressed transcripts involved in ubiquitination (e.g., UBB and UBC), as well as transcripts associated with endocytic vesicle trafficking, protein folding (e.g., HSP90AA1, HSP90AB1 and HSPA8), and JUN & FOS signaling, suggesting activation of apoptosis. [MT]

This population also expressed members of the heat shock protein family (HSPA and HSP90), as well as genes associated with dopamine secretion/metabolic processes/transport (e.g., SYT11, KCNA2 and ABAT) [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

We also observed the expression of other dopaminergic markers, such as SLC18A2 and KCNJ6. [MT]

Two-hundred and twenty differentially expressed genes were identified between the two subpopulations (FDR-adjusted p < 0.05), including established (VTA, Calb1, Calb2; SN, Kcnj6 [Girk2], Cplx1) and putative markers (SN, Ndnf, Rab3c, Rab6b; VTA, Ahi1, Nnat). [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

The top TFs ranked by AUC per DA subtype contained many TFs previously implicated in specifying DA identity, including those encoded by the genes SOX6, OTX2, SMAD1, PBX1, LMX1B, NFE2L1 and EN2 [EXTERNAL REFERENCE]. [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

First, we identified five astrocyte subpopulations characterized by high expression of VAV3, LRRC4C, ELMO1, ADGRV1 and CD44. [MT]

We recovered the astrocyte activation trajectory based on the main cell types comprising VAV3high, LRRC4Chigh, and CD44/S100A6high subpopulations. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

This population is also enriched in transcripts linked to axon development and synapse organization (e.g., UCHL1, NEFL, MAP1B and NRXN3), transcripts linked to ion transport (e.g., CNTN1 and ANK3) and the synaptic vesicle cycle (e.g., SLC18A2 and CALY). [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Microglia3 was characterized by expression of ABCA1, MITF and STARD13. [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Astrocytes4 was enriched in PD samples and expressed high levels of various metallothionein genes (e.g., MT2A, MT1E and MT3) [MT]

Astrocytes4 was enriched in PD samples and expressed high levels of various metallothionein genes (e.g., MT2A, MT1E and MT3) [MT]

Astrocytes4 was enriched in PD samples and expressed high levels of various metallothionein genes (e.g., MT2A, MT1E and MT3) [MT]

Astrocytes4 also has the highest expression of APOE, MT3 and CLU, which are associated with mitochondrial changes, oxidative stress and immune response-related processes. [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Two-hundred and twenty differentially expressed genes were identified between the two subpopulations (FDR-adjusted p < 0.05), including established (VTA, Calb1, Calb2; SN, Kcnj6 [Girk2], Cplx1) and putative markers (SN, Ndnf, Rab3c, Rab6b; VTA, Ahi1, Nnat). [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

This population is also enriched in transcripts linked to axon development and synapse organization (e.g., UCHL1, NEFL, MAP1B and NRXN3), transcripts linked to ion transport (e.g., CNTN1 and ANK3) and the synaptic vesicle cycle (e.g., SLC18A2 and CALY). [MT]

The top TFs ranked by AUC per DA subtype contained many TFs previously implicated in specifying DA identity, including those encoded by the genes SOX6, OTX2, SMAD1, PBX1, LMX1B, NFE2L1 and EN2 [EXTERNAL REFERENCE]. [MT]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Two-hundred and twenty differentially expressed genes were identified between the two subpopulations (FDR-adjusted p < 0.05), including established (VTA, Calb1, Calb2; SN, Kcnj6 [Girk2], Cplx1) and putative markers (SN, Ndnf, Rab3c, Rab6b; VTA, Ahi1, Nnat). [MT]

[SM]

The NR4A2-sorted profiles were 70-fold enriched for DA neurons, defined by a cluster with joint expression of TH, SLC6A3 and SLC18A2, genes whose products are essential for DA neurotransmission [EXTERNAL REFERENCE]. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

This revealed a gradient of expression aligning with the SN (e.g., Cplx1, Nrip3) and VTA (e.g., Calb1, Aldh1a1) of the ventral midbrain. [MT]

This population is also enriched in transcripts linked to axon development and synapse organization (e.g., UCHL1, NEFL, MAP1B and NRXN3), transcripts linked to ion transport (e.g., CNTN1 and ANK3) and the synaptic vesicle cycle (e.g., SLC18A2 and CALY). [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

Oligos3 expresses high levels of OPALIN, a marker of myelinating oligodendrocytes [EXTERNAL REFERENCES]. [MT]

Similarly, we investigated the oligodendrocyte diversity and reconstructed its differentiation trajectory. We identified five subpopulations characterized by the expression of ATP6V02, OPALIN, TRPM3, ST6GAL1, and RBFOX1. [MT]

OPALIN (also denominated as Tmem) is a marker of myelinating oligodendrocytes [EXTERNAL REFERENCES], while S100B has been associated with glial stress response in Parkinson’s disease post-mortem midbrain [EXTERNAL REFERENCES]. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

[SM]

The top TFs ranked by AUC per DA subtype contained many TFs previously implicated in specifying DA identity, including those encoded by the genes SOX6, OTX2, SMAD1, PBX1, LMX1B, NFE2L1 and EN2 [EXTERNAL REFERENCE]. [MT]

Comparison of Otx2 and Sox6 detection rate by region, demonstrating greater expression in VTA and SN, respectively. [FL]

[SM]

[SM]

While P2RY12 is highly abundant in the resting microglia [EXTERNAL REFERENCES], GPNMB [EXTERNAL REFERENCES], HSP90 [EXTERNAL REFERENCES], and IL-1β [EXTERNAL REFERENCES] are involved in the inflammatory response and have previously been linked to neurodegeneration [EXTERNAL REFERENCES] supporting the notion that the idiopathic Parkinson’s disease-specific upregulation of GPNMB and HSP90AA1 are markers of microglial activation. [MT]

We identified seven microglia subpopulations characterized by the expression of a few marker genes. The three biggest subpopulations are defined by the high expression of P2RY12, GPNMB, and HSP90AA1. [MT]

Among the markers of Microglia2, P2RY12 stands out as a P2Y receptor involved in microglial motility and migration towards (damaged) cells releasing ATP, an initiating event in neuroinflammation [EXTERNAL REFERENCES]. [MT]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

[SM]

[SM]

[SM]

The top TFs ranked by AUC per DA subtype contained many TFs previously implicated in specifying DA identity, including those encoded by the genes SOX6, OTX2, SMAD1, PBX1, LMX1B, NFE2L1 and EN2 [EXTERNAL REFERENCE]. [MT]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

PEG10, a DNA-binding protein coding gene, was another notable highly expressed cell marker [EXTERNAL REFERENCES]. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

We labelled astrocytes and oligodendrocytes with antibodies against their marker proteins GFAP and PLP1, respectively. [MT]

[SM]

[SM]

[SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

We identified ten distinct cell populations across all samples within the SN, which included (i) astrocytes (GFAP) with two subtypes: astrocyte-1 population expressing neuro-inflammatory genes (OLR1) and an astrocyte-2 (GINS3) population expressing genes associated with growth and reparative functions [EXTERNAL REFERENCES], (ii) ODCs (MOG, MOBP) with three subtypes discriminated by oligodendrocyte marker genes PALM2, LGALS1 & PPM1G, (iii) endothelial cells (RGS5), (iv) microglia cells (CSF1R), (v) OPCs (VCAN), (vi) DaNs (TH and SLC6A3), neuronal population of the SN pars compacta and (vii) GABAergic neurons, neuronal population of the SN pars reticulata expressing GABA receptors GABRA1 and GABRB2 and the enzymes GAD1 and GAD2 required for GABA neurotransmitter synthesis. [MT]

[SM]

[SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Pathway over-representation analysis, using the specific marker genes identified for this subpopulation, identified pathways predominantly associated with the metabolism of fatty acids (e.g., PTGES3, ABHD3, ADIPOR2 and ABHD2) and the UPR (e.g., BAG3, SERPINH1, DNAJB1 and HSPB1), suggesting a reactive-astrocyte identity [EXTERNAL REFERENCES]. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Spatial representation of region-specific marker expression (Calb1 is VTA; Cplx1, Aldh1a1, Rab3c are SN). [FL]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Two-hundred and twenty differentially expressed genes were identified between the two subpopulations (FDR-adjusted p < 0.05), including established (VTA, Calb1, Calb2; SN, Kcnj6 [Girk2], Cplx1) and putative markers (SN, Ndnf, Rab3c, Rab6b; VTA, Ahi1, Nnat). [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Similarly, we investigated the oligodendrocyte diversity and reconstructed its differentiation trajectory. We identified five subpopulations characterized by the expression of ATP6V02, OPALIN, TRPM3, ST6GAL1, and RBFOX1. [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

This subpopulation is the only microglial subpopulation that expressed high levels of SRGAP1, SH3PXD2A and RGL1. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

We recovered the astrocyte activation trajectory based on the main cell types comprising VAV3high, LRRC4Chigh, and CD44/S100A6high subpopulations. [MT]

Oligos5 also highly expresses S100B, which has been associated with the glial stress response in the midbrain of PD patients [EXTERNAL REFERENCES]. [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Pathway over-representation analysis, using the specific marker genes identified for this subpopulation, identified pathways predominantly associated with the metabolism of fatty acids (e.g., PTGES3, ABHD3, ADIPOR2 and ABHD2) and the UPR (e.g., BAG3, SERPINH1, DNAJB1 and HSPB1), suggesting a reactive-astrocyte identity [EXTERNAL REFERENCES]. [MT]

[SM]

This subpopulation is the only microglial subpopulation that expressed high levels of SRGAP1, SH3PXD2A and RGL1. [MT]

[SM]

[SM]

By contrasting DA neuron gene expression with other cell types, we identified strongly specific, yet understudied, markers, including Slc10a4 and Cpne7. [MT]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

The NR4A2-sorted profiles were 70-fold enriched for DA neurons, defined by a cluster with joint expression of TH, SLC6A3 and SLC18A2, genes whose products are essential for DA neurotransmission [EXTERNAL REFERENCE]. [MT]

We also observed the expression of other dopaminergic markers, such as SLC18A2 and KCNJ6. [MT]

This population is also enriched in transcripts linked to axon development and synapse organization (e.g., UCHL1, NEFL, MAP1B and NRXN3), transcripts linked to ion transport (e.g., CNTN1 and ANK3) and the synaptic vesicle cycle (e.g., SLC18A2 and CALY). [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Pathway analysis of subpopulation marker genes showed over-representation of key cellular processes known to be implicated in PD pathology, such as energy production (e.g., ATP1B1, ENO1 and ENO2), cholesterol metabolism (e.g., DHCR24, CYB5R3 and HDLBP), iron transport (e.g., FTL, FTH1 and SLC22A17), oxidative stress (e.g., CHCHD10, CLU and SOD1) and transcripts linked to the UPR (including chaperones, e.g., HSPA8 and HSP90AA1). [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

We observed the strongest expression of SLC44A1, the gene encoding the choline transporter-like protein 1, in Neurons4, whereas Neurons2 had the highest expression of serotonin 5-HT-2C receptor (HTR2C) [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Marker gene analysis revealed that Astrocytes2 showed enrichment for key genes linked to dopamine metabolism, including SLC6A3, SNCA, and importantly TH, suggesting that the vulnerability of TH enriched neurons in PD may be extended to other cell types. [MT]

The A9 group was easily identifiable by visualizing the expression of DA neuron markers TH and SLC6A3 [EXTERNAL REFERENCES]. [MT]

The NR4A2-sorted profiles were 70-fold enriched for DA neurons, defined by a cluster with joint expression of TH, SLC6A3 and SLC18A2, genes whose products are essential for DA neurotransmission [EXTERNAL REFERENCE]. [MT]

We found Neurons0 to be characterized by key markers associated with dopaminergic neurons, including TH, SLC6A3, SNCA, and ALDH1A1, highlighting that the primary subpopulation lost in PD samples is DA neurons. [MT]

Like Astrocytes2 and Microglia1, Oligos2 represents a population enriched for TH, SLC6A3 and SNCG (genes associated with dopamine metabolism) and it is largely depleted in sporadic PD samples. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

The top TFs ranked by AUC per DA subtype contained many TFs previously implicated in specifying DA identity, including those encoded by the genes SOX6, OTX2, SMAD1, PBX1, LMX1B, NFE2L1 and EN2 [EXTERNAL REFERENCE]. [MT]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Marker gene analysis revealed that Astrocytes2 showed enrichment for key genes linked to dopamine metabolism, including SLC6A3, SNCA, and importantly TH, suggesting that the vulnerability of TH enriched neurons in PD may be extended to other cell types. [MT]

We found Neurons0 to be characterized by key markers associated with dopaminergic neurons, including TH, SLC6A3, SNCA, and ALDH1A1, highlighting that the primary subpopulation lost in PD samples is DA neurons. [MT]

Like Astrocytes2 and Microglia1, Oligos2 represents a population enriched for TH, SLC6A3 and SNCG (genes associated with dopamine metabolism) and it is largely depleted in sporadic PD samples. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Pathway analysis of subpopulation marker genes showed over-representation of key cellular processes known to be implicated in PD pathology, such as energy production (e.g., ATP1B1, ENO1 and ENO2), cholesterol metabolism (e.g., DHCR24, CYB5R3 and HDLBP), iron transport (e.g., FTL, FTH1 and SLC22A17), oxidative stress (e.g., CHCHD10, CLU and SOD1) and transcripts linked to the UPR (including chaperones, e.g., HSPA8 and HSP90AA1). [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Comparison of Otx2 and Sox6 detection rate by region, demonstrating greater expression in VTA and SN, respectively. [FL]

The top TFs ranked by AUC per DA subtype contained many TFs previously implicated in specifying DA identity, including those encoded by the genes SOX6, OTX2, SMAD1, PBX1, LMX1B, NFE2L1 and EN2 [EXTERNAL REFERENCE]. [MT]

Four DA clusters preferentially expressed SOX6 while the other six expressed CALB1, recapitulating a well-defined developmental axis of variation within midbrain DA neurons [MT]

The SOX6_AGTR1 population was the most strongly enriched in the ventral tier, consistent with previous marker analyses performed on laser-capture microdissection subsets of A9 DA neurons [EXTERNAL REFERENCES], while the CALB1_GEM and CALB1_TRHR populations were strongly enriched in the dorsal tier [EXTERNAL REFERENCES]. [MT]

smFISH of the human midbrain confirmed localization of the SOX6_AGTR1 subtype to the ventral tier and types CALB1_GEM and CALB1_TRHR to the dorsal tier. [MT]

[SM]

[SM]

[SM]

[SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

[SM]

Microglia4 was characterized by the high expression of APOE and SPP1. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

This subpopulation is the only microglial subpopulation that expressed high levels of SRGAP1, SH3PXD2A and RGL1. [MT]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Similarly, we investigated the oligodendrocyte diversity and reconstructed its differentiation trajectory. We identified five subpopulations characterized by the expression of ATP6V02, OPALIN, TRPM3, ST6GAL1, and RBFOX1. [MT]

Microglia3 was characterized by expression of ABCA1, MITF and STARD13. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

This population also expressed members of the heat shock protein family (HSPA and HSP90), as well as genes associated with dopamine secretion/metabolic processes/transport (e.g., SYT11, KCNA2 and ABAT) [MT]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Marker gene analysis revealed that Astrocytes2 showed enrichment for key genes linked to dopamine metabolism, including SLC6A3, SNCA, and importantly TH, suggesting that the vulnerability of TH enriched neurons in PD may be extended to other cell types. [MT]

The A9 group was easily identifiable by visualizing the expression of DA neuron markers TH and SLC6A3 [EXTERNAL REFERENCES]. [MT]

The NR4A2-sorted profiles were 70-fold enriched for DA neurons, defined by a cluster with joint expression of TH, SLC6A3 and SLC18A2, genes whose products are essential for DA neurotransmission [EXTERNAL REFERENCE]. [MT]

As with astrocytes, we saw that one population, Microglia1, was significantly depleted in samples from patients diagnosed with sporadic PD. Marker gene analysis again revealed that this was the only microglia population enriched in markers involved in dopamine metabolism, including TH. [MT]

We found Neurons0 to be characterized by key markers associated with dopaminergic neurons, including TH, SLC6A3, SNCA, and ALDH1A1, highlighting that the primary subpopulation lost in PD samples is DA neurons. [MT]

Like Astrocytes2 and Microglia1, Oligos2 represents a population enriched for TH, SLC6A3 and SNCG (genes associated with dopamine metabolism) and it is largely depleted in sporadic PD samples. [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Microglia4 also appears to represent a population of reactive microglia, expressing genes involved in the complement cascade (e.g., C1QC, C1QB and C1QA), the HLA system (e.g., HLA-DRA and HLA-DRB1), the UPR (e.g., HSP90 and HSPA), and the oxidative stress response (e.g., HSPA1A, TREM2, GSTP1 and HSPB1). [MT]

The SOX6_AGTR1 population was the most strongly enriched in the ventral tier, consistent with previous marker analyses performed on laser-capture microdissection subsets of A9 DA neurons [EXTERNAL REFERENCES], while the CALB1_GEM and CALB1_TRHR populations were strongly enriched in the dorsal tier [EXTERNAL REFERENCES]. [MT]

smFISH of the human midbrain confirmed localization of the SOX6_AGTR1 subtype to the ventral tier and types CALB1_GEM and CALB1_TRHR to the dorsal tier. [MT]

[SM]

Similarly, we investigated the oligodendrocyte diversity and reconstructed its differentiation trajectory. We identified five subpopulations characterized by the expression of ATP6V02, OPALIN, TRPM3, ST6GAL1, and RBFOX1. [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

We also observed that the Astrocytes2 subpopulation expressed transcripts involved in ubiquitination (e.g., UBB and UBC), as well as transcripts associated with endocytic vesicle trafficking, protein folding (e.g., HSP90AA1, HSP90AB1 and HSPA8), and JUN & FOS signaling, suggesting activation of apoptosis. [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

We also observed that the Astrocytes2 subpopulation expressed transcripts involved in ubiquitination (e.g., UBB and UBC), as well as transcripts associated with endocytic vesicle trafficking, protein folding (e.g., HSP90AA1, HSP90AB1 and HSPA8), and JUN & FOS signaling, suggesting activation of apoptosis. [MT]

Pathway over-representation analysis on the markers of this population shows enrichment of terms related to oxidative stress (e.g., CRYAB, MT3, SELENOP and MAP1LC3A), the response to protein aggregates (e.g., CLU, HSPA2, HSPA1A and HSP90AB1), ATP biosynthesis (e.g., ATP5ME, ATP5F1E and ATP5MC2), mitochondrial function (e.g., MT3, UBB, UBC and UBA52) and apoptosis (e.g., FIS1, UBB, RACK1, RPS3 and NUPR1) [MT]

This population is also enriched in transcripts linked to axon development and synapse organization (e.g., UCHL1, NEFL, MAP1B and NRXN3), transcripts linked to ion transport (e.g., CNTN1 and ANK3) and the synaptic vesicle cycle (e.g., SLC18A2 and CALY). [MT]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

First, we identified five astrocyte subpopulations characterized by high expression of VAV3, LRRC4C, ELMO1, ADGRV1 and CD44. [MT]

We recovered the astrocyte activation trajectory based on the main cell types comprising VAV3high, LRRC4Chigh, and CD44/S100A6high subpopulations. [MT]

[SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

[SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.80 'Fraction of dection in cluster' and < 0.20 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

[SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]

Extracted from Supplementary table 3 using criteria > 0.85 'Fraction of dection in cluster' and < 0.15 'Fraction of detection in other clusters' (FDR was < 0.01 for all) [SM]