KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
|
| ||
| Brilliant Violet 711 Anti-Mouse/Human CD44 Antibody | BioLegend | Cat #103057; RRID: AB_2564214 |
| Ly-6A/E (Sca-1) Monoclonal Antibody | Invitrogen | Cat #17-5981-82; RRID: AB_469487 |
| Purified Anti-mouse CD45 Antibody | BioLegend | Cat #103101; RRID: AB_312966 |
| CD16/CD32 Monoclonal Antibody | eBioscience | Cat #14-0161-82; RRID: AB_2313773 |
| Anti-ScxA Antibody | Abcam | Cat #ab58655; RRID: AB_882467 |
| Collagen X Monoclonal Antibody | Invitrogen | Cat #41-9771-82; RRID: AB_2313773 |
| Osterix Antibody | Abcam | Cat #EPR21034; RRID: AB_2313773 |
| Rabbit Anti-Mouse IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 | Invitrogen | Cat #A-11059; RRID: AB_2313773 |
| Rabbit Anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 | Invitrogen | Cat #A-21239; RRID: AB_2313773 |
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| ||
| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| Acetic Acid | MilliporeSigma | Cat #695092 |
| Alcian Blue | MilliporeSigma | Cat #A3157 |
| Alizarin Red S | MilliporeSigma | Cat #A5533 |
| Alpha-MEM | Gibco | Cat #12571603 |
| BenchMark™ Fetal Bovine Serum | GeminiBio | Cat #100-106 |
| Buffered Versenate | StatLab | Cat #DCV0150 |
| Collagen, Type I Solution from Rat Tail | MilliporeSigma | Cat #C3867-1VL |
| Crystal Violet | MilliporeSigma | Cat #C0775 |
| DAPI (4′,6-diamidino-2-phenylindole) | ThermoFisher Scientific | Cat #62248 |
| DNase I, RNase & Protease Free, Solution | Worthington Biochemical Corporation | Cat #LS006342 |
| HBSS, No Calcium, No Magnesium | Gibco | Cat #14170112 |
| Hydrochloric Acid | MilliporeSigma | Cat #H1758 |
| HEPES Solution | MilliporeSigma | Cat #5401020001 |
| Isopropanol | MilliporeSigma | Cat #I9516 |
| Liberase TL Research Grade | MilliporeSigma | Cat #H0887 |
| Marcaine | Astra Zeneca | Cat #2209748 |
| Methanol | MilloporeSigma | Cat #179337 |
| Mounting Medium with DAPI | Abcam | Cat #ab104139 |
| Oil Red O | Cat #O0625 | |
| PBS (10X), pH 7.4 | Gibco | Cat #70011044 |
| Penicillin-Streptomycin-Glutamine (100X) | Gibco | Cat #10378016 |
| Pierce™ 16% Formaldehyde (w/v), Methanol-free | ThermoFisher Scientific | Cat #28906 |
| Proteinase K, Recombinant, PCR grade | ThermoFisher Scientific | Cat #EO0491 |
| RNase AWAY Decontamination Reagent | Invitrogen | Cat #10328011 |
| Sucrose | MilliporeSigma | Cat #S0389 |
| Tamoxifen | MilliporeSigma | Cat #T5648 |
| Trypsin-EDTA (0.05%), Phenol Red | Gibco | Cat #25300054 |
| UltraPure DNase/RNase-Free Distilled Water | Invitrogen | Cat #AM9920 |
| 2-Propanol | MilliporeSigma | Cat #I9516 |
| 10X RBC Lysis Buffer | eBioscience | Cat #00430054 |
|
| ||
| Critical commercial assays | ||
|
| ||
| Human Mesenchymal Stem Cell (hMSC) Chondrogenic Differentiation Medium BulletKit | Lonza | Cat #PT-3003 |
| Human Mesenchymal Stem Cell (hMSC) Osteogenic Differentiation Medium BulletKit | Lonza | Cat #PT-3002 |
| Human Mesenchymal Stem Cell (hMSC) Adipogenic Differentiation Medium BulletKit | Lonza | Cat #PT-3004 |
| Qtracker 705 Cell Labeling Kit | Invitrogen | Cat #Q25061MP |
| RNAscope Fluorescent Multiplex Reagent Kit | ACDBio | Cat #320850 |
| Safranin O Cartilage Stain Kit | StatLab | Cat #KTSFO |
| TGF Beta 3 for hMSC Chondrogenic Differentiation Kit | Lonza | Cat #PT-4124 |
|
| ||
| Deposited data | ||
|
| ||
| GSEA (Gene Set Enrichment Analysis) | N/A | http://www.gsea-msigdb.org/gsea/msigdb/collections.jsp |
| Mouse Genome Database | The Jackson Laboratory | http://www.informatics.jax.org/ |
| Mouse Genome Database | The Jackson Laboratory | http://www.informatics.jax.org/ |
| ScRNA-seq Data (10x Genomics) | This paper | GEO: GSE182997 |
| ScRNA-seq Data (96-well Plates) | This paper | GEO: GSE182997 |
|
| ||
| Experimental models: Organisms/strains | ||
|
| ||
| Mouse: B6. Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J | The Jackson Laboratory | Strain: B6.Cg-Gt(ROSA)26Sortm14 (CAG-tdTomato)Hze/J JAX: 007,914 |
| Mouse: C57BL/6J | The Jackson Laboratory | JAX: 000,664 |
| Mouse: Gli1-CreERT | The Jackson Laboratory | Strain: Gli1tm3(cre/ERT2)Alj/J JAX: 007,913 |
| Mouse: Tg(Scx-GFP)1Stzr | Tan et al., 202059 | MGI:3717419 |
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| Software and algorithms | ||
|
| ||
| Adobe Illustrator CC2018 | Adobe Systems Inc. | RRID: SCR_014199 |
| Bruker CTAn MicroCT | N/A | Bruker Software |
| Cellranger | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger |
| Colaboratory (Colab) | N/A | https://colab.research.google.com/ |
| ComplexHeatmap V2.5.6 | Gu et al., 201668 | https://jokergoo.github.io/ComplexHeatmap-reference/book/ |
| CTVOX | N/A | Bruker Software |
| DataViewer | N/A | Bruker Software |
| FCS Express™ 7 | N/A | De Novo Software |
| ggplot2 | N/A | https://ggplot2.tidyverse.org/ |
| ImageJ | N/A | https://imagej.nih.gov/ij/ |
| Monocle | Trapnell et al., 201469 | http://cole-trapnell-lab.github.io/monocle-release/ |
| Prism-GraphPad | N/A | GraphPad Software |
| Python | Python Software Foundation | https://www.python.org/ |
| R version 3.6.3 | The R Foundation | https://www.r-project.org |
| SCENIC | Aibar et al., 201731 | https://github.com/aertslab/SCENIC |
| scVelo | Bergen et al. 202034 | https://github.com/theislab/scvelo |
| Seurat v3.1.0 | Butler et al., 2018 70 | https://satijalab.org/seurat/ |
| ssGSEA | Wang et al., 201733 | https://www.sciencedirect.com/science/article/pii/S1535610817302532#mmc9 |
| SkyScan’s Volumetric NRecon Reconstruction Software | N/A | Bruker Software |
| Velocyto v0.17.16 | La Manno et al., 201871 | http://velocyto.org/ |
|
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| Other | ||
|
| ||
| RNAscope Probe- Mm-Cebpd | ACDbio | Cat #556661 |
| RNAscope Probe- Mm-Cd34-C3 | ACDbio | Cat #319161-C3 |
| RNAscope Probe- Mm-Foxa3 | ACDbio | Cat #573031 |
| RNAscope Probe- Mm-Ly6a-C2 | ACDbio | Cat #427571-C2 |
| RNAscope Probe- Mm-Mef2a | ACDbio | Cat #443911 |
| RNAscope Probe- Mm-Nfatc1-C3 | ACDbio | Cat #436161-C3 |
| RNAscope Probe- Mm-Runx2-C3 | ACDbio | Cat #414021-C3 |
| Tap Windows | Electron Microscopy Sciences | Cat #62800-72 |