KEY RESOURCES TABLE
| REAGENT or RESOURCESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CD3-BUV805 clone UCHT1 | BD Biosciences | cat# 565515; RRID:AB_2739277 |
| CD4-BB700 clone SK3 | BD Biosciences | cat# 566392; RRID:AB_2744421 |
| CD8-BUV496 clone RPA-T8 | BD Biosciences | cat# 564804; RRID:AB_2744460 |
| CD14-BV510 clone M5E2 | Biolegend | cat# 301842; RRID:AB_2561946 |
| CD19-BV510cloneHIB19 | Biolegend | cat# 302242; RRID:AB_2561668 |
| CD25-BUV737 clone 2A3 | BD Biosciences | cat# 564385; RRID:AB_2744342 |
| CD27-BV570 clone O323 | Biolegend | cat# 302825; RRID:AB_11149686 |
| CD38-BUV661 clone HIT2 | BD Biosciences | cat# 565069; RRID:AB_2744377 |
| CD45RA-BUV563 clone HI100 | BD Biosciences | cat# 565702; RRID:AB_2744407 |
| CD69-PE clone FN50 | BD Biosciences | cat# 555531; RRID:AB_395916 |
| CD95-BV711 clone DX2 | Biolegend | cat# 305644; RRID:AB_2632623 |
| CD127-BV480 clone HIL-7R-M21 | BD Biosciences | cat# 566101 |
| CCR4-PE-CF594 clone 1G1 | BD Biosciences | cat# 565391; RRID:AB_2739215 |
| CCR5-BV650 clone 3A9 | BD Biosciences | cat# 564999; RRID:AB_2739037 |
| CCR6-BV421 clone 11A9 | BD Biosciences | cat# 562515; RRID:AB_11154229 |
| CCR7-APC-Cy7 clone G043H7 | Biolegend | cat# 353211; RRID:AB_10915272 |
| CXCR3-AF700 clone G025H7 | Biolegend | cat# 353731; RRID:AB_2563532 |
| CXCR4-PE Cy5 clone 12G5 | BD Biosciences | cat# 555975; RRID:AB_396268 |
| CXCR5-BB515 clone RF8B2 | BD Biosciences | cat# 564624; RRID:AB_2738871 |
| HLA DR-BV605 clone G46-6 | BD Biosciences | cat# 562845; RRID:AB_2744478 |
| FoxP3-PE Cy7 clone 236A/E7 | eBioscience | cat# 25-4777-42; RRID:AB_2573450) |
| Ki67-BUV395 clone B56BDBiosciencescat# 56 | BD Biosciences | cat# 564071; RRID:AB_2738577 |
| PD-1-BV785 clone EH12.2H7 | Biolegend | cat# 329930; RRID:AB_2563443 |
| SLeX (CD15s)-AF647 clone CSLEX1 | BD Biosciences | cat# 563526; RRID:AB_2738258 |
| CLA-AF647 clone HECA-452 | Biolegend | cat# 321309; RRID:AB_2563661 |
| CD19-142Nd clone HIB19 | Fluidigm | cat# 3142001; RRID: AB_2651155 |
| CD8-146Nd clone RPAT8 | Fluidigm | cat# 3146001B; RRID: AB_2687641 |
| CD62L-153Eu clone DREG56 | Fluidigm | cat# 3153004B; RRID: AB_2810245 |
| TIGIT-154Sm clone MBSA43 | Fluidigm | cat# 3154016B; RRID: NA |
| CCR7-159Tb clone G043H7 | Fluidigm | cat# 3159003A; RRID: AB_2714155 |
| CD27-167Er clone L128 | Fluidigm | cat# 3167006B; RRID: AB_2811093 |
| CD45RA-169Tm clone HI100 | Fluidigm | cat# 3169008B; RRID: NA |
| CD3-170Er clone UCHT1 | Fluidigm | cat# 3170001B; RRID: AB_2811085 |
| CD4-174Yb clone SK3 | Fluidigm | cat# 3174004B; RRID: AB_2687862 |
| Human Survivin Antibody clone 91630 | R&D Systems | cat# MAB886, RRID:AB_2243438 |
| HIV-1 core antigen-FITC, clone KC57 | Beckman Coulter | cat# 6604665, RRID:AB_1575987 |
| Human Fucosyltransferase 7/FUT7 Antibody clone 795116 | R&D Systems | cat# MAB64091 |
| B4GALT5 polyclonal antibody | Novus | cat# NBP2-14882 |
| GAPDH antibody, clone 14C10 | Cell Signaling Technology | cat# 2118, RRID:AB_561053 |
| Peroxidase AffiniPure Donkey Anti-Rabbit IgG (H+L) | Jackson ImmunoResearch | cat# 711–035-152, RRID:AB_10015282 |
| FUT6 Polyclonal Antibody | Thermo Fisher | cat# PA5-96261, RRID:AB_2808063 |
| Bacterial and Virus Strains | ||
| dfHIV | Generously provided to us by Dr. Leonard Chavez at Vitalant Research Institute | N/A |
| HIV-1 1MB | The Virus and Reservoirs Core at Penn Center for AIDS Research | N/A |
| HIV-1 89.6 | The Virus and Reservoirs Core at Penn Center for AIDS Research | N/A |
| HIV-1 DH12 | The Virus and Reservoirs Core at Penn Center for AIDS Research | N/A |
| HIV-1 NL43 | The Virus and Reservoirs Core at Penn Center for AIDS Research | N/A |
| Biological Samples | ||
| CD4+ T cells isolated from PBMC of HIV-infected antiretroviral therapy (ART)-suppressed individuals | External Quality Assurance Program Oversight Laboratory (EQAPOL)- Duke Human Vaccine Institute’s Immunology and Virology Quality | N/A |
| CD4+ T cells isolated from PBMC of HIV-infected ART-suppressed individuals | The Wistar Institute and Philadelphia FIGHT | N/A |
| PBMCs from HIV-infected viremic and ART-treated individuals | INER-CIENI (Mexico) | N/A |
| PBMC from healthy individuals | University of Pennsylvania Human Immunology Core | N/A |
| Normal mouse serum | Thermo Fisher | cat# 501121171 |
| Normal rat serum | Thermo Fisher | cat# 10710C |
| Human serum | Sigma-Aldrich | cat# H4522-20ML |
| Chemicals, Peptides, and Recombinant Proteins | ||
| RPMI1640 medium | Corning | cat# 10-040-CM |
| Penicillin-Streptomycin | GIBCO | cat# 15140163 |
| Fetal Bovine Serum | GIBCO | cat# 10437028 |
| Recombinant Human IL-2 | Prepotech | cat# 200-20 |
| Recombinant Human TNF-α | Prepotech | cat# 300-01A |
| cis-Diammineplatinum(II) dichloride | Sigma-Aldrich | cat# P4394-25MG |
| AOL-biotin conjugated | TCI America | cat# A26591 ML |
| APC Streptavidin | Biolegend | cat# 405207 |
| Ulex Europaeus Agglutinin I (UEA I), Fluorescein | Vector Labs | cat# FL-1061-2 |
| Critical Commercial Assays | ||
| TaqMan Universal Master Mix II, with UNG | Applied Biosystems | cat# 4440038 |
| TaqMan Copy Number Reference Assay, human, TERT | Applied Biosystems | cat# 4403316 |
| TaqMan RNA-to-CT 1-Step Kit | Applied Biosystems | cat# 4392656 |
| Human RPLP0 (Large Ribosomal Protein) Endogenous Control | Applied Biosystems | cat# 4310879E |
| Brilliant Stain Buffer Plus | BD BioSciences | cat# 566385 |
| Fixation/Permeabilization Solution Kit | BD BioSciences | cat# 554714 |
| Perm/Wash Buffer | BD BioSciences | cat# 554723 |
| Blotting-Grade Blocker | BIO-RAD | cat# 1706404 |
| Falcon 48-well Clear Flat Bottom TC-treated Cell Culture Plate | Corning | cat# 353230 |
| Foxp3/Transcription Factor Staining Buffer Set | eBioscience | cat# 00-5523-00 |
| Cell-ID 20-Plex Pd Barcoding Kit | Fluidigm | cat# 201060 |
| CyFACS buffer | Fluidigm | cat# MB-008 |
| Cell-IDTM DNA Intercalator-Ir | Fluidigm | cat# 201192A |
| Maxpar cell staining buffer | Fluidigm | cat# 201068 |
| Maxpar PBS | Fluidigm | cat# 201058 |
| Maxpar Cell Acquisition Solution | Fluidigm | cat# 201240 |
| EQTM calibration beads | Fluidigm | cat# 201078 |
| Cy®3 Mono 5-pack | GE Healthcare | cat# GEPA23001 |
| Dynabeads Human T-Activator CD3/CD28 for T Cell Expansion and Activation | GIBCO | cat# 11131D |
| eBioscience Foxp3 / Transcription Factor Staining Buffer Se | Invitrogen | cat# 00-5523-00 |
| LIVE/DEAD Fixable Violet Dead Cell Stain Kit, for 405 nm excitation | Invitrogen | cat# L34955 |
| ProteoExtract Subcellular Proteome Extraction Kit | Merck | cat# 539790 |
| DEAE-dextran | MilliporeSigma | cat# D-9885 |
| Anti-rat kappa MicroBeads | Miltenyi Biotec | cat# 130-047-401 |
| LS columns | Miltenyi Biotec | cat# 130-042-401 |
| QuadroMACS Separator | Miltenyi Biotec | cat# 130-090-976 |
| MACS MultiStand | Miltenyi Biotec | cat# 130-042-303 |
| HIV Infectivity Enhancement Reagent | Miltenyi Biotec | cat# 130-095-093 |
| NEBNext Ultra RNA Library Prep Kit for Illumina | New England Biolabs | cat# E7530S |
| Bright-Glo Luciferase Assay System | Promega | cat# E2610 |
| AllPrep DNA/RNA/miRNA Universal Kit | QIAGEN | cat# 80224 |
| RNase-Free DNase Set | QIAGEN | cat# 79254 |
| Bovine Serum Albumin | R&D Systems | cat# 5217 |
| CyFACS buffer | Rockland | cat# MB-008 |
| EasySep Human CD4+ T Cell Isolation Kit | Stem Cell | cat# 17952 |
| NuPAGE 4-12% Bis-Tris Protein Gels, 1.0 mm, 12-well | Thermo Fisher | cat# NP0322BOX |
| NuPAGE Sample Reducing Agent (10X) | Thermo Fisher | cat# NP0004 |
| NuPAGE LDS Sample Buffer (4X) | Thermo Fisher | cat# NP0007 |
| iBlot 2 Transfer Stacks, nitrocellulose, mini | Thermo Fisher | cat# IB23002 |
| Novex Sharp Pre-stained Protein Standard | Thermo Fisher | cat# LC5800 |
| SuperSignal West Pico PLUS Chemiluminescent Substrate | Thermo Fisher | cat# 34580 |
| RIPA Lysis and Extraction Buffer | Thermo Fisher | cat# 89900 |
| Bicinchoninic acid (BCA) assay | Thermo Fisher | cat# 23235 |
| Halt Protease Inhibitor Cocktail (100X) | Thermo Fisher | cat# 87786 |
| CL-XPosure Film, 8 × 10 in. (20 × 25 cm) | Thermo Fisher | cat# 34091 |
| Deposited Data | ||
| RNaseq data | Deposited to GEO (https://www.ncbi.nlm.nih.gov/geo/) | Accession number GSE151453 |
| Experimental Models: Cell Lines | ||
| ACH-2 | NIH AIDS Reagent Program | cat# 349 |
| H9 | NIH AIDS Reagent Program | cat# 87 |
| TZM-bl | NIH AIDS Reagent Program | cat# 8129 |
| Oligonucleotides | ||
| F522-43 (5′ GCC TCA ATA AAG CTT GCC TTGA3′ | IDT | (Kumar et al., 2007) |
| R626-43 (5′ GGG CGC CAC TGC TAG AGA3′ | IDT | (Kumar et al., 2007) |
| FAM-BQ probe (5′ CCA GAG TCA CAC AAC AGA CGG GCA CA 3′ | IDT | (Kumar et al., 2007) |
| Software and Algorithms | ||
| FlowJo software (Tree Star). | https://www.flowjo.com/ | RRID:SCR_008520 |
| bowtie2 | http://bowtie-bio.sourceforge.net/index.shtml | RRID:SCR_005476 |
| RSEM v1.2.12 | http://deweylab.biostat.wisc.edu/rsem/ | RRID:SCR_013027 |
| DESeq2 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html | RRID:SCR_015687 |
| QIAGEN’s Ingenuity® Pathway Analysis software | https://digitalinsights.qiagen.com/ | RRID:SCR_008653 |
| Prism 6.0 and 7.0 | http://www.graphpad.com/ | RRID:SCR_002798 |
| Rstudio | https://rstudio.com/ | RRID:SCR_000432 |
| FACSDiva software | http://www.bdbiosciences.com/instruments/software/facsdiva/index.jsp | RRID:SCR_001456 |
| HiSeq control software | https://www.illumina.com/systems/sequencing-platforms/hiseq-2500/products-services/hiseq-control-software.html | N/A |