KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| B2M-FITC | Biolegend | 316304; RRID:AB_492837 |
| B2M-PE | Biolegend | 316305; RRID:AB_492840 |
| B2M-APC | Biolegend | 316311; RRID:AB_10643412 |
| CD8-PeCy7 | BD Biosciences | 557746; RRID:AB_396852 |
| CD4-FITC | Biolegend | 300505; RRID:AB_314073 |
| TCRa/b-BV421 | Biolegend | 306721; RRID:AB_2562077 |
| Ghost Dye red 780 | Tonbo | 13-0865-T100 |
| Ghost Dye violet 450 | Tonbo | 13-0863-T100 |
| eBioscience Fixable Viability Dye eFluor 780 | Thermo Fisher Scientific | 65-0865-14 |
| CD25 PE-Cy7 | BD | 557741; RRID:AB_396847 |
| CD69 PerCP | BioLegend | 310927; RRID:AB_10696423 |
| 4-1BB BV711 | BioLegend | 309831; RRID:AB_2650990 |
| TNF-a Pacific Blue | BioLegend | 502920; RRID:AB_528965 |
| IL-2 APC | BD | 341116; RRID:AB_400574 |
| IFN-g FITC | BioLegend | 502505; RRID:AB_315230 |
| anti-FLAG | Sigma | F3165; RRID:AB_259529 |
| anti-p24 | Abcam | Ab9071; RRID:AB_306981 |
| IR680RD IgG | LI-COR | 926-68070; RRID:AB_1095658 |
| IR800CW IgG | LI-COR | 925-32211; RRID:ab_2651127 |
| Bacterial and virus strains | ||
| Mach1 chemically competent E. Coli | UC Berkeley QB3 MacroLab | https://qb3.berkeley.edu/facility/qb3-macrolab/services/#services-molecular-biology-reagents |
| Biological samples | ||
| Human PBMCs | Blood Centers of the Pacific, University of California, San Francisco | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Cas9-NLS recombinant protein | UC Berkeley QB3 MacroLab | https://qb3.berkeley.edu/facility/qb3-macrolab/projects/#projects-cas9-nls-purified-protein |
| Cas9 crRNA and tracrRNA | Horizon Discovery | https://horizondiscovery.com/en/gene-editing/gene-editing-reagents/crispr-guide-rna |
| Polyethylenimine | Polysciences Inc. | 24314 |
| P3 Primary Cell Nucleofector Solution | Lonza | V4SP-3096 |
| SE. Nucleofector Solution | Lonza | V4SC-1096 |
| eBioscience Brefeldin A Solution | Invitrogen | 00-4506-51 |
| QuickExtract | Lucigen | QE09050 |
| Q5 polymerase | NEB | M0491S |
| PrimeStar GXL DNA polymerase | Takara Bio | R050B |
| SPRI beads | UC Berkeley Sequencing Core | https://ucberkeleydnasequencing.com/reagents-for-sale |
| Critical commercial assays | ||
| EasySep magnetic Cell Isolation kit | STEMCELL | 17951 |
| Lenti-X p24 rapid titer kits | Takara Bio | 632200 |
| Cell Line Optimization 4D-Nucleofector X Kit | Lonza | V4XC-9064 |
| MycoAlert mycoplasma detection kit | Lonza | LT07-118 |
| CellTrace Violet Cell Proliferation Kit | Thermo Fisher Scientific | C34557 |
| FIX & PERM Cell Fixation & Cell Permeabilization Kit | Thermo Fisher Scientific | GAS003 |
| Deposited data | ||
| Raw MiSeq sequencing files for analysis of genome editing | This paper | NIH NCBI Bioproject PRJNA680046 |
| Experimental models: Cell lines | ||
| Jurkats | UC Berkeley Cell Culture Facility | https://bds.berkeley.edu/facilities/cell-culture |
| A549 | UC Berkeley Cell Culture Facility | https://bds.berkeley.edu/facilities/cell-culture |
| 293T | UC Berkeley Cell Culture Facility | https://bds.berkeley.edu/facilities/cell-culture |
| Lenti-X | UC Berkeley Cell Culture Facility | https://bds.berkeley.edu/facilities/cell-culture |
| CCRF-CEM | UC Berkeley Cell Culture Facility | https://bds.berkeley.edu/facilities/cell-culture |
| HuT 78 | UC Berkeley Cell Culture Facility | https://bds.berkeley.edu/facilities/cell-culture |
| Oligonucleotides | ||
| See Tables S1–S3 | IDT | N/A |
| Recombinant DNA | ||
| Plasmids generated for this paper (Gag-Cas9, HIV-1 envelope, lentiviral expression of guide RNA plasmids transient expression of guide RNA plasmids) | This paper | Addgene plasmid #171060, 171061, 171625, 171628, 171632, 171633, 171634, 171635, 171636, 171637 |
| psPax2 | psPAX2 was a gift from Didier Trono | Addgene plasmid #12260 |
| pCMV-VSV-G | pCMV-VSV-G was a gift from Bob Weinberg | Addgene plasmid #8454 |
| pCF221 | pCF221 was a gift from David Savage | Addgene plasmid #121669 |
| Software and algorithms | ||
| Prism v7 or v8 | Graphpad | https://www.graphpad.com/scientific-software/prism/ |
| Inference of CRISPR Edits (ICE) | Synthego | https://ice.synthego.com |
| CRISPResso2 | https://github.com/pinellolab/CRISPResso2 | |