KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-human CD3-PE, Clone HIT3a | BioLegend | Cat. #300308 |
| anti-human CD4-Alexa Fluor700, Clone RPA-T4 | BioLegend | Cat. #300526 |
| anti-human CD8-APC/Cy7, Clone RPA-T8 | BioLegend | Cat. #301016 |
| anti-human CD19-BV421, Clone HIB19 | BioLegend | Cat. #302233 |
| anti-human CD45-FITC, Clone HI30 | BioLegend | Cat. #304006 |
| anti-mouse CD45-APC, Clone 30F11 | BioLegend | Cat. #103112 |
| anti-human CCR7(CD197)-PE, Clone G043H7 | BioLegend | Cat. #353203 |
| anti-human HLA-A,B,C-APC, Clone W6/32 | BioLegend | Cat. #311410 |
| Bacterial and Virus Strains | ||
| HIV-1 NL43 Nef-IRES-GFP (BaL envelope) | Murooka et al. 2012 | N/A |
| HIV-1 NL43 Nef-IRES-Tomato (BaL envelope) | This paper | N/A |
| HIV-1 NL43 Nef-IRES-GFP-ΔNef (BaL envelope) | This paper | N/A |
| HIV-1 NL43 Nef-IRES-GFP-NefF191A (BaL envelope) | This paper | N/A |
| HIV-1 NL43 Nef-IRES-GFP-NefLLAA (BaL envelope) | This paper | N/A |
| HIV-1 NL43 Nef-IRES-GFP-ΔEnv (BaL envelope) | This paper | N/A |
| HIV-1 NL43 Nef-IRES-GFP-ΔEnv ΔNef (BaL envelope) | This paper | N/A |
| HIV-1 NL43 Nef-IRES-GFP-ΔVpu (BaL envelope) | This paper | N/A |
| HIV-1 NL43-NefF191A (BaL envelope) | This paper | N/A |
| HIV-1 NL43-ΔNef (BaL envelope) | This paper | N/A |
| Biological Samples | ||
| Human de-identified peripheral blood mononuclear cells | MGH Blood Bank | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Critical Commercial Assays | ||
| QIAamp viral RNA kit | Qiagen | Cat. #52904 |
| QIAquick PCR Purification Kit | Qiagen | Cat. #28106 |
| AllPrep DNA/RNA Mini Kit | Qiagen | Cat. #80204 |
| QuantiFast SYBR Green RT-PCR Kit | Qiagen | Cat. #204154 |
| QuantiTect SYBR Green RT-PCR kit | Qiagen | Cat. #204243 |
| FastStart Essential DNA Green Master mix | Roche | Prod. #06924204001 |
| SuperScript® III One-Step RT-PCR System with Platinum® Taq High Fidelity DNA Polymerase | Thermo Fisher | Cat. #12574030 |
| TaKaRa Ex Taq® DNA Polymerase Hot-Start Version | Clontech | Cat. #RR006A |
| GenElute HP Plasmid Maxiprep Kit | Sigma | Prod. #NA0310-1KT |
| Deposited Data | ||
| Experimental Models: Cell Lines | ||
| HEK 293T Cells | ATCC | Cat. #CRL-11268 |
| MAGI CCR5+ Cells | NIH AAARP | Cat. #3580 |
| TZM-bl Cells | NIH AAARP | Cat. #8129 |
| Experimental Models: Organisms/Strains | ||
| NOD-scid mice | Jackson Laboratories | Stock #001303 |
| NOD-scid × γc−/− mice | Jackson Laboratories | Stock #005557 |
| Oligonucleotides | ||
| Refer to Table S1 | ||
| Recombinant DNA | ||
| Software and Algorithms | ||
| Imaris 8.2 | Bitplane | http://www.bitplane.com |
| ImageJ | Freeware/NIH | https://imagej.nih.gov/ij/ |
| Prism 6 | GraphPad | https://www.graphpad.com |
| FlowJo | Treestar | https://www.flowjo.com/ |
| Other | ||