Resource Type,Resource Name,Source,Identifier,New/Reuse,Additonal Information 
Antibodies,Mouse anti-NeuN-488,Millipore Sigma ,Cat# MAB377X; RRID AB_2149209,Reuse,1 to 500
Antibodies,Rabbit anti-Foxp2,Abcam ,Cat# ab16046; RRID AB_2107107,Reuse,1:10k
Antibodies,Guinea Pig anti-Pou6f2,Thomas Jessell Laboratory; HHMI Columbia University,"Cat# CU1795, RRID:AB_2665425",Reuse,1:2k
Antibodies,Rabbit anti-GFP-488,Invitrogen,Cat# A-21311; RRID AB_221477,Reuse,1:1k
Antibodies,chicken anti-GFP,Aves labs,Cat# GFP-1020; RRID AB_2307313,Reuse,1:2k
Antibodies,Rabbit anti-RFP,Rockland ,Cat# 600-401-379; RRID AB_2209751,Reuse,1:2k
Antibodies,Rat anti-mCherry,Invitrogen ,Cat# M11217; AB_2536611,Reuse,1:2k
Antibodies,Mouse anti-TH ,Immunostar ,Cat# 22941; RRID AB_572268,Reuse,1:10k
Antibodies,Chicken anti-Myc,Invitrogen,Cat# A21281; RRID AB_2535826 ,Reuse,1 to 250
Antibodies,Goat anti-Chicken 488,Invitrogen,Cat# A-11039; RRID AB_2534096,Reuse,
Antibodies,Goat anti-Guinea Pig 568 ,Invitrogen,Cat# A-11075; RRID AB_2534119,Reuse,
Antibodies,Goat anti-Mouse 488,Invitrogen,Cat# A-11029; RRID AB_2534088,Reuse,
Antibodies,Goat anti-Mouse 568,Invitrogen,Cat# A-11004; RRID AB_2534072,Reuse,
Antibodies,Goat anti-Rabbit 568,Invitrogen,Cat# A-11011; RRID AB_143157,Reuse,
Antibodies,Goat anti-Rabbit 647,Invitrogen,Cat# A-21244; RRID AB_2535812,Reuse,
Antibodies,Goat anti-Rat 568,Invitrogen,Cat# A-11077; RRID AB_2534121,Reuse,
Cell Line,HEK293T,ATCC,"ATCC Cat# CRL-1573, RRID:CVCL_0045",Reuse,
Critical commercial assay,RNAscope Multiplex Fluorescent Reagent Kit v2,ACD biosciences,323136,Reuse,
Oligonucleotide,RNAscope Probe-Mm-Scn5a,ACD biosciences,429881- C1,Reuse,
Oligonucleotide,Pou6f2,ACD biosciences,839401- C1,Reuse,
Oligonucleotide,RNAscope Probe-Mm-Zfpm2,ACD biosciences,554031-C1,Reuse,
Oligonucleotide,RNAscope Probe-Mm-Foxp2,ACD biosciences,428791-C2 ,Reuse,
Oligonucleotide,RNAscope Probe-Mm-Slc32a1,ACD biosciences,319191-C2 ,Reuse,
Oligonucleotide,RNAscope Probe-Mm-Pax5,ACD biosciences,541761-C2,Reuse,
Oligonucleotide,RNAscope Probe-Mm-Tmem132c ,ACD biosciences,591841-C2,Reuse,
Oligonucleotide,RNAscope Probe-Mm-Th,ACD biosciences,317621-C3 ,Reuse,
Oligonucleotide,RNAscope Probe-EGFP,ACD biosciences,400281-C3,Reuse,
Oligonucleotide,RNAscope Probe-tdTomato,ACD biosciences,317041-C3 ,Reuse,
Oligonucleotide,RNAscope Probe-Mm-Pvalb ,ACD biosciences,421931-C3,Reuse,
Critical commercial assay,Opal 520,Akoya biosciences,FP1487001KT,Reuse,
Critical commercial assay,Opal 620,Akoya biosciences,FP1495001KT,Reuse,
Critical commercial assay,Opal 690,Akoya biosciences,FP1497001KT,Reuse,
Plasmids,AAVretro-hSyn-H2B-mCherry ,Salk Institute,RRID:SCR_014847,Reuse,
Plasmids,AAVretro-hSyn-H2B-GFP,Columbia University Zuckerman Institute Molecular Tools Core Facility,RRID:SCR_026201,Reuse,
Plasmids,AAV(DJ)-hSyn-Con/Fon EYFP-WPRE ,UNC Vector Core,RRID:SCR_023280,Reuse,
Plasmids,AAV-DJ-EF1a-ConFon-Synaptophysin-10Xmyc-WPRE,Columbia University Zuckerman Institute Molecular Tools Core Facility,RRID:SCR_026201,Reuse,
Plasmids,AAV-DJ-hSyn-FLEX_FRT-mGFP-2A-synaptophysin.mRuby,Stanford Vector Core,Cat# GVVC-AAV-101; RRID:SCR_023250,Reuse,
Plasmids,AAVretro-EF1a-Flpo ,Addgene ,Cat#55637-AAVrg; RRID:Addgene_55637,Reuse,
Plasmids,AAV8-Con/Fon-TVA-mCherry,Stanford Vector core,Cat# GVVC-AAV-197; RRID:SCR_023250,Reuse,
Plasmids,EnVA-N2c∆G-GFP,"Thomas Jefferson, Center for Neuroanatomy with Neurotropic Viruses (CNNV)",RRID:SCR_024984,Reuse,
Plasmids,EnVA-N2c∆G-tdTomato ,"Thomas Jefferson, Center for Neuroanatomy with Neurotropic Viruses (CNNV)",RRID:SCR_024984,Reuse,
Plasmids,pAAV-Con/Fon-N2cG (AAV8-Con/Fon-N2cG),Columbia University Zuckerman Institute Molecular Tools Core Facility,RRID:SCR_026201,NEW,RRID:Addgene_234709
Plasmids,pAAVDJ-Esyn-FlpX-TVA950-EYFP-WPRE,Columbia University Zuckerman Institute Molecular Tools Core Facility,RRID:SCR_026201,NEW,RRID:Addgene_234710
Plasmids,pAAVDJ-CAG-FlpX-mKate2.0-N2cG,Columbia University Zuckerman Institute Molecular Tools Core Facility,RRID:SCR_026201,NEW,RRID:Addgene_234711
Plasmids,pAAV-Ef1a-Con/Fon oG,Addgene ,Cat#131778; RRID:Addgene_131778,Reuse,
Plasmids,pCAGGS-N2c(G),Addgene ,Cat#73481; RRID:Addgene_73481,Reuse,
Plasmids,pAAV-EnhancedSynapsin-DIO-TVA950-EYFP-WPRE,Addgene ,Cat#120269; RRID:Addgene_120269,Reuse,pAAV-DIO-TVA950-eYFP
Plasmids,mKate2 (pPB-CAG-Brainbow3.2-PGK-PuroTK),Addgene ,Cat#159928; RRID:Addgene_159928,Reuse,
Experimental model: Organism/strain,C57BL/6J ,Jackson Laboratories ,Cat#000664; RRID:IMSR_JAX:000664,Reuse,
Experimental model: Organism/strain,B6.Cg-Foxp2tm1.1(cre)Rpa/J (e.g. Foxp2-Cre),Jackson Laboratories ,Cat#030541; RRID:IMSR_JAX:030541,Reuse,
Experimental model: Organism/strain,B6.Cg-Slc32a1tm1.1(flpo)Hze/J (e.g. Vgat-Flp),Jackson Laboratories ,Cat#029591; RRID:IMSR_JAX:029591,Reuse,
Experimental model: Organism/strain,B6.Cg-Gt(ROSA)26Sortm65.2(CAG-tdTomato)Hze/J (e.g. Ai65F),Jackson Laboratories ,Cat#032864; RRID:IMSR_JAX:032864,Reuse,
Experimental model: Organism/strain,Pou6f2-Flp,10.1016/j.neuron.2024.11.019,Gift from Jay Bikoff ,Reuse,
Software,Imaris,Oxford Insturments,RRID:SCR_007370,Reuse,http://www.bitplane.com/imaris/imaris
Software,Image J,National Institutes of Health (NIH),RRID:SCR_003070,Reuse,https://imagej.net/
Software,Fiji,National Institute of Health (NIH),RRID:SCR_002285,Reuse,https://fiji.sc/
Software,MapMyCells,Allen Brain Cell (ABC) Atlas,RRID:SCR_024672,Reuse,https://portal.brain-map.org/atlases-and-data/bkp/mapmycells
Software,Seurat v4.3,Satija Lab and Collaborators,RRID:SCR_016341,Reuse,https://satijalab.org/seurat/get_started.html
Software,R,R Foundation,RRID:SCR_001905,Reuse,http://www.r-project.org/
Software,Clustree,R Foundation,RRID:SCR_016293,Reuse,https://CRAN.R-project.org/package=clustree
Software,Harmony,PerkinElmer,RRID:SCR_023543,Reuse,https://portals.broadinstitute.org/harmony/index.html
Software,GraphPad,Dotmatics,RRID:SCR_000306,Reuse,http://graphpad.com/
Software,MATLAB,MathWorks,RRID:SCR_001622,Reuse,http://www.mathworks.com/products/matlab/
Software,BrainJ,"GitHub	",10.5281/zenodo.7626693,Reuse,https://github.com/lahammond/BrainJ
Software,ilastik,GitHub,RRID:SCR_015246,Reuse,http://ilastik.org/
Software,Elastix,Stefan Klein & Marius Staring,RRID:SCR_009619,Reuse,https://elastix.dev/
Software,STAR,GitHub,RRID:SCR_004463,Reuse,http://code.google.com/p/rna-star/
Software,Cell Ranger,10X Genomics ,RRID:SCR_017344,Reuse,https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
Software,CRIS.py,Connelly et al 2019,10.1038/s41598-019-40896-w,Reuse,https://github.com/patrickc01/CRIS.py
Datasets,Single nucleus RNA sequencing of projection-defined SNr neurons,Gene Expression Omnibus,GSE277660,New,
Datasets,Single nucleus RNA sequencing of SNr neurons,Gene Expression Omnibus,GSE277661,New,
Datasets,Human RNA sequencing data,Gene Expression Omnibus,GSE178265,Reuse,"A molecular census of midbrain dopaminergic neurons in Parkinsons disease; Kamath et al., 2022"
Datasets,Allen Brain Atlas Common Coordinate Framework,Allen Institute,RRID:SCR_020999,Reuse,https://atlas.brain-map.org/
Datasets,Enhanced and Unified Atlas,Kim Lab,RRID:SCR_019267,Reuse,http://kimlab.io/brain-map/atlas/
Datasets,Raw images of SNr molecular anatomy,Zenodo,10.5281/zenodo.14884056,NEW,https://zenodo.org/records/14884057
Datasets,Quantification tables of SNr molecular organization,Zenodo,10.5281/zenodo.14826481,NEW,https://zenodo.org/records/14826482
Protocol,Histology (Immunohistochemsitry protocol),Protocols.io,dx.doi.org/10.17504/protocols.io.kxygxwqywv8j/v1,New,Immunohistochemistry (Histology + Imaging)-Mendelsohn et al 2025
Protocol,Histology (In Situ Hybridization protocol),Protocols.io,dx.doi.org/10.17504/protocols.io.kxygxwq5ov8j/v1,New,In Situ Hybridization -Mendelsohn et al 2025
Protocol,Imaging,Protocols.io,dx.doi.org/10.17504/protocols.io.kxygxwqywv8j/v1,New,Immunohistochemistry (Histology + Imaging)-Mendelsohn et al 2025
Protocol,Stereotaxic viral injections,Protocols.io,dx.doi.org/10.17504/protocols.io.kxygxy6j4l8j/v1,New,Costa Lab Nanoject Virus Injections-CU
Protocol,Nuclear isolation and 10x sequencing of SNr neurons,Allen Institute,dx.doi.org/10.17504/protocols.io.7dxhi7n,Reuse,Isolation of Nuclei from Adult Mouse Brain Tissue Protocol V.1 
Protocol,10x library prep and sequencing (user guide #CG000204),10X Genomics ,n/a,Reuse,https://www.10xgenomics.com/support/universal-three-prime-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry
Protocol,Nuclear isolation and plate-based sequencing after retrograde labeling,Allen Institute,dx.doi.org/10.17504/protocols.io.7dxhi7n,Reuse,Isolation of Nuclei from Adult Mouse Brain Tissue Protocol V.1; using steps without NeuN staining 
Code ,Code for analysis of anatomical data ,Zenodo,10.5281/zenodo.14787957,NEW,Matlab scripts used to plot anatomical data related to the study: Segregated basal ganglia output pathways correspond to genetically divergent neuronal subclasses. ; https://zenodo.org/records/14787958