Appendix 1—key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Biological sample (Homo sapiens) | Aqueous humor (AqH) | Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands |
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| Biological sample (Homo sapiens) | Blood Plasma (EDTA tubes) | Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands |
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| Antibody | Anti-human CD14-FITC Clone: TÜK4 (mouse monoclonal) |
Miltenyi | CAT# 130-080-701 | (Dilution:) 1:50 |
| Antibody | Anti-human CCR2-BV421 Clone: K036C2 (mouse monoclonal) |
BioLegend | CAT# 357210 | (Dilution:) 1:150 |
| Antibody | Anti-human CD11c-PerCP-Cy5.5 Clone: Bu15 (mouse monoclonal) |
BioLegend | CAT# 337210 | (Dilution:) 1:200 |
| Antibody | Anti-human CD123-FITC Clone: 6 H6 (mouse monoclonal) |
eBioscience | CAT# 11-1239-42 | (Dilution:) 1:20 |
| Antibody | Anti-human CD14-PerCP-Cy5.5 Clone: HCD14 (mouse monoclonal) |
BioLegend | CAT# 325622 | (Dilution:) 1:100 |
| Antibody | Anti-human CD14-BV785 Clone: M5E2 (mouse monoclonal) |
BioLegend | CAT# 301840 | (Dilution:) 1:100 |
| Antibody | Anti-human CD141 BDCA3-APC Clone: AD5-14H12 (mouse monoclonal) |
Miltenyi | CAT# 130-090-907 | (Dilution:) 1:20 |
| Antibody | Anti-human CD163-BV510 Clone: GHI/61 (mouse monoclonal) |
BioLegend | CAT# 333628 | (Dilution:) 1:25 |
| Antibody | Anti-human CD180-PE/Cy7 Clone: MHR73-11 (mouse monoclonal) |
BioLegend | CAT# 312910 | (Dilution:) 1:100 |
| Antibody | Anti-human CD19-eF450 Clone: HIB19 (mouse monoclonal) |
eBioscience | CAT# 48-0199-42 | (Dilution:) 1:25 |
| Antibody | Anti-human CD19-BV605 Clone: SJ25C1 (mouse monoclonal) |
BD | CAT# 562653 | (Dilution:) 1:50 |
| Antibody | Anti-human CD19-AF700 Clone: HIB19 (mouse monoclonal) |
eBioscience | CAT# 56-0199-42 | (Dilution:) 1:50 |
| Antibody | Anti-human CD1c-APC Clone: L161 (mouse monoclonal) |
eBioscience | CAT# 17-0015-42 | (Dilution sorting cohort 2:) 1:50 |
| Antibody | Anti-human CD1c BDCA1-BV421 Clone: L161 (mouse monoclonal) |
BioLegend | CAT# 331526 | (Dilution:) 1:25 |
| Antibody | Anti-human CD1c BDCA1-APC Clone: L161 (mouse monoclonal) |
eBioscience | CAT# 17-0015-42 | (Dilution purity check cohort 1:) 1:20 |
| Antibody | Anti-human CD20-PE Clone: 2 H7 (mouse monoclonal) |
eBioscience | CAT# 12-0209-42 | (Dilution:) 1:50 |
| Antibody | Anti-human CD3-AF700 Clone: UCHT1 (mouse monoclonal) |
BioLegend | CAT# 300424 | (Dilution:) 1:50 |
| Antibody | Anti-human CD304 BDCA4-PE Clone: AD5-17F6 (mouse monoclonal) |
Miltenyi | CAT# 130-090-533 | (Dilution:) 1:20 |
| Antibody | Anti-human CD36-PE Clone: CB38 (mouse monoclonal) |
BD | CAT# 555455 | (Dilution:) 1:200 |
| Antibody | Anti-human CD4-BV711 Clone: OKT4 (mouse monoclonal) |
BioLegend | CAT# 317440 | (Dilution:) 1:50 |
| Antibody | Anti-human CD45-PerCP Clone: HI30 (mouse monoclonal) |
BioLegend | CAT# 304026 | (Dilution:) 1:100 |
| Antibody | Anti-human CD5-BB515 Clone: UCHT2 (mouse monoclonal) |
BD | CAT# 564647 | (Dilution:) 1:100 |
| Antibody | Anti-human CD56-AF700 Clone: B159 (mouse monoclonal) |
BD | CAT# 557919 | (Dilution:) 1:50 |
| Antibody | Anti-human CD8-V500 Clone: RPA-T8 (mouse monoclonal) |
BD | CAT# 560774 | (Dilution:) 1:50 |
| Antibody | Anti-human CX3CR1-PE/Dazzle594 Clone: 2 A9-1 (rat monoclonal) |
BioLegend | CAT# 341624 | (Dilution:) 1:100 |
| Antibody | Anti-human HLA-DR-BV605 Clone: G46-6 (mouse monoclonal) |
BD | CAT# 562845 | (Dilution:) 1:150 |
| Other | Viability dye and labelling reagent. Live/Dead-APC-eF780 |
eBioscience | CAT# 65-0865-14 | (Dilution:) 1:1000 |
| Chemical compound, drug | R848 | Invivogen | CAT# tlrl-r848 | (Concentration:) 1 µg/ml |
| Chemical compound, drug | Lipoteichoic acid (LTA) | Sigma-Aldrich | CAT# L2515-5MG | (Concentration:) 1 µg/ml |
| Chemical compound, drug | Lipopolysaccharide (LPS) | Invivogen | CAT# tlrl-3pelps | (Concentration:) 10 ng/ml |
| Chemical compound, drug | Pam3CSK4 | Invivogen | CAT# tlrl-pms | (Concentration:) 5 µg/ml |
| Chemical compound, drug | oxLDL | Cell Biolabs | CAT# STA-214 | (Concentration:) 50 µg/ml |
| Chemical compound, drug | TGFβ-b2 | R&D Systems | CAT# 302-B2-002/CF | (Concentration:) 100 ng/ml |
| Chemical compound, drug | FLT3L | Cellgenix | CAT# 1415-05 | (Concentration:) 100 ng/ml |
| Chemical compound, drug | TNFα | R&D Systems | CAT# 210-TA-020 | (Concentration:) 100 ng/ml |
| Chemical compound, drug | S100A12 (EN-RAGE) | R&D Systems | CAT# 1052-ER-050 | (Concentration:) 1 µg/ml |
| Chemical compound, drug | IL-4 | R&D Systems | CAT# 204-IL-50 | (Concentration:) 10 ng/ml |
| Chemical compound, drug | IFNα-2a | Cell Sciences | CAT# CRI003B | (Concentration:) 1000 U/ml |
| Chemical compound, drug | GM-CSF | R&D Systems | CAT# 215 GM-500 | (Concentration:) 800 U/ml |
| Commercial assay or kit | Olink Target 96 Immuno-Oncology | Olink | CAT# 95311 | Olink Targeted Proteomics analysis |
| Commercial assay or kit | TruSeq RNA Library Prep Kit | Illumina | CAT#RS-122-2001 | RNA-seq |
| Commercial assay or kit | AllPrep DNA/RNA/miRNA Universal Kit | QIAGEN | CAT# 80224 | RNA isolations |
| Commercial assay or kit | CD1c (BDCA-1)+Dendritic Cell Isolation Kit, human |
Miltenyi Biotec | CAT#130-119-475 | isolation of CD1c+ DCs from PBMCs. |
| Commercial assay or kit | CD19 MicroBeads, human | Miltenyi Biotec | CAT#130-050-301 | Depletion of CD19+ B cells from PBMCs |
| Commercial assay or kit | CD304 (BDCA-4/Neuropilin-1) MicroBead Kit, human |
Miltenyi Biotec | CAT#130-090-532 | Depletion of plasmacytoid dendritic cells from PBMCs |
| Commercial assay or kit | Human IL-23 Quantikine ELISA Kit | R&D Systems | CAT# D2300B | Quantification of IL-23 in supernatant of CD1c+ DC cultures |
| Recombinant DNA reagent | CD36 FW (Sequence 5′–3′) AAAGAGGTCCTTATACGTACAGAGTTCGT |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | CD36 RV (Sequence 5′–3′) AGCCTTCTGTTCCAACTGATAGTGA |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | RUNX3 FW (Sequence 5′–3′) CAATGACGAGAACTACTCCGC |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | RUNX3 RV (Sequence 5′–3′) GAAGCGAAGGTCGTTGAACC |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | GUSB FW (Sequence 5′–3′) CACCAGGGACCATCCAATACC |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | GUSB RV (Sequence 5′–3′) GCAGTCCAGCGTAGTTGAAAAA |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | CCR2 FW (Sequence 5′–3′) CCACATCTCGTTCTCGGTTTATC |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | CCR2 RV (Sequence 5′–3′) CAGGGAGCACCGTAATCATAATC |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | CX3CR1 FW (Sequence 5′–3′) AGTGTCACCGACATTTACCTCC |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | CX3CR1 RV (Sequence 5′–3′) AAGGCGGTAGTGAATTTGCAC |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | IRF8 FW (Sequence 5′–3′) CGACGCGCACCATTCA |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | IRF8 RV (Sequence 5′–3′) GCTTGCCCCCATAGTAGAAGCT |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | TLR7 FW (Sequence 5′–3′) CAAGAAAGTTGATGCTATTGGGC |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | TLR7 RV (Sequence 5′–3′) TGGTTGAAGAGAGCAGAGCA |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | CCR5 FW (Sequence 5′–3′) TGCTACTCGGGAATCCTAAAAACT |
Integrated DNA Technologies | qPCR primer | |
| Recombinant DNA reagent | CCR5 RV (Sequence 5′–3′) TTCTGAACTTCTCCCCGACAAA |
Integrated DNA Technologies | qPCR primer | |
| Software, algorithm | R Project for Statistical Computing; R version 4.0.3 (2020-10-10) |
https://www.r-project.org/ | RRID:SCR_001905 | RNA-seq,flowSOM, statistical analysis |
| Software, algorithm | FlowJo v10.6.1 | BD Biosciences; https://www.flowjo.com/solutions/flowjo |
RRID:SCR_008520 | Flow cytometry |
| Software, algorithm | Seurat v3.1.5 |
Stuart et al., 2019; http://seurat.r-forge.r-project.org/ |
RRID:SCR_007322 | scRNA-seq analysis |
| Software, algorithm | DESeq2 v1.30.1 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html | RRID:SCR_015687 | RNA-seq analysis |
| Software, algorithm | WGCNA v 1.70-3 | http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/ | RRID:SCR_003302 | Co-expression network analysis |
| Software, algorithm | flowSOM | https://github.com/SofieVG/FlowSOM, Van Gassen et al., 2023 | RRID:SCR_016899 | Flowcytometry analysis using a Self-Organizing Map. |
| Software, algorithm | UCell v1.3.1 | https://github.com/carmonalab/UCell, Andreatta and Carmona, 2023 | scRNAseq Module score | |
| Software, algorithm | scGate v1.0.0 | https://github.com/carmonalab/scGate, Andreatta et al., 2023 | Purification of intraocular CD1c+ DCs in scRNAseq data |