KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| FITC anti-mouse Lineage Cocktail | Biolegend | Cat#133301 |
| Biotin anti-mouse Lineage Panel | Biolegend | Cat#133307 |
| Rat anti-mouse cKit (CD117) | Biolegend | Cat#105808; RRID: AB_313217 |
| Rat anti-mouse Sca1 (Ly6-A/E) | Biolegend | Cat#122514; RRID: AB_756199 |
| Armenian Hamster anti-mouse CD48 | Biolegend | Cat#103426; RRID: AB_10612755 |
| Rat anti-mouse CD150 | Biolegend | Cat#115922; RRID: AB_2303663 |
| Rat anti-mouse CD16/CD32 | Biolegend | Cat#101324; RRID: AB_1877267 |
| Armenian Hamster anti-mouse CD34 | Biolegend | Cat#128612; RRID: AB_10553896 |
| Rat anti-mouse CD135 | Biolegend | Cat#135310, 135315; RRID: AB_2107050, AB_2571919 |
| Rat anti-mouse CD41 | Biolegend | Cat#133912; RRID: AB_2650893 |
| Armenian Hamster anti-mouse CD61 | Biolegend | Cat#104316; RRID: AB_2561734 |
| Rat anti-mouse CD11b | BD Pharmingen™ | Cat# 552850; RRID: AB_394491 |
| Rat anti-mouse Gr-1(Ly-6G/C) | eBioscience™ | Cat#48-5931-82; RRID: AB_1548788 |
| Rat anti-mouse CD45 | Biolegend | Cat#103132; RRID: AB_893340 |
| Rat anti-mouse CD19 | Biolegend | Cat#115508; RRID: AB_313643 |
| Rat anti-mouse CD3 | Biolegend | Cat#100236; RRID: AB_2561456 |
| Mouse anti-mouse CD45.1 | Biolegend | Cat#110728; RRID: AB_893346 |
| Mouse anti-mouse CD45.2 | Biolegend | Cat#109828; RRID: AB_893350 |
| Rat anti-mouse Ly6G | Biolegend | Cat#127614, 127604; RRID: AB_2227348, AB_1186108 |
| Rat anti-mouse Ly6C | Biolegend | Cat#128008, 128004; RRID: AB_1186132, AB_1236553 |
| Armenian Hamster anti-mouse CD11c | Biolegend | Cat#117306; RRID: AB_313775 |
| Rat anti-mouse CD115 | Biolegend | Cat#135526; RRID: AB_2566462 |
| Rat anti-mouse CXCR4 | Biolegend | Cat#146508; RRID: AB_2562785 |
| Rat anti-mouse CXCR2 | Biolegend | Cat#149610; RRID: AB_2565690 |
| Arthritogenic monoclonal antibodies (5-clone collagen antibody cocktail) | Chondrex | Cat#53010 |
| Chemicals, Enzymes, Reagents and recombinant proteins | ||
| Collagenase IV | Gibco | Cat#17104019; CAS: 9001-12-1 |
| ACK Lysing Buffer | Gibco | Cat#A1049201 |
| Percoll gradient | GE Healthcare | Cat#17-0891-01 |
| Tamoxifen | Sigma-Aldrich | Cat#T5648 |
| Tamoxifen-containing (0.5 mg/g) diet | Envigo | Cat#TD.130857 |
| Nonidet P40 Substrate | Sigma-Aldrich | Cat#74385 |
| Nuclei Buffer | 10x Genomics | Cat#2000153 |
| Streptavidin microBeads | Miltenyi Biotec | Cat# 130-048-101 |
| Anti-biotin microbeads | Miltenyi Biotec | Cat# 130-090-485 |
| LPS-EB (LPS from E. coliO111:B4) | Invivogen | Cat# tlrl-eblps |
| DAPI (4’,6-Diamidino-2-Phenylindole,Dihydrochloride) | ThermoFisher Scientific | Cat# D1306 |
| TRIzol™ Reagent | Invitrogen | Cat# 15596026 |
| Mouse recombinant G-CSF | R&D Systems | Cat# 414-CS-005/CF |
| Critical commercial assays | ||
| IL-6 mouse ELISA kit | Invitrogen | Cat# 88-7064-88 |
| IL-1β mouse ELISA kit | Invitrogen | Cat# 88-7013-88 |
| IFN-γ mouse ELISA kit | Invitrogen | Cat# 88-7314-88 |
| IL-12p70 mouse ELISA kit | Invitrogen | Cat# 88-7121-88 |
| IL-10 mouse ELISA kit | Invitrogen | Cat# 88-7105-88 |
| Mouse G-CSF ELISA | RayBiotech | Cat# ELM-GCSF-1 |
| High-Capacity RNA-to-cDNA Kit | Applied Biosystems | Cat# 4387406 |
| TURBO DNA-free Kit | Invitrogen | Cat# AM1907 |
| Chromium Next GEM Chip H Single Cell Kit v1.1 | 10x Genomics | Cat#1000162 |
| Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 | 10x Genomics | Cat#1000176 |
| NGS High Sensitivity Fragment Analysis Kit | Agilent | Cat#DNF-474 |
| NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles) | Illumina | Cat#20028401 |
| Chromium Next GEM Single Cell 3ʹ Kit v3.1, 16 rxns | 10x Genomics | Cat# PN-1000268 |
| ATAC-Seq Kit | Active Motif | Cat#53150 |
| Deposited data | ||
| RNA sequencing data | This paper | GEO: GSE180002 |
| Single cell ATAC sequencing data | This paper | GEO: GSE180025 |
| Single cell RNA sequencing data | This paper | GEO: GSE196808 |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6 | The Jackson Laboratory | Stock#000664 |
| Mouse: C57BL/6-CD45.1 B6.SJL-Ptprca Pepcb/BoyJ | The Jackson Laboratory | Stock#002014 |
| Mouse: B6.129(Cg)-Il1r1tm1.1Rbl/J (Il1r1fl/fl mice) | The Jackson Laboratory | Stock#028398 |
| Mouse: HSC-SCL-Cre-ERT | Donated by Dr. Joachim R. Göthert, University Hospital Essen | N/A |
| Software and algorithms | ||
| GraphPad Prism 8 | Graphpad Software | N/A |
| STAR | (Dobin et al., 2013) | http://code.google.com/p/rna-star/ |
| Ingenuity Pathway Analysis | QIAGEN | https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/ |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| NovoExpress software | ACEA Biosciences | https://www.aceabio.com |
| Cell Ranger ATAC version 1.2.0 | 10x Genomics | https://support.10xgenomics.com/single-cell-atac/software/overview/welcome |
| R package ArchR v1.0.1 | (Granja et al., 2021) | https://github.com/GreenleafLab/ArchR/releases/tag/v1.0.1 |
| R package Seurat | (Stuart et al., 2019) | https://github.com/satijalab/seurat/releases/tag/v3.0.0 |
| R package Signac | (Stuart et al., 2020) | https://github.com/timoast/signac/releases/tag/1.2.1 |
| Monocle 3 v1.0.0 | (Cao et al., 2019) | https://github.com/cole-trapnell-lab/monocle3/releases/tag/1.0.0 |
| Cicero v1.4 | (Pliner et al., 2018) | https://github.com/stjude/CICERO/releases/tag/v1.4.0 |