KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
|
| ||
| Antibodies | ||
|
| ||
| anti-Human CD1c (Mouse monoclonal) | 3ioLegend | Cat# 331547; Clone L161; RRID: AB_2800871 |
| anti-Human CD163 (Mouse monoclonal) | 3ioLegend | Cat# 333637; Clone GHI/61; RRID: AB_2810510 |
| anti-Human CD141 (Mouse monoclonal) | 3ioLegend | Cat# 344125; Clone M80; RRID: AB_2810541 |
| anti-Human CD11a (Mouse monoclonal) | 3ioLegend | Cat# 350617; Clone TS2/4; RRID: AB_2800935 |
| anti-Human CD197 (Mouse monoclonal) | 3ioLegend | Cat# 353251;Clone G043H7; RRID: AB_2800943 |
| anti-Human CD14 (Mouse monoclonal) | 3ioLegend | Cat# 301859; Clone M5E2; RRID:AB_2800736 |
| anti-Human CD16 (Mouse monoclonal) | BioLegend | Cat# 302065; Clone 3G8; RRID: AB_2800738 |
| anti-Human CD19 (Mouse monoclonal) | BioLegend | Cat# 302265; Clone HIB19; RRID: AB_2800741 |
| anti-Human CD45RO (Mouse monoclonal) | BioLegend | Cat# 304259; Clone UCHL1; RRID: AB_2800766 |
| anti-Human CD2 (Mouse monoclonal) | BioLegend | Cat# 309231; Clone TS1/8; RRID: AB_2810464 |
| anti-Human CD138 (Mouse monoclonal) | BioLegend | Cat# 356539; Clone MI15; RRID: AB_2810567 |
| anti-Human CD303 (Mouse monoclonal) | BioLegend | Cat# 354241; Clone 201A; RRID: AB_2814295 |
| anti-Human CD56 (Mouse monoclonal) | BioLegend | Cat# 362559; Clone5.1h11; RRID: AB_2801002 |
| anti-Human CD4 (Mouse monoclonal) | BioLegend | Cat# 300567; Clone RPA-T4; RRID: AB_2800725 |
| anti-Human CD3 (Mouse monoclonal) | BioLegend | Cat# 300479; Clone UCHT1; RRID: AB_2800723 |
| anti-Human CD45RA (Mouse monoclonal) | BioLegend | Cat# 304163; Clone HI100; RRID: AB_2800764 |
| anti-Human CD39 (Mouse monoclonal) | BioLegend | Cat# 328237;Clone A1; RRID: AB_2800853 |
| anti-Human CD279 (Mouse monoclonal) | BioLegend | Cat# 329963;Clone EH12.2H7; RRID: AB_2800862 |
| anti-Human CD8 (Mouse monoclonal) | BioLegend | Cat# 344753; Clone SK1; RRID: AB_2800922 |
| anti-Human CD27 (Mouse monoclonal) | BioLegend | Cat# 302853; Clone O323; RRID: AB_2800747 |
| anti-Human CD20 (Mouse monoclonal) | BioLegend | Cat# 302363; Clone 2H7; RRID: AB_2800743 |
| anti-Human HLA-A/B/C (Mouse monoclonal) | BioLegend | Cat# 311449; Clone W6/32; RRID: AB_2800816 |
| anti-Human IgM (Mouse monoclonal) | BioLegend | Cat# 314547; Clone MHM-88; RRID: AB_2800835 |
| anti-Human CD127 (Mouse monoclonal) | BioLegend | Cat# 351356; Clone A019D5; RRID: AB_2800937 |
| anti-Human CD195 (Rat monoclonal) | BioLegend | Cat# 359137; Clone J418F1; RRID: AB_2810570 |
| anti-Human HLA-DR (Mouse monoclonal) | BioLegend | Cat# 307663; Clone L243; RRID: AB_2800795 |
| anti-Human IgG (Fc) (Rat monoclonal) | BioLegend | Cat# 410727; Clone M1310G05; RRID: AB_2801087 |
| anti-Human TCR Vd2 (Mouse monoclonal) | BioLegend | Cat# 331435; Clone B6; RRID: AB_2800864 |
| anti-Human TCR Va7.2 (Mouse monoclonal) | BioLegend | Cat# 351735;Clone 3C10; RRID: AB_2810556 |
| anti-Human TCR Va24-Ja18 (Mouse monoclonal) | BioLegend | Cat# 342925; Clone 6B11; RRID: AB_2810539 |
| anti-Human TCR g/d (Mouse monoclonal) | BioLegend | Cat# 331231; Clone B1; RRID AB_2814199 |
| anti-Human TCR Vg9 (Mouse monoclonal) | BioLegend | Cat# 331313; Clone B3; RRID: AB_2814203 |
| anti-Human CD7 (Mouse monoclonal) | BioLegend | Cat# 343127; Clone CD7–6B7; RRID: AB_2800914 |
| anti-Human CD11c (Mouse monoclonal) | BioLegend | Cat# 371521; Clone S-HCL-3; RRID: AB_2801018 |
| anti-Human CD185 (Mouse monoclonal) | BioLegend | Cat# 356939,;Clone J252D4; RRID: AB_2800968 |
| anti-Human CD1d (Mouse monoclonal) | BioLegend | Cat# 350319; Clone 51.1; RRID: AB_2800934 |
| anti-Human IgD (Mouse monoclonal) | BioLegend | Cat# 348245; Clone IA6–2; RRID: AB_2810553 |
| anti-Human CD11b (Mouse monoclonal) | BioLegend | Cat# 301359; Clone ICRF44; RRID: AB_2800732 |
| anti-Human CD62L (Mouse monoclonal) | BioLegend | Cat# 304851; Clone DREG-56; RRID: AB_2800770 |
| anti-Human CD66a/c/e (Mouse monoclonal) | BioLegend | Cat# 342325; Clone ASL-32; RRID: AB_2810538 |
| anti-Human CD15 (Mouse monoclonal) | BioLegend | Cat# 323053; Clone W6D3; RRID: AB_2800847 |
| anti-Human CD32 (Mouse monoclonal) | BioLegend | Cat# 303225; Clone FUN-2; RRID: AB_2814129 |
| anti-Human CD57 (Mouse monoclonal) | BioLegend | Cat# 393321; Clone QA17A04; RRID: AB_2801030 |
| anti-Human CD73 (Mouse monoclonal) | BioLegend | Cat# 344031; Clone AD2; RRID: AB_2800916 |
| anti-Human CD123 (Mouse monoclonal) | BioLegend | Cat# 306045; Clone 6H6; RRID: AB_2800789 |
| anti-Human Mouse IgG1, k Isotype Ctrl (Mouse monoclonal) | BioLegend | Cat# 400187; Clone MOPC-21; RRID: AB_2888921 |
| anti-Human Mouse IgG2a, k Isotype Ctrl (Mouse monoclonal) | BioLegend | Cat# 400293; Clone MOPC-173; RRID: AB_2888922 |
| anti-Human Mouse IgG2b, k Isotype Ctrl (Mouse monoclonal) | BioLegend | Cat# 400381; Clone MPC-11; RRID: AB_2888923 |
| anti-Human Rat IgG2b, k Isotype Ctrl (Rat monoclonal) | BioLegend | Cat# 400677; Clone RTK4530: RRID: AB_2894967 |
| anti-Human CD28 (Mouse monoclonal) | BioLegend | Cat# 302963; Clone CD28.2; RRID:AB_2800751 |
| anti-Human CD161 (Mouse monoclonal) | BioLegend | Cat# 339947; Clone HP-3G10; RRID: AB_2810532 |
| anti-Human CD95 (Mouse monoclonal) | BioLegend | Cat# 305651; Clone DX2; RRID: AB_2800787 |
| anti-Human CD38 (Mouse monoclonal) | BioLegend | Cat# 303543; Clone HIT2; RRID: AB_2800758 |
| anti-Human KLRG1 (Syrian hamster monoclonal) | BioLegend | Cat# 138433; Clone 2F1/KLRG1; RRID: AB_2800649 |
| anti-Human CD25 (Mouse monoclonal) | BioLegend | Cat# 302649; Clone BC96; RRID: AB_2800745 |
| anti-Human CD41 (Mouse monoclonal) | BioLegend | Cat# 303739; Clone HIP8; RRID: AB_2814134 |
| anti-Human CD184 (Mouse monoclonal) | BioLegend | Cat# 306533; Clone 12G5; RRID: AB_2800791 |
| anti-Human CD137 (Mouse monoclonal) | BioLegend | Cat# 309839; Clone 4B4–1; RRID: AB_2800807 |
| anti-Human CD24 (Mouse monoclonal) | BioLegend | Cat# 311143; Clone ML5; RRID: AB_2800813 |
| anti-Human CD274 (Mouse monoclonal) | BioLegend | Cat# 329751; Clone 29E.2A3; RRID: AB_2800860 |
| anti-Human CD96 (Mouse monoclonal) | BioLegend | Cat# 338423; Clone NK92.39; RRID: AB_2810531 |
| anti-Human CD194 (Mouse monoclonal) | BioLegend | Cat# 359425; Clone L291H4; RRID: AB_2800988 |
| anti-Human CD152 (Mouse monoclonal) | BioLegend | Cat# 369621; Clone BNI3; RRID: AB_2801015 |
| Hashl: anti-Human CD298 S b2-microglobulin (Mouse monoclonals) | BioLegend | Cat# 394661; Clone LNH-94; 2M2; RRID: AB_2801031 |
| Hash2: anti-Human CD298 S b2-microglobulin (Mouse monoclonals) | BioLegend | Cat# 394663; Clone LNH-94; 2M2; RRID: AB_2801032 |
| Hash3: anti-Human CD298 S b2-microglobulin (Mouse monoclonals) | BioLegend | Cat# 394665; Clone LNH-94; 2M2; RRID: AB_2801033 |
| Hash4: anti-Human CD298 S b2-microglobulin (Mouse monoclonals) | BioLegend | Cat# 394667; Clone LNH-94; 2M2; RRID: AB_2801034 |
| Hash5: anti-Human CD298 S b2-microglobulin (Mouse monoclonals) | BioLegend | Cat# 394669; Clone LNH-94; 2M2; RRID: AB_2801035 |
| Hash6: anti-Human CD298 S b2-microglobulin (Mouse monoclonals) | BioLegend | Cat# 394671; Clone LNH-94; 2M2; RRID: AB_2820042 |
| Hash7: anti-Human CD298 S b2-microglobulin (Mouse monoclonals) | BioLegend | Cat# 394673; Clone LNH-94; 2M2; RRID: AB_2820043 |
| Hash8: anti-Human CD298 S b2-microglobulin (Mouse monoclonals) | BioLegend | Cat# 394675; Clone LNH-94; 2M2, RRID: AB_2820044 |
| Hash9: anti-Human CD298 S b2-microglobulin (Mouse monoclonals) | BioLegend | Cat# 394677; Clone LNH-94; 2M2; RRID: AB_2820045 |
| Hash10: anti-Human CD298 S b2-microglobulin (Mouse monoclonals) | BioLegend | Cat# 394679; Clone LNH-94; 2M2; RRID: AB_2820046 |
| Mouse anti-human CD3 FITC | Becton Dickinson | Cat# 555332; Clone UCHT1; RRID: AB_395739 |
| Mouse anti-human CD8 PerCP-eF710 | eBiosciences | Cat# 46–0087-42; Clone SK1; RRID: AB_1834411 |
| Mouse anti-human CD14 V500 | Becton Dickinson | Cat# 562693; Clone M5E2; RRID: AB_2737727 |
| Mouse anti-human CD45RO eF650NC | eBiosciences | Cat# 95–0457-42; Clone UCHL1; RRID: AB_1603247 |
| Mouse anti-human CD4 APC | Becton Dickinson | Cat# 561841; Clone RPAT4; RRID: AB_395739 |
| Mouse anti-human CD45RA APC-H7 | Becton Dickinson | Cat# 560674; Clone HI100; RRID: AB_1727497 |
| Mouse anti-human CD19 PE-Cy5 | Invitrogen | Cat# MHCD1918; Clone SJ25-C1; RRID: AB_10373840 |
| Mouse anti-human CD56 PE-Cy7 | Becton Dickinson | Cat# 335809; Clone NCAM16.2; RRID: AB_399984 |
| Mouse IgG isotype control | Caltag | Cat# 10400C; RRID: AB_2532980 |
|
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| Biological samples | ||
|
| ||
| PBMC from MHRP RV217 donors | M. Robb | Robb et al., 2016 |
| PBMC from MHRP RV254 donors | D. Hsu | Ananworanich et al., 2013; De Souza et al., 2015 |
| PBMC from MHRP RV152 donors | A. Schuetz | Rerks-Ngarm et al., 2013 |
| PBMC from CDC BMCS donors | A. Hickey | van Griensven et al., 2013 |
|
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| Chemicals, peptides, and recombinant proteins | ||
|
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| Cell Staining Buffer | BioLegend | Cat# 420201 |
| TruStain FcX Blocking Reagent, human | BioLegend | Cat# 422301 |
| Acridine Orange | ThermoFisher Scientific | Cat# A3568 |
| Ethidium Homodimer | ThermoFisher Scientific | Cat# E1169 |
| Glycerin (Glycerol), 50% (v/v) | Ricca Chemical Co | Cat# 3290–16 |
| Buffer EB | Qiagen | Cat# 19086 |
| Tween 20, 10% (v/v) | Bio-Rad | Cat# 1610781 |
| SPRIselect beads | Beckman Coulter | Cat# 823318 |
| Guava ViaCount Reagent | Millipore Corp | Cat# 4000–0041 |
| Live/Dead Fixable Aqua | ThermoFisher | Cat# L34957 |
|
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| Critical commercial assays | ||
|
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| Chromium Single Cell 5’ Library & Gel Bead kit, v2 | 10x Genomics | Cat# 1000006 |
| Chromium Single Cell 5’ Feature Barcode Library kit | 10x Genomics | Cat# 1000080 |
| Single Index kit N, Set A | 10x Genomics | Cat# 1000212 |
| Single Index kit T, Set A | 10x Genomics | Cat# 1000213 |
| PhiX Control kit, v3 | Illumina | Cat# FC-110–3001 |
| High Sensitivity DNA kit | Agilent | Cat# 5067–4626 |
| Qubit dsDNA HS Assay kit | ThermoFisher Scientific | Cat# Q32854 |
| SMART-Seq v4 UltraLow Input RNA kit | Takara | Cat# 634891 |
| Single Cell RNA Purification kit | Norgen Biotek | Cat# 51800 |
| Nextera XT DNA Sample Preparation kit | Illumina | Cat# FC-131–1096 |
| ERCC RNA Spike-in Mix 1 | Life Technologies | Cat# 4456740 |
| NovaSeq 6000 S4 Reagent kit, 300 cycles, v1.5 | Illumina | Cat# 20028312 |
| MiSeq Reagent Nano kit, 500 cycles, v2 | Illumina | Cat# MS-103–1003 |
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| Deposited data | ||
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| RNA-seq analysis of human peripheral blood cells collected at multiple timepoints during the course of acute HIV-1 infection (RV217) | This paper | GEO: GSE192384; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE192384 |
| R code and data files for figures | This paper | https://doi.org/10.6084/m9.figshare.c.5728400 |
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| Software and algorithms | ||
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| FlowJo | FlowJo, LLC | https://www.flowjo.com/ |
| bcl2fastq | Illumina | https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2–20.html |
| featureCounts | Liao et al., 2014 | http://subread.sourceforge.net/ |
| Cell Ranger | Zheng et al., 2017 | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads |
| R | https://www.r-project.org/ | |
| DSB | Mulè et al., 2022 | https://github.com/niaid/dsb |
| edgeR | Robinson et al., 2010 | https://bioconductor.riken.jp/packages/devel/bioc/html/edgeR.html |
| geepack | H0jsgaard et al., 2006 | https://cran.r-project.org/web/packages/geepack/index.html |
| Seurat | Hao et al., 2021 | https://cran.r-project.org/web/packages/Seurat/index.html |
| GSEA | Subramanian et al., 2005 | https://www.gsea-msigdb.org/gsea/index.jsp |
| Metascape | Zhou et al., 2019 | https://metascape.org |
| Arlequin | Excoffier and Lischer, 2010 | http://cmpg.unibe.ch/software/arlequin35/Arl35Downloads.html |