KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rat monoclonal anti-CD3 | Biolegend | Cat# 100243 |
| Armenian hamster monoclonal anti-CD3 | eBioscience | Cat# 15–0031-82 |
| Rat monoclonal anti-CD4 | eBioscience | Cat# 15–0042-82 |
| Rat monoclonal anti-CD4 | eBioscience | Cat# 13–0042-82 |
| Rat monoclonal anti-CD8a | eBioscience | Cat# 15–0081-82 |
| Rat monoclonal anti-CD8a | eBioscience | Cat# 36–0081-85 |
| Rat monoclonal anti-CD11b (Mac-1) | eBioscience | Cat# 15–0112-82 |
| Rat monoclonal anti-CD11b (Mac-1) | eBioscience | Cat# 25–0112-82 |
| Rat monoclonal anti-CD11b (Mac-1) | Biolegend | Cat# 101203 |
| Rat monoclonal anti-Ly6G/Ly6C (Gr1) | eBioscience | Cat# 35–5931-82 |
| Rat monoclonal anti-Ly6G/Ly6C (Gr1) | eBioscience | Cat# 47–5931-82 |
| Rat monoclonal anti-Ly6G/Ly6C (Gr1) | eBioscience | Cat# 13–5931-82 |
| Rat monoclonal anti-IgM | eBioscience | Cat# 15–5790-82 |
| Rat monoclonal anti-IgM | Biolegend | Cat# 406503 |
| Rat monoclonal anti-Ter119 | eBioscience | Cat# 15–5921-82 |
| Rat monoclonal anti-Ter119 | Biolegend | Cat# 116203 |
| Rat monoclonal anti-Ly-6A/E (Sca1) | eBioscience | Cat# 25–5981-82 |
| Rat monoclonal anti-CD117 (c-Kit) | eBioscience | Cat# 17–1171-82 |
| Rat monoclonal anti-CD135(Flt3/Flk2) | eBioscience | Cat# 13–1351-82 |
| Rat monoclonal anti-Cd34 | eBioscience | Cat# 11–0341-82 |
| Armenian Hamster monoclonal anti-CD48 | Biolegend | Cat# 103418 |
| Rat monoclonal anti-CD150 | Biolegend | Cat# 115904 |
| Rat monoclonal anti-CD150 | eBioscience | Cat# 12–1502-82 |
| Armenian Hamster monoclonal anti-CD49b | Biolegend | Cat# 103506 |
| Armenian Hamster monoclonal anti-CD49b | Biolegend | Cat# 103516 |
| Armenian Hamster monoclonal anti-CD49b | eBioscience | Cat# 11–0491-82 |
| Mouse monoclonal anti-CD45.1 | eBioscience | Cat# 15–0453-81 |
| Mouse monoclonal anti-CD45.2 | eBioscience | Cat# 11–0454-82 |
| Rat monoclonal anti-CD3 | eBioscience | Cat# 17–0032-82 |
| Rat monoclonal anti-B220 | eBioscience | Cat# 12–0452-82 |
| Rat monoclonal anti-B220 | eBioscience | Cat# 13–0452-82 |
| Rat monoclonal anti-CD45 | eBioscience | Cat# 17–0451-82 |
| Rat monoclonal anti-CD31 | eBioscience | Cat# 17–0311-82 |
| Rat monoclonal anti-PDGFRα-biotin | eBioscience | Cat# 13–1401-82 |
| Mouse monoclonal anti-LepR Biotinylated | R&D systems | Cat# BAF497 |
| Rat monoclonal anti-CD51-biotin | Biolegend | Cat# 104104 |
| Brilliant Violet 421 Streptavidin | Biolegend | Cat# 405225 |
| Rat monoclonal anti-CD41-biotin | eBioscience | Cat# MA1–82655 |
| Rat monoclonal anti-Endomucin | Abcam | Cat# Ab106100 |
| Rat monoclonal anti-Endomucin | SCBT | Cat# sc-65495 |
| Rat monoclonal anti-VE-cadherin | eBioscience | Cat # 17–1441-82 |
| Streptavidin, Alexa Fluor 405 conjugate | Invitrogen | Cat# S32351 |
| Mouse monoclonal anti-BrdU | GE Healthcare | Cat# RPN202 |
| Rabbit polyclonal anti-Aggrecan | Millipore | Cat# AB1031 |
| Rabbit polyclonal anti-Perilipin | Cell Signaling | Cat# 9349S |
| Goat polyclonal anti-Osteopontin | R&D systems | Cat# AF808 |
| Donkey-anti-goat Alexa Fluor 647 | Invitrogen | Cat# A-21447 |
| Donkey-anti-goat Alexa Fluor 488 | Invitrogen | Cat# A-11055 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| 7-aminoactinomycin D (7-AAD) | Life technologies | Cat# A1310 CAS: 7240–37-1 |
| SYTOX Green | Life technologies | Cat# S34860 CAS: 67–68-5 |
| 5-Bromo-2′-deoxyuridine | Sigma | Cat# B9285 CAS: 59–14-3 |
| 5-Fluorouracil | Sigma | Cat# F6627 CAS: 51–21-8 |
| Diphtheria toxin | Sigma | Cat# D0564 |
| Deoxyribonuclease I | Sigma | Cat# D5025 CAS: RN 9003–98-9 |
| Collagenase I | Worthington | Cat# LS004197 |
| Dispase | STEMCELL Technologies | Cat# 07913 |
| Oil Red O | Sigma | Cat# O0625 CAS: 1320–06-5 |
| Toluidine blue | Sigma | Cat# 89640 CAS: 6586–04-5 |
| Liberase DL | Roche | Cat# 5466202001 |
| Critical Commercial Assays | ||
| Annexin A5 Apoptosis Detection Kit | Biolegend | Cat# 640928 |
| APC BrdU Flow Kit | BD PharMingen | Cat# 552598 |
| VECTOR Red Alkaline Phosphatase (Red AP) Substrate Kit | VECTOR LABORATORIES | Cat# SK-5100 |
| StemPro Osteogenesis Differentiation Kit | GIBCO | Cat# A1007201 |
| StemPro Chondrogenesis Differentiation Kit | Cat# A1007101 | |
| StemPro Adipogenesis Differentiation Kit | Cat# A1007001 | |
| Deposited Data | ||
| Raw and analyzed data | This paper | GSE104887 |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6-Gt(ROSA)26Sortm1(HBEGF)Awai/J(iDTR) | The Jackson Laboratory | JAX: 007900 |
| Mouse: B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J(R26R-tdT) | The Jackson Laboratory | JAX: 007914 |
| Mouse: B6.Cg-Gt(ROSA)26Sortm6(CAG-ZsGreen1)Hze/J(R26R-ZsG) | The Jackson Laboratory | JAX: 007906 |
| Mouse: B6.129X1t(ROSA)26Sortm1(EYFP)Cos/J | The Jackson Laboratory | JAX: 006148 |
| Mouse: B6.Cg-Tg(Col1a1*2.3-GFP)1Rowe/J | The Jackson Laboratory | JAX: 013134 |
| Mouse: B6.129X1t(ROSA)26Sortm1(EYFP)Cos/J | ||
| Mouse: Tg(Cspg4-DsRed.T1)1Akik/J | The Jackson Laboratory | JAX: 008241 |
| Mouse: B6;FVB-Tg(Cspg4-cre)1Akik/J | JAX: 008533 | |
| Mouse: Cxcl12tm2.1Sjm/J | The Jackson Laboratory | JAX: 022458 |
| Mouse: Cxcl12tm1.1Sjm/J | The Jackson Laboratory | JAX: 022457 |
| Mouse: B6.129(Cg)-Leprtm2(cre)Rck/J | The Jackson Laboratory | JAX: 008320 |
| Mouse: Kitltm2.1Sjm/J | The Jackson Laboratory | JAX: 017861 |
| Mouse: Tg(Nes-EGFP)33Enik | MGI | 5523870 |
| Mouse: Pecam-GFP | This paper | This paper |
| Mouse: N-cad-TdT | This paper | This paper |
| Mouse: N-cad-CreERT | This paper | This paper |
| Software and Algorithms | ||
| Grid/Collection stitching plugin | Preibisch et al., 2009 | https://academic.oup.com/bioinformatics/article/25/11/1463/332497 |
| ImageJ custom plugin | This paper | http://research.stowers.org/imagejplugins |
| Tophat2 | Kim et al., 2013 | https://ccb.jhu.edu/software/tophat/index.shtml |
| Cufflinks | Trapnell et al., 2010 | http://cole-trapnell-lab.github.io/cufflinks/ |
| Htseq-count | Anders et al., 2015 | https://htseq.readthedocs.io/en/master/count.html |
| EdgeR | Robinson et al., 2010 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |