KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| LNMC samples from study participants living with HIV | This study, Centre hospitalier universitaire vaudois (CHUV), Lausanne Switzerland | N/A |
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| Flow Cytometry | ||
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| APC-H7-conjugated mouse anti-human anti-HLA-DR (G46-6) | Becton Dickinson | 561358 |
| APC conjugated mouse anti-human anti-CD4 (RPA-T4) | Becton Dickinson | 555349 |
| ECD-conjugated mouse anti-human anti-CD3 (UCHT1) | Beckman Coulter | A07748 |
| PE-Cy7-conjugated mouse anti-human anti-CD11c (B-ly6) | Becton Dickinson | 561356 |
| PerCP-Cy5.5 conjugated mouse anti-human anti-CD45 (H-I30) | Becton Dickinson | 332784 |
| Alexa Fluor 700 conjugated mouse anti-human anti-CCR7 (150503) | Becton Dickinson | 561143 |
| FITC-conjugated mouse anti-human anti-CD20 (clone 2H7). | Becton Dickinson | 555622 |
| BV421 conjugated mouse anti-human CD279 (EH12) | Becton Dickinson | 565935 |
| PerCP-Cy5.5 conjugated mouse anti-human anti-CD8 (SK1) | Becton Dickinson | 341050 |
| PE-CF594-conjugated mouse anti-human anti-CD45RA (HI100) | Becton Dickinson | 562298 |
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| Mass Cytometry | ||
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| Ultra-LEAF™ Purified anti-human CD8a (RPA-T8) | Biolegend | 301073 |
| Ultra-LEAF™ Purified anti-human CD4 (RPA-T4) | Biolegend | 300570 |
| Purified anti-human CD45 Antibody (HI30) | Biolegend | 304002 |
| Purified anti-human CD19 (HIB19) | Biolegend | 302202 |
| Purified anti-human/mouse/rat CD278 (ICOS) (C398.4A) | Biolegend | 313502 |
| Purified IRF4 (IRF4.3E4) | Biolegend | 646402 |
| Purified anti-human CCR5 (J418F1) | Biolegend | 359102 |
| SAMHD1 antibody (AA 426-657) (FITC) | Antibodies-online.com | ABIN7177151 |
| Purified anti-human CD163 (GHI/61) | Biolegend | 3145010B |
| Purified anti-human IgD (IA6-2) | Biolegend | 348202 |
| Purified anti-human BIRC3 (C-IAP2) | Biolegend | 667702 |
| Anti-Human CD274/PD-L1 (29E.2A3)-148Nd | Fluidigm | 3148017B |
| Anti-Human CD127/IL-7Ra (A019D5)-149Sm | Fluidigm | 3149011B |
| Anti-Human CD134/OX40 (ACT35)-150Nd | Fluidigm | 3150023B |
| Purified anti-human CD123 (6H6) | Biolegend | 306002 |
| Purified anti-human CD21 (Bu32) | Biolegend | 354902 |
| Purified anti-human DC-SIGN (9E9A8) | Biolegend | 330102 |
| Anti-Human CD27 (L128)-155Gd | Fluidigm | 3155001B |
| Anti-Human CD86/B7.2 (IT2.2)-156Gd | Fluidigm | 3156008B |
| Anti-Human CD169 (7-239)-158Gd | Fluidigm | 3158027B |
| Anti-Human CD197/CCR7 (G043H7)-159Tb | Fluidigm | 3159003A |
| Anti-Human CD14 (M5E2)-160Gd | Fluidigm | 3160001B |
| Purified anti-human CD1c (L161) | Biolegend | 331502 |
| Anti-Human CD11c (Bu15)-162Dy | Fluidigm | 3162005B |
| Purified anti-human CD85j (GHI/75) | Biolegend | 333702 |
| APC-conjugated anti-IRF8 (V3GYWCH) | Invitrogen | 17-9852-82 |
| Anti-APC (APC003)-163Dy | Fluidigm | 3163001B |
| Anti-FITC (FIT-22)-144Nd | Fluidigm | 3144006B |
| Anti-Human CD185/CXCR5 (RF8B2)-164 | Fluidigm | 3164029B |
| Anti-Human CD40 (5C3)-165Ho | Fluidigm | 3165005B |
| Purified anti-human CD155 (PVR) (SKII.4) | Biolegend | 337602 |
| Purified anti-human CD38 (HIT2) | Biolegend | 303502 |
| Anti-Human CD45RA (HI100)-169Tm | Fluidigm | 3169008B |
| Anti-Human CD3 (UCHT1)-170Er | Fluidigm | 3170001B |
| Anti-Human CD273/PDL2 (24F.10C12)-172Yb | Fluidigm | 3172014B |
| Anti-Human CD184/CXCR4 (12G5)-173Yb | Fluidigm | 3173001B |
| Purified anti-human HLA-DR (L243) | Biolegend | 307602 |
| Purified anti-human PD-1(EH12.2H7) | Biolegend | 329925 |
| Anti-Human CD11b/Mac-1 (ICRF44)-209Bi | Fluidigm | 3209003B |
| Purified NA/LE Mouse Anti-Human CD3 | Becton Dickinson | 555329 |
| Purified Mouse Anti-Human CD28 | Becton Dickinson | 555726 |
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| Virus strainss | ||
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| Human Immunodeficiency Virus Type 1 (HIV-1) BaL | HIV reagent program | 510 |
| Human Immunodeficiency Virus Type 1 (HIV-1)-CCR5 EGFP | Gift From Nicola Manel | Ref. 68; Manel et al.63 |
| Human Immunodeficiency Virus Type 1 (HIV-1)-CXCR4 EGFP | Gift From Nicola Manel | Ref. 68; Manel et al.63 |
| VpX Lentivirus | Gift from Fabio Condotti | Bobadilla et al. (2013).64 Gene Therapy |
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| Reagents, chemicals, peptides, recombinant proteins | ||
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| HIV peptides | JPT Peptide Technology | Customized |
| TLR-7/8 agonist | InvivoGen | CL264 |
| SEB | Sigma-Aldrich | S4881 |
| Human IL-2 IS, research grade | Miltenyi | 130-097-743 |
| Emtricitabine | NIH Reagents Program | HRP-10071 |
| Thymidine, [Methyl-3H], in 2% ethanol, 1 mCi | perkinelmer | NET027W001MC |
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| Critical commercial assays | ||
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| Single cell RNAseq (Seq-well; refer to Gierahn et al.36) | ||
| polydimethylsiloxane (PDMS) | ChemGenes Corporation, Wilmington, MA, USA | #MACOSKO201110 |
| polycarbonate membrane | Sterlitech Corporation, Auburn, WA, USA | #PCT00162X22100 |
| barcoded with mRNA capturing beads | ChemGenes Corporation, Wilmington, MA, USA). | #MACOSKO201110 |
| cDNA library preparation - Nextera XT DNA Library Preparation Kit) | Illumina, Inc., San Diego, CA, USA | #FC-131-1024 |
| NGS HIV resistance testing (Sentosa SQ HIV Genotyping Assay) | Vela Diagnostics, Hamburg | |
| DNeasy Blood and Tissue Kit | Qiagen | 69504 |
| MIPseq protocol | Refer to Einkauf et al.38 | |
| EasySep Human CD8+ Tcell IsolationKit | Stemcell | 17953 |
| EasySep™ Human CD4+ T Cell Isolation Kit | Stem Cell | 17952 |
| Human IFNγ ELISpotPRO assay KIT | MABTECH | 3420-2APW-2 |
| Cobas 6800 | Cobas HIV-1; Roche Diagnostics AG | KIT COBAS 6800/8800 HIV 96T IVD; Référence : 7000995190 |
| HIV-1 P24 Electrochemiluminiscence assay | Elecsys HIV Duo de Roche | 08 836 973 190 (300 tests) |
| IFNγ ELISpot assay KIT | MABTECH | 3420-2APW-2 |
| LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit | Invitrogen | L34957 |
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| Software and algorithms | ||
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| STAR aligner software | ENCODE, version 2.7 | https://www.encodeproject.org/software/star/ |
| R package | R Core Team and R Foundation for Statistical Computing, version 4.0.2 | https://www.r-project.org |
| Seurat package for R (v.4.0.0) | ||
| DropEst (version 0.8.5) | ||
| SmartGene ASP-IDNS®−5 pipeline for NGS data using the ‘‘Provirus Pipeline’’ version 2.0.5_HIV1_v1.4 | ||
| ANRS algorithm | http://www.hivfrenchresistance.org | |
| MIPseq data analysis | Refer to Einkauf et al.38 | N/A |
| FlowJo 10 | FlowJo, LLC | https://www.flowjo.com |
| Graphpad Prism 9 | Graphpad | https://graphpad.com |
| Cytobank software package | Cytobank | https://premium.cytobank.org/cytobank/ |
| Prism | Graphpad, version 8.2.1 | https://www.graphpad.com/scientific-software/prism |
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| Sequence | ||
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| RNAseq sequences for LN DCs | Gene Expression Omnibus (GEO) | GSE196066 |
| Near-full length proviral sequences obtained from LN DC subpopulations and CD4 T cells | GenBank | OM795243-OM795291. |
| Protease/reverse transcriptase and Integrase sequences from HIV virion-associated RNA | Sequence Read Archive (SRA) database | SMN35564308-315 |