KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-FLAG M2 antibody | Sigma-Aldrich | F1804; RRID:AB_262044 |
| Mouse monoclonal anti-RUNX2 antibody (used for Western blotting and EMSA) | Abcam | ab76956; RRID:AB_1565955 |
| Rabbit polyclonal anti- RUNX2 antibody (used for immunohistochemistry) | Santa Cruz Biotechnology | sc-10758; RRID:AB_2184247 |
| Rabbit polyclonal anti-SP7 antibody | Abcam | ab22552; RRID:AB_2194492 |
| Mouse monoclonal anti-FOXA2 antibody | Merck | 17–10258; RRID:AB_11204693 |
| Rabbit polyclonal anti-C-JUN antibody | Abcam | ab31419; RRID:AB_731605 |
| Rabbit polyclonal anti-CBFb antibody | Abcam | ab195411 |
| Mouse monoclonal anti-CRISPR-Cas9 antibody | Abcam | ab191468; RRID:AB_2692325 |
| Rabbit polyclonal to Histone H3 antibody | Abcam | ab1791; RRID:AB_302613 |
| Alexa Fluor 488 secondary antibody | Invitrogen | A-11034; RRID:AB_2576217 |
| Alexa Fluor 546 secondary antibody | Invitrogen | A-11030; RRID:AB_2534089, A-11035; RRID:AB_2534093 |
| Alexa Fluor 647 secondary antibody | Invitrogen | A-21245; RRID:AB_2535813 |
| Goat Anti-Mouse IgG (H + L), HRP Conjugate | Promega | W402B; RRID:AB_430834 |
| Goat Anti-Rabbit IgG (H + L), HRP Conjugate | Promega | W401B; RRID:AB_430833 |
| Chemicals, peptides, and recombinant proteins | ||
| Recombinant human BMP2 | R&D | 355-BM |
| Critical commercial assays | ||
| Tagment DNA Enzyme 1 | Illumina | 15027865 |
| ThruPLEX®-FD Prep Kit | Rubicon Genomics | R40012 |
| TruSeq Illumina kit | illumina | RS-122-2001 |
| SMARTer Stranded Total RNA-seq Kit v2 Pico Input Mammalian | Takara | 634411 |
| Chromium Single Cell 3′ Library & Gel Bead Kit | 10x Genomics | PN-120237 |
| Chromium Single Cell A Chip Kits | 10x Genomics | PN-120236 |
| Chromium Multiplex Kit | 10x Genomics | PN-120262 |
| Deposited data | ||
| Raw and analyzed ChIP-seq, ATAC-seq and bulk RNA-seq data | This paper | GSE178293 |
| Raw and analyzed scRNA-seq data | This paper | DDBJ BioProject database: PRJDB8387 |
| Mouse osteoblast Sp7 ChIP-seq and Sp7-positive osteoblast RNA-seq data | GEO | GSE76187 |
| Mouse chondrocyte Jun ChIP-seq data | GEO | GSE73372 |
| Experimental models: Cell lines | ||
| MC3T3-E1 | ATCC | CRL-2593 |
| NIH3T3 | ATCC | CRL-1658 |
| HEK293T | ATCC | CRL-3216 |
| COS7 | ATCC | CRL-1651 |
| Plat-E | Cell Biolabs | RV-101 |
| Experimental models: Organisms/strains | ||
| Col2-ECFP transgenic reporter mice | (Chokalingam et al., 2009) | N/A |
| Col10-mCherry transgenic reporter mice | (Maye et al., 2011) | N/A |
| Sp7/Osx-EGFP∷Cre BAC transgenic reporter mice | (Rodda and McMahon, 2006), The Jackson laboratory | Stock No: 006361 |
| R26RtdTomato reporter mice | The Jackson laboratory | Stock No: 007905 |
| Runx2BioFL/+ mice | This paper, The Jackson laboratory | Stock No: 029512 |
| Runx2flox/+ mice | Nagata K et al., unpublished | N/A |
| Sp7Enh-Ob-lacZ∷GFP transgenic reporter mice | This paper | N/A |
| Sp7Enh-Ob+/− mice | This paper | N/A |
| Recombinant DNA | ||
| pMx-GFP | (Hojo et al., 2016) | N/A |
| pMx-Runx2-BioFL | This paper | N/A |
| pKLV2-EF1aBsd2ACas9-W | (Tzelepis et al., 2016) | Addgene 67978 |
| pKLV2.2-mU6gRNA5(SapI)-hU6gRNA5(BbsI)-PGKpuroBFP-W | (Tzelepis et al., 2016) | Addgene 72667 |
| CROPseq-Guide-Puro | (Datlinger et al., 2017) | Addgene 86708 |
| psPAX2 | Unpublished | Addgene 12260 |
| pMD2.G | Unpublished | Addgene 12259 |
| pGL4.23-Sp7Enh-Ob | This paper | N/A |
| pGL4.23- Sp7Enh-Ob-mut | This paper | N/A |
| caALK6 | (Ohba et al., 2008) | N/A |
| Smad1 | (Ohba et al., 2008) | N/A |
| Software and algorithms | ||
| CisGenome software v.2.0 | (Ji et al., 2008) | http://www.biostat.jhsph.edu/~hji/cisgenome/ |
| Trimmomatic v.0.33 | (Bolger et al., 2014) | http://www.usadellab.org/cms/?page=trimmomatic |
| Bowtie v.1.1.2 | (Langmead et al., 2009) | http://bowtie-bio.sourceforge.net/index.shtml |
| Tophat-2 v.2.1.0 | (Trapnell et al., 2009) | https://ccb.jhu.edu/software/tophat/index.shtml |
| Cufflinks v.2.2.1 | (Trapnell et al., 2010) | http://cole-trapnell-lab.github.io/cufflinks/ |
| HOMER v.3 | (Heinz et al., 2010) | http://homer.ucsd.edu/homer/ |
| factoextra v.1.0.7 | (Kassambara and Mundt, 2020) | https://cran.r-project.org/web/packages/factoextra/index.html |
| ggplot2 v.3.3.2 | (Hadley, 2016) | https://ggplot2.tidyverse.org/ |
| Java TreeView | (Saldanha, 2004) | http://jtreeview.sourceforge.net/ |
| GREAT v.3.0.0 | (McLean et al., 2010) | http://great.stanford.edu/public/html/ |
| BEDTools v.2.16.2 | (Quinlan and Hall, 2010) | https://bedtools.readthedocs.io/en/latest/ |
| DiffBind v.2.10.0 | (Ross-Innes et al., 2012) | https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
| Cellranger v.2.0.0 | (Zheng et al., 2017) | https://bioconductor.org/packages/release/bioc/html/DEsingle.html |
| DEsingle | (Miao et al., 2018) | https://bioconductor.org/packages/release/bioc/html/DEsingle.html |
| g:Profiler | (Raudvere et al., 2019) | https://biit.cs.ut.ee/gprofiler/gost |