| Reagent/Resource | Reference or Source | Identifier or Catalog Number |
|---|---|---|
| Experimental Models | ||
| Prrx1‐Cre | Logan et al (2002) | JAX: 005584 |
| Lepr‐Cre | DeFalco et al (2001) | JAX: 008320 |
| Loxp‐STOP‐loxp‐tdTomato | Madisen et al (2010) | JAX: 007914 |
| Col2.3‐GFP | Kalajzic et al (2002) | JAX: 013134 |
|
Recombinant DNA | ||
| pLKO.1 ‐ TRC Cloning Vector | Addgene | Cat# 10878 |
| pLKO.1_Hoxb2_1 | This study | |
| pLKO.1_Hoxb2_2 | This study | |
| pLKO.1_Npdc1_1 | This study | |
| pLKO.1_Npdc1_2 | This study | |
| Antibodies | ||
| Anti‐CD45‐APC (Clone 30‐F11) | eBioscience | Cat# 17‐0451‐83 |
| Anti‐Ter119‐APC (Clone TER‐119) | eBioscience | Cat# 17‐5921‐82 |
| Anti‐Tie2‐APC (Clone TEK4) | Biolegend | Cat# 124010 |
| Anti‐Pdgfra‐Biotin Antibody (Clone APA5) | eBioscience | Cat# 13‐1401‐82 |
| Anti‐Notch 3 Armenian Hamster Monoclonal Antibody (Clone HMN3‐133) | Biolegend | Cat# 130512 |
| Anti‐Ly‐6A/E (Sca‐1)‐PerCP/Cy5.5 (Clone E13‐161.7) | Biolegend | Cat# 122524 |
| FITC anti‐BrdU Antibody (Clone 3D4) | Biolegend | Cat# 364104 |
| Anti‐CD31‐biotin (Clone MEC13.3) | Biolegend | Cat# 102504 |
| Mouse/Rat CD31/PECAM‐1 Antibody | R&D system | Cat# AF3628‐SP |
| Anti‐Ly‐6A/E‐Alexa Fluor 647 (Clone E13‐16.7) | Biolegend | Cat# 122518 |
| Rabbit anti‐Aggrecan Antibody | Millipore | Cat# AB1031 |
| Rabbit anti‐Perilipin Antibody | Sigma | Cat# P1873 |
| Donkey anti‐rabbit‐Alexa Fluor 488 | Invitrogen | Cat# A21206 |
| Donkey anti‐goat‐Alexa Fluor 488 | Invitrogen | Cat# A‐11055 |
| Donkey anti‐rabbit‐Alexa Fluor 647 | Invitrogen | Cat# A‐31573 |
|
Oligonucleotides and other sequence‐based reagents | ||
| Acan (NM_007424.2) | This study | qPCR primers |
| F: TGA AGC AGA AGG TCT GGA CA | ||
| R: CCA GAA GGA ATC CCA CTA ACA | ||
| Col2a1 (NM_031163.3) | This study | qPCR primers |
| F: GTC CCC CTG GCC TTA GTG | ||
| R: CCA CCA GCC TTC TCG TCA | ||
| Adipoq (NM_001310597.1) | This study | qPCR primers |
| F: TGT TCC TCT TAA TCC TGC CCA | ||
| R: CCA ACC TGC ACA AGT TCC CTT | ||
| Pparg (NM_011146.3) | This study | qPCR primers |
| F: ACC ACT CGC ATT CCT TTG AC | ||
| R: TGG GTC AGC TCT TGT GAA TG | ||
| Sp7 (NM_001348205.1) | This study | qPCR primers |
| F: CAA GAG TGA GCT GGC CTG A | ||
| R: TGG AGC CAT AGT GAG CTT CTT | ||
| Bglap (NM_007541.3) | This study | qPCR primers |
| F: TGA GGA CCA TCT TTC TGC TCA | ||
| R: TGG ACA TGA AGG CTT TGT CA | ||
| Hoxb2 (NM_134032.2) | This study | qPCR primers |
| F: CGA GGT CGG ATC ACC ATC | ||
| R: GGT ACT TAT TGA AGT GGA ACT CCT TCT | ||
| Npdc1 (NM_008721.4) | This study | qPCR primers |
| F: GTG CCA AGG AAA CA CTA TCTT | ||
| R: CTC CTT CAG TGC CAG TTC CT | ||
| ShRNA_Hoxb2_1 | This study | shRNA‐sequence |
| CCGGGTCTGGTCCTCCTTGGCTGTTCTCGAGAACAGCCAAGGAGGACCAGACTTTTTG | ||
| ShRNA_Hoxb2_2 | This study | shRNA‐sequence |
| AATTCAAAAAGCCTTCTCCACTCGTGGATACCTCGAGGTATCCACGAGTGGAGAAGGC | ||
| ShRNA_Npdc1_1 | This study | shRNA‐sequence |
| AATTCAAAAAGCTTTCTGCTTAGCAAGCTCACTCGAGTGAGCTTGCTAAGCAGAAAGC | ||
| ShRNA_Npdc1_2 | This study | shRNA‐sequence |
| AATTCAAAAAGGCATAAGGAACCTCCAAAGGCTCGAGCCTTTGGAGGTTCCTTATGCC | ||
| Chemicals, Enzymes and other reagents | ||
| Anti‐Biotin Microbeads | Miltenyi Biotec | Cat# 130‐090‐485 |
| LS Columns | Miltenyi Biotec | Cat# 130‐042‐401 |
| Type I Collagenase | Worthington | Cat# LS004197 |
| Dispase II | Sigma‐Aldrich | Cat# 04942078001 |
| DNase I | Sigma‐Aldrich | Cat# D4527‐200KU |
| GelMA | Engineering for Life | EFL‐GM‐90 |
| Sodium pyruvate solution | Gibco | Cat# S8636 |
| Bovine serum albumin (BSA) | Sigma‐Aldrich | Cat# A9647 |
| Fetal bovine serum (FBS) | HyClone | Cat# SH30070.03 |
| MEM alpha medium | Thermo Fisher Scientific | Cat# 12561‐056 |
| Penicillin‐Streptomycin Solution | Thermo Fisher Scientific | Cat# 15140‐122 |
| LM‐DMEM | Corning | Cat# 10‐014‐CV |
| DMEM with 4.5 g/l glucose l‐glutamine & sodium pyruvate | Corning | Car# 10‐013‐CVR |
| L‐Ascorbic acid 2‐phosphate sesquimagnesium salt hydrate, ≥95% | Sigma‐Aldrich | Cat# A8960‐5G |
| L‐proline | Sigma‐Aldrich | Cat# P0380 |
| Recombinant human TGF‐b3 | PeproTech | Cat# 100‐36E |
| Indomethacin | Sigma‐Aldrich | Cat# I7378 |
| Alizarin Red S | Sigma‐Aldrich | Cat# A5533 |
| Oil Red O solution | Sigma‐Aldrich | Cat# O1391 |
| Alcian blue 8GX | Sangon Biotech | Cat# A600298‐0001 |
| Crystal Violet | Solarbio | Cat# C8470 |
| 5X All‐In‐One MasterMix Kit | ABM | Cat# G492 |
| APC BrdU Flow Kit | BD Bioscience | Cat# 552598 |
| 5‐Bromo‐2′‐deoxyuridine ≥ 99% (HPLC) | Sigma‐Aldrich | Cat# B5002‐5G |
| RQ1 RNase‐Free Dnase, | Promega, | Cat# M6101 |
| Matrigel | Corning | Cat# 354234 |
| Chromium Single Cell 3’ Library and Gel Bead Kit V2 | 10× Genomics | Cat# PN‐120237 |
| Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit V3.1 | 10× Genomics | Cat# 1000128 |
| iTaq Universal SYBR Green Supermix | BioRad | Cat# 172‐5125 |
| Software | ||
| Zen 2.3 software | Zeiss | |
| FlowJo V10.1 | FlowJo LLC | https://www.flowjo.com/ solutions/flowjo |
| GraphPad Prism 7.0 | GraphPad | https://www.graphpad.com/ |
| Image J: Fiji | Image J | https://imagej.nih.gov/ij/ |
| Snapgene V2.3.2 | Snapgene | https://www.snapgene.com |
| Cell Ranger v3.0.1 | 10× Genomics | https://support.10xgenomics.com |
| Python 3 | N/A | www.python.org |
| R 3.5.0 | R‐Project | https://cran.r‐project.org/ mirrors.html |
| Seurat v2.3.4 | Satija et al (2015) | https://satijalab.org/seurat/ |
| Scanpy v1.4 | Wolf et al (2018) | https://github.com/theislab/scanp |
| SCENIC | Aibar et al (2017) | https://github.com/aertslab/SCENIC |
| jvenn | Bardou et al (2014) | http://jvenn.toulouse.inra.fr/app/example.html |
| ClusterProfiler v3.2.14 | Yu et al (2012) | https://guangchuangyu.github.io/software/clusterProfiler/ |
| TACS | Kernfeld et al (2018) | N/A |
| CellphoneDB v2.0.0 | Vieira Braga et al (2019) | www.cellphonedb.org |
| Cytoscape v3.6 | Otasek et al (2019) | www.cytoscape.org |
| GSEA v2.2.4 |
Subramanian et al (2005), Mootha et al (2003) |
|
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