| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Monoclonal mouse anti-human CD31/PECAM-1, Clone JC/70a | DAKO, Agilent | Cat# GA61051-2 |
| Mouse anti-CD20, Clone L26 | Ventana Roche | Cat# 760-2531 |
| Monoclonal mouse anti-human CD3, Clone LN10 | Leica Biosystems | Cat# CD3-565-L-CE; RRID: AB_563541 |
| Monoclonal mouse anti-human CD68, Clone PG-M1 | DAKO, Agilent | Cat# GA61361-2 |
| Monoclonal mouse anti-human CD138, Clone MI15 | DAKO, Agilent | Cat# GA64261 |
| Monoclonal mouse anti-Human CD15, Clone Carb-3 | DAKO, Agilent | Cat# GA06261-2 |
| APC anti-human CD45 | BioLegend | Cat# 982304; RRID: AB_2650648 |
| PE anti-human CD64 | BioLegend | Cat# 399504; RRID: AB_2861005 |
| BV421™ anti-human CD11b | BioLegend | Cat# 393114; RRID: AB_2750257 |
| Alexa Fluor® 700 anti-human CD3 | BioLegend | Cat# 317340; RRID: AB_2563408 |
| BV785™ anti-human CD19 | BioLegend | Cat# 363028; RRID: AB_2564257 |
| anti-Podoplanin-BB700 | BD Biosciences | BD OptiBuild Cat# 749715; RRID: AB_2873969 |
| anti-CD31-BUV395 | BD Biosciences | BD Horizon Cat# 565290; RRID: AB_2739159 |
| anti-CD45-PE/Fire810 | Sony Biotechnology | Cat# 1116435 |
| anti-CD14-cFluorB548 | Cytek Biosciences | Cat# R7-20115 |
| anti-CD3-BV605 | BD Biosciences | BD OptiBuild Cat# 742623; RRID: AB_2740919 |
| anti-CD8b-PE | BioLegend | Cat# 387307; RRID: AB_3068193 |
| anti-CD4-PE-Cy7 | BioLegend | Cat# 317413; RRID: AB_571958 |
| anti-CD19-BB515 | BD Biosciences | BD Horizon Cat# 564457; RRID: AB_2744309 |
| Biological samples | ||
| Human synovial tissue biopsy | University Hospital Zürich, Zurich, Switzerland | N/A |
| Human synovial tissue biopsy | Hospital Santa Maria, CAML, Lisbon, Portugal | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Liberase™ TL Research Grade | Roche | Cat# 05401020001 |
| DNase I – from bovine pancreas | Roche | Cat# 11284932001 |
| Red Blood Cell Lysis Solution (10x) | Miltenyi Biotec | Cat# 130-094-183 |
| UltraPure™ BSA (50 mg/ml) | Thermo Fisher Scientific | Cat# AM2616 |
| Acridine Orange PI | BioCat | Cat# F23002-LG |
| Cell Staining Buffer | BioLegend | Cat# 420201 |
| Human TruStain FcX™ | BioLegend | Cat# 422301 |
| Zombie Green™ Fixable Viability Dye | BioLegend | Cat# 423111 |
| BD™ CompBeads Anti-Mouse Igκ/Negative Control Compensation Particle Set | BD Biosciences | Cat# 552843 |
| autoMACS® Rinsing Solution | Miltenyi Biotec | Cat# 130-091-222 |
| MACS BSA Stock Solution | Miltenyi Biotec | Cat# 130-091-376 |
| BD Horizon™ Brilliant Stain Buffer | BD Horizon | Cat# 563794 |
| FcR Blocking Reagent, human | Miltenyi Biotec | Cat# 130-059-901 |
| UltraComp eBeads™ Compensation Beads | Invitrogen | Cat# 01-2222-42 |
| Critical commercial assays | ||
| Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 | 10x Genomics | PN-1000075 |
| Chromium Single Cell B Chip Kit | 10x Genomics | PN-1000073 |
| Chromium i7 Multiplex Kit | 10x Genomics | PN-120262 |
| Chromium Next GEM Single Cell 3’ GEM, Library & Gel bead kit v3.1 | 10x Genomics | PN-1000121 |
| Chromium Next GEM Chip G Single Cell Kit | 10x Genomics | PN-1000120 |
| Single Index Kit T Set A | 10x Genomics | PN-1000213 |
| Deposited data | ||
| scRNA-seq data Edalat G. S. et al. | This paper ArrayExpress |
ArrayExpress: E-MTAB-11791 Samples 28, 50 data also Accession #: GSE181082 |
| Published scRNA-Seq datasets | Stephenson et al.17, dbGaP | dbGap: phs001529.v1.p1 |
| Published scRNA-Seq datasets | Wei et al.23 | https://portals.broadinstitute.org/single_cell/study/SCP469 |
| Original code and instructions | This paper |
https://retogerber.pages.uzh.ch/protocol_synovial https://retogerber.pages.uzh.ch/synovialscrnaseq |
| Software and algorithms | ||
| FlowJo v10.10.0 | BD Biosciences | https://www.bdbiosciences.com/en-us/products/software/flowjo-v10-software |
| FACSDiva v9.0.1 | BD Biosciences | https://www.bdbiosciences.com/en-us/products/software/instrument-software/bd-facsdiva-software |
| SonyID7000™ V2.0.2 | Sony Biotechnology | https://www.sonybiotechnology.com/us/instruments/id7000-spectral-cell-analyzer/software/ |
| GraphPad Prism v10.1.2 | GraphPad, Dotmatics | https://www.graphpad.com/updates/prism-10-1-2-release-notes |
| R v4.0.3 | R Core Team | https://cran.r-project.org/bin/windows/base/old/4.0.3/ |
| Bioconductor v3.12 | Bioconductor | https://bioconductor.org |
| Cell Ranger v6.0.0 | 10X Genomics | https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-release-notes |
| Other | ||
| ART™ wide bore filtered pipette tips | Thermo Fisher Scientific | Cat# 2069G |
| Blunt cannula 80 mm, 16 G, Ø 1.6 mm | APPLIMED SA | Cat# 8001741 |
| BD Plastipak™ Syringe | BD | Cat# 303172 |
| Corning® 40μm Cell Strainer | Corning | Cat# 431750 |
| Corning® 70μm Cell Strainer | Corning | Cat# 431751 |
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