| Antibodies |
|
|
|
| Mouse anti-human CD206 BV421 (clone 19.2) |
Becton Dickinson |
Cat# 566281; RRID:AB_2739655 |
| Mouse anti-human CD11c PerCP-Cy5.5 (clone B-ly6) |
Becton Dickinson |
Cat# 565227; RRID:AB_2739122 |
| Mouse anti-human CD16 APC (clone 3G8) |
Biolegend |
Cat# 302012; RRID:AB_314212 |
| Mouse anti-human CD11b BV650 (clone ICRF44) |
Becton Dickinson |
Cat# 740566; RRID:AB_2740267 |
| Mouse anti-human CD14 FITC (clone M5E2) |
Biolegend |
Cat# 301804; RRID:AB_314186 |
| Mouse anti-human β2-Microglobulin PE (clone TU99) |
Becton Dickinson |
Cat# 551337; RRID:AB_394152 |
| Mouse anti-human HLA-DR Pacific Blue (TU36) |
Life Technologies |
Cat# MHLDR28; RRID: AB_10401403 |
| Human anti-human CD14 PE (clone REA599) |
Miltenyi Biotec |
Cat# 130-110-519; RRID:AB_2655051 |
| Human anti-human CD16 APC (clone REA423) |
Miltenyi Biotech |
Cat# 130-106-705; RRID:AB_2655406 |
| Ghost Dye™ Violet 510 |
Tonbo Biosciences |
Cat# 13-0870-T100 |
| Ghost Dye™ Violet 780 |
Tonbo Biosciences |
Cat# 13-0865-T100 |
| Human TruStain FcX (Fc Receptor Blocking Solution) |
Biolegend |
Cat# 422302 |
| Rabbit recombinant monoclonal Anti-ATP6V1A |
Abcam |
Cat# EPR19270; RRID: AB_199326 |
| Rabbit polyclonal anti-CSE1L |
Proteintech |
Cat# 22219-1-AP; RRID:AB_10950892 |
| Rabbit polyclonal anti-GNE |
Proteintech |
Cat# 25079-1-AP |
| Rabbit monoclonal anti-β-Actin |
Cell Signaling Technology |
Cat# 4970P; RRID:AB_2223172 |
| Mouse monoclonal anti-GAPDH |
Sigma |
Cat# G8795; RRID:AB_1078991 |
| Mouse monoclonal anti-p24 |
AIDS Reagent |
Cat# 183-H12-5C; RRID:AB_2819250 |
| Rabbit polyclonal anti-SAMHD1 |
Proteintech |
Cat# 12586-1-AP; RRID:AB_2183496 |
| Donkey anti-mouse Alexa Fluor 488 |
Invitrogen |
Cat# A-21202; RRID:AB_141607 |
|
| Bacterial and virus strains |
|
|
|
| HIV LAI-YU2 |
Gummuluru, Boston University |
N/A |
|
M. tuberculosis (Erdman Strain pMV261-eGFP) |
Stanley Lab, UC Berkeley |
ATCC #35801 |
|
M. bovis bacillus Calmette-Guerin (BCG) δAg85B/Ag85B-mCherry |
Ernst Lab, UCSF |
N/A |
|
| Biological samples |
|
|
|
| Leukoreduction chambers from healthy human donors |
Vitalant |
N/A |
| 1/10 Leukapheresis pack |
STEMCELL |
200-0092 |
|
| Chemicals, peptides, and recombinant proteins |
|
|
|
| Cas9-NLS purified protein |
QB3 Macrolab |
N/A |
| GM-CSF Human Recombinant |
Life Technologies |
Cat# PHC2015 |
| IL-4 Human Recombinant Protein |
Life Technologies |
Cat# PHC0045 |
| Triton™ X-100 (for molecular biology) |
Sigma-Aldrich |
Cat# T8787 |
| NaCl |
Corning |
Cat# 46-032-CV |
| PEG-6000 |
Millipore Sigma |
Cat# 8074911000 |
| Glycerol |
Sigma-Aldrich |
Cat# G7893 |
| Tween-80 |
N/A |
N/A |
| PolyJet |
Signagen |
Cat# SL100688 |
| Penicillin/Streptomycin |
Corning |
Cat# 30-002-Cl |
| Ficoll-Paque Density Gradient |
Sigma-Aldrich |
Cat# GE17-1440-03 |
| Hygromycin B |
N/A |
N/A |
| Kanamycin |
N/A |
N/A |
| Albumin |
Sigma |
Cat# A1470-100G |
| Dextrose |
Fisher |
Cat# D16500
|
| Catalase |
Sigma |
Cat# C9322-5G |
| Saponin |
Sigma |
Cat# 47036 |
| Phusion Hot Start 2X Master Mix |
New England Biolabs |
Cat# M0536L |
| HCS CellMask™ Green Stain |
ThermoFisher Scientific |
Cat# H32714
|
| HCS CellMask™ Deep Red Stain |
ThermoFisher Scientific |
Cat# H32721
|
| Hoechst 33258 |
Sigma-Aldrich |
Cat# 861405 |
| RPMI 1640 with 1x L-Glutamine |
Corning |
MT10040CV |
| HEPES |
VWR |
16777-032 |
| Sodium Pyruvate |
Fisher |
MT 25-000-CI |
| PMA |
Fisher |
BP685-1 |
|
| Critical commercial assays |
|
|
|
| StemCell™ Human Monocyte Isolation Kit |
STEMCELL Technologies |
Cat# 19359 |
| P2 Primary Cell 4D-Nucleofector™ X Kit L |
Lonza |
Cat# V4XP-2024 |
| CellTiter-Glo Luminescent Cell Viability Assay |
Promega |
Cat# G7570 |
| RNeasy 96 QIAcube HT Kit |
QIAGEN |
Cat# 74171 |
| QuantSeq 3′ mRNA-seq Library Prep Kit FWD for Illumina |
Lexogen |
Cat# 015 |
|
| Experimental models: cell lines |
|
|
|
|
Homo sapiens: 293T/17 |
UCSF CCF |
N/A |
|
Homo sapiens: THP-1 |
ATCC |
TIB-202 |
|
| Oligonucleotides |
|
|
|
| Primer: PPIA Forward TGTTGACAGGGTGGTGACTTCA |
IDT |
N/A |
| Primer: PPIA Reverse ACTTAATTggttgggcgcagtg |
IDT |
N/A |
| Primer: CXCR4 Forward AGAGGAGTTAGCCAAGATGTGACTTTGAAACC |
IDT |
N/A |
| Primer: CXCR4 Reverse GGACAGGATGACAATACCAGGCAGGATAAGGCC |
IDT |
N/A |
| Primer: CCR5 Forward TGCTTGGCCAAAAAGAGAGTTA |
IDT |
N/A |
| Primer: CCR5 Reverse TTTAAAGCAAACACAGCATGGA |
IDT |
N/A |
| Primer: SAMHD1-01 Forward #1 GTAGCCATGCAGCGAGCCGATT |
IDT |
N/A |
| Primer: SAMHD1-01 Reverse #1 AGGGACCCGAGTCTCGCTTGTC |
IDT |
N/A |
| Primer: SAMHD1-01 Forward #2 TTTGAGGACGACTGGACTGC |
IDT |
N/A |
| Primer: SAMHD1-01 Reverse #2 CTCCCATCCTACGAATCGCC |
IDT |
N/A |
| Primer: SAMHD1-02 Forward CGGTGGAGAAGCAGTTGTCT |
IDT |
N/A |
| Primer: SAMHD1-02 Reverse TGGGAAGCTAAAATCGTTCCA |
IDT |
N/A |
| Primer: SAMHD1-03 Forward TCAAATAGCTTTGACTTTGCAC |
IDT |
N/A |
| Primer: SAMHD1-03 Reverse GCCTCAATTTTCTCATCAATAAA |
IDT |
N/A |
| Primer: SAMHD1-04 Forward ACATCTTGTCATTTCCGTTAGT |
IDT |
N/A |
| Primer: SAMHD1-04 Reverse GCCTCAATTTTCTCATCAATAAAA |
IDT |
N/A |
| Primer: SAMHD1-05 Forward TGGCTTTACTAATCTGCCTCCTCA |
IDT |
N/A |
| Primer: SAMHD1-05 Reverse TCACGGAGAGACCTGGCTGT |
IDT |
N/A |
| tracrRNA |
Dharmacon |
Cat# U-002005-0050 |
| Non-targeting crRNA GTCGACGTTATTGCCGGTCG |
Dharmacon |
Cat# U-007503-01-0020 |
| SAMHD1 crRNA 1 GTGCTGCTGAAGAACATCCG |
Dharmacon |
Cat# CM-013950-01-0020 |
| SAMHD1 crRNA 2 CTTACCTGTCAGCTTAGTAT |
Dharmacon |
Cat# CM-013950-02-0020 |
| SAMHD1 crRNA 3 CGATACATCAAACAGCTGGG |
Dharmacon |
Cat# CM-013950-03-0020 |
| SAMHD1 crRNA 4 GTGTATCAATGATTCGGACG |
Dharmacon |
Cat# CM-013950-04-0020 |
| SAMHD1 crRNA 5 GGTGTAAAGAGTTGCGAGTG |
Dharmacon |
Cat# CM-013950-05-0020 |
| CXCR4 crRNA GAAGCGTGATGACAAAGAGG |
Dharmacon |
N/A (Custom synthesis) |
| CCR5 crRNA CCTGCCTCCGCTCTACTCAC |
Dharmacon |
N/A (Custom synthesis) |
| β2-microglobulin crRNA GAGTAGCGCGAGCACAGCTA |
Dharmacon |
N/A (Custom synthesis) |
| PPIA crRNA ACTGCCAAGACTGAGTGGTA |
Dharmacon |
CM-004979-03-0020 |
| AAVS1 crRNA GTCACCAATCCTGTCCCTAG |
Dharmacon |
N/A (Custom synthesis) |
|
| Recombinant DNA |
|
|
|
| HIV LAI-YU2 plasmid |
Gummuluru Lab, Boston University |
N/A |
|
| Software and algorithms |
|
|
|
| GraphPad Prism v8.3.0 |
GraphPad Software, LLC |
RRID: SCR_002798 https://www.graphpad.com
|
| TIDE: Tracking of Indels by DEcomposition |
(Brinkman et al., 2014) |
http://tide.nki.nl/ |
| Benchling |
Benchling [Molecular Biology]. (2020). |
https://www.benchling.com |
| BioRender |
BioRender. (2020). |
https://www.biorender.com |
| ImageJ |
https://imagej.nih.gov/ij/ |
RRID: SCR_003070 https://imagej.nih.gov/ij/
|
| FlowJo 10 v10.6.1 |
Becton Dickinson |
RRID: SCR_008520 https://www.flowjo.com
|
| Primer3 |
|
https://primer3.org |
| Attune™ NxT Software v3.1.2 |
Life Technologies |
https://www.thermofisher.com/us/en/home/life-science/cell-analysis/flow-cytometry/flow-cytometers/attune-acoustic-focusing-flow-cytometer/attune-cytometer-software.html |
| HCS Studio™ Cell Analysis Software v6.6.0 |
ThermoFisher Scientific |
Cat# SX00041A |
| R: A Language and Environment for Statistical Computing |
R Development Core Team (2020) |
www.R-project.org/ |
|
| Other |
|
|
|
| Iscove’s Modified Dulbecoo’s Medium |
GIBCO |
Cat# 12440053 |
| RPMI 1640 Medium |
GIBCO |
Cat# 11-875-093 |
| Heat Inactivated Human AB Serum (lot 7J2616) |
Valley Biomedical Products & Services |
Cat# HP1022HI |
| Fetal Bovine Serum, Qualified One Shot™ |
GIBCO |
Cat# A3160502 |
| 4–20% Criterion TGX Gel |
Bio-Rad |
Cat# 567-1094 |
| PVDF Membrane |
Bio-Rad |
Cat# 1620177 |
| HyBlot CLR Audiogradiography Film |
Thomas Scientific |
Cat# 1159T41 |
| Pierce™ ECL Western Blotting Substrate |
ThermoFisher Scientific |
Cat# 32106 |
| 7H9 Middlebrook Medium |
BD Difco |
Cat# 271310 |
| Middlebrook OADC Growth Supplement |
Sigma-Aldrich |
Cat# M0678 |
| UltraComp eBeads Compensation Beads |
Life Technologies |
Cat# 01-2222-42 |
| Accutase Enzyme Cell Detachment Medium |
ThermoFisher Scientific (Invitrogen™)
|
Cat# 00-4555-56 |
| Falcon® 96-well Clear Flat Bottom Not Treated Cell Culture Microplate, With Lid, Sterile |
Corning |
Cat# 351178 |
| Falcon® 96-well Clear Flat Bottom Not Treated Cell Culture Microplate, With Lid, Sterile |
Corning |
Cat# 351172 |
| TempPlate Non-Skirted 96-well PCR Plate |
USA Scientific |
Cat# 1402-9598 |
| Konica Minolta SRX-101A Medical Film Processor |
Konica Minolta |
Cat# SRX-101A |
