Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Reelin (CR-50) | MBL International | D223–3 |
| P73 (EP436Y) | Abcam | ab40658 |
| Olig2 | EMD Millipore | AB9610 |
| SOX2 | Santa Cruz | sc-365823 |
| Cleaved Caspase-3 Antibody (Asp175) | Cell Signaling Technology | 9661S |
| SKOR2 | Novus Biologicals | NBP2–14565 |
| TFAP2A | Santa Cruz | sc-12726 |
| Calbindin D28k (CALB1) | Synaptic Systems | 214 005 |
| HNA | Abcam | ab191181 |
| Anti-GFP | GeneTex | GTX13970 |
| MAP2 | Sigma-Aldrich | M4403–50UL |
| FOXP2 | Santa Cruz | sc-517261 |
| CLIC2 | Abcam | ab175230 |
| KI67 | BioLegend | 350504 |
| PAX6 | Sigma-Aldrich | AB2237 |
| BARHL1 | Sigma-Aldrich | HPA004809 |
| TCF7L2 | Cell Signaling Technology | 2569S |
| Bacterial and virus strains | ||
| AAV-DJ-hSYN1::eYFP | Stanford Gene Vector and Virus Core | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| CHIR 99021 | Selleckchem | S1263 |
| SAG | Millipore | 566660 |
| BMP4 | PeproTech | 120–05ET |
| BMP7 | PeproTech | 120–03P |
| FGF2 | R&D Systems | 233-FB |
| FGF4 | PeproTech | 100–31 |
| FGF8 | PeproTech | 100–25 |
| Retinoic Acid | Sigma-Aldrich | R2625 |
| IWP2 | STEMCELL Technologies | 72124 |
| LDN-193189 | Selleckchem | S7507 |
| Dorsomorphin | Sigma-Aldrich | P5499 |
| SB | Tocris | 3748 |
| Y-27632 | Selleck chem | S1049 |
| EGF | R&D Systems | 236-EG |
| DAPT | STEMCELL Technologies | 72082 |
| Vitronectin | Thermo Fisher Scientific | A14700 |
| E8 medium | Life Technologies | A1151700 |
| Human recombinant BDNF | Peprotech | 450–02 |
| Human recombinant NT3 | Peprotech | 450–03 |
| L-Ascorbic Acid 2-phosphate Trisodium Salt | Wako | 323–44822 |
| N6, 2’-O-Dibutyryladenosine 3’, 5’ -cyclic monophosphate sodium salt (cAMP) | Millipore Sigma | D0627 |
| N-2 supplement | Life Technologies | 17502048 |
| Essential 6 medium | Life Technologies | A1516401 |
| Neurobasal A | Life Technologies | 10888 |
| B-27 supplement without Vit A | Life Technologies | 12587 |
| Glutamax | Thermo Fisher Scientific | 35050079 |
| Penicillin and streptomycin | Thermo Fisher Scientific | 15140122 |
| Accutase | Innovate Cell Technologies | AT–104 |
| Activin A | PeproTech | 120–14P |
| SR11237 | Tocris | 3411 |
| Critical commercial assays | ||
| Chromium Single cell 3′ GEM, Library & Gel Bead Kit v3 | 10x Genomics | PN: 1000075 |
| Evercode Whole Transcriptome Kit | Parse Biosciences | ECW02030 |
| Parse Biosciences Cell Fixation | Parse Biosciences | ECF2001 |
| Deposited data | ||
| Spatial transcriptomics data | This paper | Zenodo: https://doi.org/10.5281/zenodo.13835782 |
| Single cell RNA sequencing data | This paper | GEO: GSE233574 https://cells-test.gi.ucsc.edu/?ds=morphogen-screen |
| Human fetal brain scRNA-seq dataset | Braun et al. 37 | https://github.com/linnarsson-lab/developing-human-brain |
| Human fetal cerebellum scRNA-seq dataset | Aldinger et al.52 | https://cells.ucsc.edu/?ds=cbl-dev |
| Primate TAC3-IN scRNA-seq dataset | Schmitz et al.28 | https://dev-inhibitory-neurons.cells.ucsc.edu/ |
| Human fetal striatum scRNA-seq dataset | Bhaduri et al.65 | https://data.nemoarchive.org/biccn/grant/u01_devhu/kriegstein/transcriptome/scell/10x_v2/human/processed/counts/ |
| Experimental models: Cell lines | ||
| Human iPSC line 2242–1 | Pasca Lab | N/A |
| Human iPSC line Q-0306–1 | Pasca Lab | N/A |
| Human iPSC line Q-0294–2 | Pasca Lab | N/A |
| Human iPSC line NIH2788 | Pasca Lab | N/A |
| Experimental models: Organisms/strains | ||
| FOXN1−/− rats | Charles River Laboratories | Crl:NIH-Foxn1rnu |
| Software and algorithms | ||
| ImageJ (Fiji) | Schindelin et al., 2012 66 | https://imagej.net/Fiji |
| Cell Ranger v6.1.0, v7.1.0 | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger |
| Seurat v4.3.0 | Satija Lab; Hao et al., 2021 67 | https://satijalab.org/seurat/ |
| MERlin spatial transcriptomics processing pipeline | Emanuel et al., 2020 68 | https://github.com/emanuega/merlin |
| Cellpose segmentation algorithm | Stringer et al., 2021 69 | https://www.cellpose.org/ |
| Other | ||
| 10 cm ultra-low attachment plates | Corning | 3262 |
| 6-well ultra-low attachment plates | Corning | 3471 |
| White PLA filament | Prusa | PRM-PLA-175-WHT |
| Original Prusa i3 MK3S+ 3D Printer | Prusa | PRI-MK3S-COM-ORG-PEI |
| FLOWMI Cell Strainer (40, 70uM) | SP Bel Art | 136800070 |
| MERSCOPE | Vizgen | https://vizgen.com/ |
| AggreWell 800 plates | STEMCELL Technologies | 34815 |