| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CRYAA | gift from Roy Quinlan | |
| CRYAB | Abcam | Cat# ab76467; RRID: AB_1523120 |
| CRX | Abnova | H00001406-MO2; RRID: AB_606098 |
| Ki67 | Abcam | Cat# ab15580; RRID: AB_443209 |
| KRT13 | Abcam | Cat# ab92551; RRID: AB_2134681 |
| KRT15 | Abcam | Cat# ab52816; RRID: AB_869863 |
| Lumican | Santa Cruz Biotechnology | Cat# sc-166871; RRID: AB_10607817 |
| MT2A | Sigma-Aldrich | Cat# SAB1402848; RRID: AB_10737934 |
| NP63 | Abcam | Cat# ab735; RRID: AB_305870 |
| Goat Anti-Mouse Alexa488 | Jackson Immuno Research Laboratories | Cat# 115-545-146; RRID: AB_2307324 |
| Goat Anti-Rabbit Cy3 | Jackson Immuno Research Laboratories | Cat# 111-165-003; RRID: AB_2338000 |
| Chemicals, peptides, and recombinant proteins | ||
| Accutase | Thermo Fisher Scientific | Cat# A1110501 |
| B27 Supplement | Thermo Fisher Scientific | Cat# 17504001 |
| Bluing Buffer | Dako | Cat# CS702 |
| Bovine serum albumin (BSA) | Sigma-Aldrich | Cat# A2153 |
| Chemically Defined Lipid Concentrate | Thermo Fisher Scientific | Cat# 11905031 |
| DMEM/F-12 | Thermo Fisher Scientific | Cat# 11320033 |
| Ethanol | VWR | Cat# 85651.320 |
| Eosin solution | Sigma-Aldrich | Cat# HT110216 |
| Fetal Bovine Serum (FBS) used in combination with the Neurosphere dissociation kit | Miltenyi Biotec | Cat# 130-091-376 |
| Fetal Bovine Serum (FCS) used for RO differentiation | Thermo Fisher Scientific | Cat# A5256801 |
| Fungizone | Thermo Fisher Scientific | Cat# 15290018 |
| GlutaMAX™ Supplement | Thermo Fisher Scientific | Cat# 35050087 |
| Hanks' Balanced Salt Solution | Thermo Fisher Scientific | Cat# J67763-AP |
| Hematoxylin | Dako | Cat# S3309 |
| Hoechst | Thermo Fisher Scientific | Cat# H3570 |
| IGF-1 | Merck | Cat# SRP3069 |
| Isopropanol | VWR | Cat# 20880 |
| Knockout Serum Replacement (KOSR) | Thermo Fisher Scientific | Cat# 10828028 |
| Lipidure | AMSbio | Cat# AMS.52000011GB1G |
| Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix | CORNING | Cat# 354230 |
| mTeSR™ 1 | Stem Cell Technologies | Cat# 85850 |
| Methanol | VWR | Cat# 20846.326 |
| N2 Supplement | Thermo Fisher Scientific | Cat# 17502001 |
| Non-Essential AminoAcids | Thermo Fisher Scientific | Cat# 11140050 |
| Normal Goat Serum | Millipore | Cat# S26-100ml |
| OCT embedding matrix | CellPath | Cat# KMA-0100-00A |
| Paraformaldehyde | Sigma-Aldrich | Cat# 158127 |
| Phosphate Buffered Saline (PBS) | Thermo Fisher Scientific | Cat# 14190250 |
| Penicillin/Streptomycin | Thermo Fisher Scientific | Cat# 15140130 |
| Protease IV | ACD | Cat# 322336 |
| Retinoic acid | Merck | Cat# R2625 |
| ROCK inhibitor (Y-27632) | CHEMDEA | Cat# CD0141 |
| T3 | Merck | Cat# 709719 |
| Taurine | Merck | Cat# T8691 |
| Triton X-100 | Sigma-Aldrich | Cat# T8787 |
| Vectashield | Vector Laboratories | Cat# H-1000 |
| Critical commercial assays | ||
| Chromium Next GEM Chip G Single Cell kit | 10x Genomics | Cat#1000120 |
| Chromium Next GEM Chip H Single Cell Kit v1.1 | 10x Genomics | Cat#1000162 |
| Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit, version 1.1 | 10x Genomics | Cat#1000175 |
| Chromium Next GEM Single Cell 3’ Kit, version 3.1 | 10x Genomics | Cat#1000268 |
| Chromium Single Cell 3’ Library & Gel Bead Kit, version 3.1 | 10x Genomics | Cat#1000121 |
| Neurosphere dissociation kit | Miltenyi Biotech | Cat#130-095-943; RRID:SCR_020290 |
| Visium Spatial Gene Expression Kit, version 1 | 10x Genomics | Cat#1000184; RRID:SCR_023571 |
| Visium Spatial Tissue Optimization Kit | 10x Genomics | Cat#1000193 |
| Deposited data | ||
| GEO | GEO: GSE235577 | |
| Zenodo | Zenodo: https://doi.org/10.5281/zenodo.10658110 | |
| Experimental models: Cell lines | ||
| hiPSCs (WT2) | Laboratory of Prof Majlinda Lako, Newcastle University | Melguizo-Sanchis et al.56, Buskin et al.57 |
| Oligonucleotides | ||
| Hs-ZIC1-C2 | ACD | Cat#542991-C2 |
| Hs-HES6-C3 | ACD | Cat#521301-C3 |
| Opal 520 | Akoya Biosciences | Cat#FP1487001KT |
| Opal 650 | Akoya Biosciences | Cat#FP1496001KT |
| Positive control probe | ACD | Cat#320861 |
| Negative control probe | ACD | Cat#320871 |
| Software and algorithms | ||
| ZEN software | Zeiss, Germany | |
| Spaceranger (version 1.0) | 10x Genomics | |
| Seurat (version 4.3.0) | https://satijalab.org/seurat/ | RRID:SCR_016341 |
| Monoclone 3 (version 1.3.1) | Bioconductor | |
| Cellranger ATAC software (version 1.2) | 10x Genomics | |
| Bedtools merge (version 2.30) | Bedtools | RRID:SCR_006646 |
| Cellranger (Version 3.01) | 10x Genomics | |
| Ingenuity Pathway Analysis (IPA) software | Qiagen | RRID:SCR_008653 |
| SCENIC+ (Version 1.0.1) | https://github.com/aertslab | |
| Python, scanpy (version 1.9.5) | https://github.com/scverse/scanpy | RRID:SCR_018139 |
| DoubletFinder (Version 2.0.3) | Bioconductor | RRID:SCR_018771 |
| Harmony (Version 0.1.1) | Bioconductor | RRID:SCR_022206 |
| cell2Location (Version 0.13) | https://github.com/BayraktarLab/cell2location | |
| Spaniel (Version 1.12) | Bioconductor | |
| Signac (Version 1.6) | Bioconductor | RRID:SCR_021158 |
| Chromvar (Version 1.20) | Bioconductor | |
| ComplexHeatmap (Version 2.14) | Bioconductor | RRID:SCR_017270 |
| Other | ||
| 6 Well plate | Helena/TTP | Cat#92406 |
| 96-well plates (U-bottom) | Helena/TPP | Cat#92697T |
| 6-well low attachment plates | CORNING | Cat#3471 |
| Axio Observer.Z1 | Zeiss, Germany | |
| Countess II FL Automated Cell Counter | Life Technologies | RRID:SCR_020236 |
| Nikon ECLIPSE Ti inverted microscope | Nikon Instruments Inc., USA | RRID:SCR_021242 |
| Zeiss Axio Imager.Z1 microscope | Zeiss, Germany | RRID:SCR_018876 |
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