KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| AMBN | Santa Cruz | sc-271012; RRID: AB_10613795 |
| AMELX | Santa Cruz | sc-365284; RRID: AB_10843799 |
| DSPP | Santa Cruz | sc-73632; RRID: AB_2230660 |
| ENAM | Thermo Fisher | PA5–25734; RRID: AB_2543234 |
| KRT14 | Thermo Fisher | LL002; RRID: AB_306091 |
| KRT5 | Sigma-Aldrich | HPA059479; RRID:AB_2684034 |
| ZO-1 | Invitrogen | 33–9100; RRID: AB_87181 |
| anti-GFP | Invitrogen | A-1112; RRID:AB_221569 |
| SP6 | Atlas Antibodies | HPA024516; RRID: AB_10960551 |
| VIMENTIN | Cell Signalling | 5741S; RRID: AB_10695459 |
| Human Nuclei | Millipore | MAB1281; RRID:AB_94090 |
| CD144 | BD Biosciences | 555661, RRID: AB_396015 |
| CD146 (MCAM) | Abcam | ab75769; RRID: AB_2143375 |
| DAPI | Thermo Fisher | D1306, RRID: AB_2629482 |
| Mouse IgG (Alexa Flour 488) | Thermo Fisher | A11001; RRID: AB_2534069 |
| Rabbit IgG (Alexa Flour 488) | Thermo Fisher | A-32731; RRID:AB_2633280 |
| Mouse IgG (Alexa Flour 568) | Thermo Fisher | A-11004; RRID:AB_2534072 |
| Rabbit IgG (Alexa Flour 568) | Thermo Fisher | A-11036, RRID:AB_10563566 |
| Mouse IgG (Alexa Flour 647) | Thermo Fisher | A32728, RRID:AB_2633277 |
| Rabbit IgG (Alexa Flour 647) | Thermo Fisher | A32733, RRID:AB_2633282 |
| See File S for concentrations | N/A | N/A |
| Bacterial and virus strains | ||
| chemically competent E. coli Lemo21 | NEB | C2528J |
| Biological samples | ||
| Human fetal jaw tissues | UW Birth Defect Research Laboratory (BDRL) | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Matrigel | Corning | #356231; |
| β-mercaptoethanol (BME) | Sigma | #M7522 |
| Smoothened agonist (SAG) | Selleckchem | # S7779 |
| Bone morphogenic protein-4 (BMP4) | rndsystems | #314-BP-010 |
| BMP-I inhibitor (LDN-193189) | Tocris | # 6053 |
| GSK3-Inhibitor (CHIR99021) | Selleckchem | # 4423 |
| Epidermal growth factor (EGF) | rndsystems | #236-EG |
| Supplement S7 | Thermo Fisher | #S0175 |
| Neurotrophin-4 (NT4) | rndsystems | #268-N4 |
| Transforming growth factor beta 1(TGFβ1) | rndsystems | #7754-BH |
| ROCKi (Y-27632) | Selleckchem | #S1049 |
| Ascorbic acid | Sigma | #A8960 |
| β-Glycerophosphate | Sigma | #35675 |
| Dexamethasone | Sigma | #D2915 |
| FGFR-mb | Cao et al., 202260 | NA |
| Calcein | Sigma | #C0875 |
| Alizarin red S stain | Sigma | #A5533 |
| Sodium Thiosulfate | Sigma | #217263 |
| Silver Nitrate | Sigma | #209139 |
| Paraformaldehyde | EMS | #15710 |
| Tissue-Tek O.C.T. | Sakura | #4583 |
| 2-methylbutane | EMD | #MX0760–1 |
| RPMI 1640 Medium | Thermo Fisher | #11875093 |
| EpiCult-C media | StemCell Technologies | #05630 |
| EpiLife | Thermo Fisher Scientific | #MEPI500CA |
| mTeSR1 stem cell medium | StemCell Technologies | #85850 |
| Critical commercial assays | ||
| RNAscope Intro Pack for HiPlex12 Reagents Kit (488, 550,650,750) - Human | Advanced Cell Diagnostics, Inc | 324442 |
| Deposited data | ||
| Raw and analyzed data | This paper | GEO: GSE184749 |
| RNAscope raw and processed data | This paper | https://datadryad.org/stash/share/TiKnbN_96SrgYmHHJ7kHa4kH8AYjAFcMXG0BsMlVOeE |
| Human reference genome NCBI build 38, GRCh38 | Genome Reference Consortium | https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.38/ |
| Experimental models: Cell lines | ||
| WTC-11 human induced pluripotent stem cells) | Coriell | #GM25256 |
| Dental Pulp Stem Cells | Macrin et al., 201989 | N/A |
| Experimental models: Organisms/strains | ||
| Mouse: CB17.Cg-PrkdcscidLystbg-J/Crl | Charles River Laboratories | RRID: IMSR_CRL:250 |
| Oligonucleotides | ||
| See File S for all primers | N/A | N/A |
| Recombinant DNA | ||
| pET-29b(+) | GeneScript | N/A |
| Software and algorithms | ||
| Seurat 4.0 package | Hao et al., 202164 | https://satijalab.org/seurat/ |
| networkD3 | Allaire et al., 201787 | https://cran.r-project.org/package=networkD3 |
| Monocle3 | Cao et al., 201924; Qiu77 et al., 2017; Trapnell et al., 201433 | https://cole-trapnell-lab.github.io/monocle3/ |
| STAR | (Dobin et al., 2013)76 | https://github.com/alexdobin/STAR |
| Fiji (ImageJ2 v2.3.0) | Schindelin et al., 201291; Schindelin et al., 201592 | https://imagej.net/software/fiji/ |
| UMAP algorithm | McInnes et al., 201878 | https://github.com/lmcinnes/umap |
| Leiden Algorithm | Levine et al., 201579; Traag et al., 201980. | https://github.com/vtraag/leidenalg |
| UpSetR | Conway et al., 201783 | https://github.com/hms-dbmi/UpSetR |
| ComplexHeatmap R package | Gu et al., 201681 | https://github.com/jokergoo/ComplexHeatmap |
| ViSEAGO R package | Brionne et al., 201936 | https://bioconductor.org/packages/release/bioc/html/ViSEAGO.html |
| simplifyEnrichment R package | Gu and Hübschmann, 202182 | https://github.com/jokergoo/simplifyEnrichment |
| talklr R package | Wang, 202049 | https://github.com/yuliangwang/talklr |
| DEsingle R package | Miao et al., 201850 | https://github.com/miaozhun/DEsingle |
| scMLnet R package | Cheng et al., 202151 | https://github.com/SunXQlab/scMLnet |
| LIGER R package | Welch et al., 201965 | https://github.com/welch-lab/liger |
| QuPath (v0.3.0) | Bankhead et al., 201788 | https://qupath.github.io/ |
| BioRender | BioRender | https://www.biorender.com/ |
| NIS-Elements | Nikon | RRID:SCR_014329 |
| Custom R codes | This paper | https://github.com/Ruohola-Baker-lab/Tooth_sciRNAseq.(DOI: 10.5281/zenodo.8076442) |