Reagents and tools table
| Reagent/Resource | Reference or Source | Identifier or Catalog Number |
|---|---|---|
| Experimental models | ||
| BRGS HIS (M. musculus) | Li et al, 2018 (PMID30065364) | N/A |
| HEK-293T cells (H. sapiens) | ATCC | CRL-3216™ |
| Primary CD34+ cells (H. sapiens) | This study | N/A |
| THP-1 cells (H. sapiens) | ATCC | TIB-202™ |
| Recombinant DNA | ||
| pCMV-VSV-G | Addgene | #8454 |
| pHIV-1(BRU)-Δenv-IN(HA) |
Petit et al, 1999 (PMC112553) Petit et al, 2000 (PMC112230) |
N/A |
| pHIV-1(BRU)-Δenv-IN(HA)-Δnef-MS2 | Scoca et al, 2022 (PMC10117160) | N/A |
| pHIV-1(BRU)-Δenv-Δnef-IRESGFP | Rensen et al, 2021 (PMC7780146) | N/A |
| pMS2-GFP-NLS | Tantale et al, 2016 (PMC4974459) | N/A |
| pSD-GP-NDK | PlasmidFactory | N/A |
| pSIV3+ | Durand et al, 2013 (PMC3536400) | N/A |
| Antibodies | ||
| Donkey anti-mouse IgG (CY3) | Jackson Lab | #715-165-150 |
| Donkey anti-rabbit IgG (CY3) | Jackson Lab | #711-165-152 |
| Goat-anti-mouse gold-conjugated (6 nm) | Aurion | #806.022 |
| Goat anti-rabbit IgG (A488) | Invitrogen | #A32731 |
| Goat anti-rabbit IgG (A647) | Invitrogen | #A32795 |
| Goat-anti-rabbit gold-conjugated (10 nm) | Aurion | #810.011 |
| Goat anti-rat IgG (A647) | Invitrogen | #A-21247 |
| Mouse anti-human CD3 (BV510) | BioLegend | #344828 |
| Mouse anti-human CD4 (APC) | BD Biosciences | #555349 |
| Mouse anti-human CD8/CD8a (BV785) | BioLegend | #103108 |
| Mouse anti-human CD19 (PE6CF594) | BD Biosciences | #562294 |
| Mouse anti-human CD45 (BUV395) | BD Biosciences | #563792 |
| Mouse anti-p24 | NIH reagent | #ARP-3537 |
| Rabbit anti-CPSF6 | Novus Biologicals | #NBP1- 85676 |
| Rat anti-HA | Roche | #11867423001 |
| Rat anti-mouse CD45 (FITC) | BioLegend | #103108 |
| Oligonucleotides and other sequence-based reagents | ||
| Primary smiFISH probes against HIV-1 pol (x 24) | Integrated DNA Technologies | N/A |
| Secondary RNA FISH probe CY5 FLAP | Eurofins Genomics | N/A |
| Chemicals, Enzymes and other reagents | ||
| BD Cytofix Fixation Buffer | BD Biosciences | #554655 |
| Bovine Serum Albumin (BSA) | Sigma-Aldrich | #A9647 |
| Calcium Chloride solution | Sigma-Aldrich | #21115 |
| cOmplete, EDTA free (tablet) | Roche | #11873580001 |
| Deionized Formamide | Bio Basic | #FB0211 |
| DMEM (1X) + GlutaMAX™-I | Gibco | #31966 |
| DPBS (1X) | Gibco | #14190 |
| Ethylenediamine tetra-acetic acid disodium salt solution (EDTA) | Sigma-Aldrich | #E7889 |
| Ficoll-Paque™ PLUS | Cytiva | #17144003 |
| Fetal Bovine Serum (FBS) | Serana® | #S-FBS-SA-015 |
| Formaldehyde 4% | Sigma-Aldrich | #1004965000 |
| Gelatin | Merck | #104070 |
| Glutaraldehyde | Merck | #112179 |
| Glycine | Sigma-Aldrich | #G8898 |
|
HEPES-buffered saline, pH 7.0 (2X for transfection) |
Thermo Scientific Chemicals | #J62623.AK |
| HEPES solution (for cell culture) | Gibco | #15630 |
| Hoechst 33342 | Invitrogen | #H3570 |
| Human GM-CSF | Miltenyi Biotec | #130-093-862 |
| Human M-CSF | Miltenyi Biotec | #130-093-963 |
| Methylcellulose | Sigma-Aldrich | #M6385-250G |
| MEM Non-essential Amino Acid Solution | Sigma-Aldrich | #M7145 |
| NEBuffer™ 3 | New England BioLabs | #B7003S |
| Nevirapine | Sigma-Aldrich | #SML0097 |
| Paraformaldehyde 32% Aqueous Solution | Electron Microscopy Sciences | #15714 |
| PBS (RNase-free) | Invitrogen | #AM9625 |
| PBS | Gibco | #18912-014 |
| Penicillin Streptomycin (P/S) | Gibco | #15140 |
| PF74 | Sigma-Aldrich | #SML0835 |
| Phorbol 12-myristate 13-acetate (PMA) | Sigma-Aldrich | #P8139 |
| ProLong™ Diamond Antifade Mountant | Invitrogen | #P36970 |
| RIPA buffer | Sigma-Aldrich | #R0278 |
| RNaseZAP™ | Sigma-Aldrich | #R2020 |
| RPMI Medium 1640 (1X) + GlutaMAX™-I | Gibco | #61870 |
| Sodium Pyruvate | Gibco | #11360 |
| Stellaris® RNA FISH Hyb. Buffer | Biosearch™ Technologies | #SMF-HB1 |
| Stellaris® RNA FISH Wash Buffer A | Biosearch™ Technologies | #SMF-WA1 |
| Stellaris® RNA FISH Wash Buffer B | Biosearch™ Technologies | #SMF-WB1 |
| Sucrose | Sigma-Aldrich | #S0389-1KG |
| Triton™ X-100 | Sigma-Aldrich | #T8787 |
| Trypsin 0.05%-EDTA (1X) | Gibco | #253000 |
| TURBO DNase™ | Invitrogen | #AM2238 |
| UltraPure™ Distilled Water (H2O) | Invitrogen | #10977 |
| Uranyl acetate | Merck | #8473 |
| Vanadyl Ribonucleoside Complexes (VRC) | Sigma-Aldrich | #94742 |
| 5-Ethynyl-2′-deoxyuridine (EdU) | Invitrogen | #A10044 |
| Software | ||
| Digital micrograph suite (V3.43.3213.0) | https://www.gatan.com/products/tem-analysis/gatan-microscopy-suite-software | |
| SerialEM (v4.0.11) | University of Colorado, https://bio3d.colorado.edu/SerialEM/ | RRID:SCR_017293 |
| IMOD (v4.11.64) | University of Colorado, https://bio3d.colorado.edu/imod/ | RRID:SCR_003297 |
| UCSF ChimeraX (v1.7.1) | UCSF, https://www.cgl.ucsf.edu/chimerax/ | RRID:SCR_015872 |
| Ilastik (v1.4.0) | https://www.ilastik.org/ | RRID:SCR_015246 |
| Fiji (v1.54f) |
https://imagej.net/software/fiji/ Schindelin et al, 2012 (PMC3855844) |
|
| FlowJo™ Software (v10.8.1) |
BD Life Sciences |
|
| Icy (v2.5.2) |
https://icy.bioimageanalysis.org/download/ de Chaumont et al, 2012 (PMID22743774) |
|
| Prism (v10.2.2) |
https://www.graphpad.com/scientific-software/prism/ GraphPad Software |
|
| Other | ||
| CD14+ Magnetic beads | Miltenyi Biotec | #130-050-201 |
| Click-iT™ Plus Alexa Fluor™ 647 picolyl azide toolkit | Invitrogen | #C10643 |
| Ficoll Paque Plus density gradient | Cytiva | #17-1440-03 |
| QIAamp® DNA Micro Kit | QIAGEN | #56304 |
| Rneasy Mini Kit | QIAGEN | #74106 |
| SepMate™-50 | Stemcell Technologies | #85450 |
| SuperScript™ III Platinum™ SYBR™ Green One-Step qRT-PCR | Invitrogen | #11736059 |
| 2’,3’-Cyclic GAMP Enzyme Immunoassay Kit | Arbor Assays | #K067-H1 |
| Centrifuge | Thermo Scientific | Sorvall ST4 Plus |
| BD SYRINGE 60 ml (no needle) | Dutscher | #309653 |
| Confocal microscope | Zeiss | LSM700 inverted |
| Confocal microscope 63´ objective | Zeiss | Objective Plan-Apochromat 63x/1.4 Oil DIC M27 |
| EVOS® LED cube, GFP | Life Technologies | #AMEP4651 |
| EVOS® LED cube, RFP | Life Technologies | #AMEP4652 |
| EVOS® Live microscope | ThermoFisher Scientific | EVOS® FL Color |
| EVOS® microscope 10´ objective | ThermoFisher Scientific | EVOS™ 10X Objective, fluorite, LWD, 0.30NA/7.13WD |
| Falcon® Cell culture 24-well plate | Dutscher | #353047 |
| Flow Cytometer | ThermoFisher Scientific | Attune NxT Flow Cytometer |
| Formvar/carbon-coated nickel grids | Delta microscopies | #G150HEX-Ni |
| Glasstic™ Slide 10 with Grids | KOVA™ | #87144E |
| High tilt Holder | JEOL | #EM-21311 HTR |
| Transmission electron microscope 120 kV JEM-1400Plus | JEOL | JEM-1400Plus |
|
Transmission electron microscope 200 kV Tecnai F20 (FEG-TEM) |
FEI | Tecnai F20 D2216, Institut Pasteur |
| Falcon2 direct electron detector | FEI | Institut Pasteur |
| LS Columns | Miltenyi Biotec | #130-042-401 |
| Minisart™ NML Syringe Filter 0.45 μm | Sartorius | #16555 |
| MS Columns | Miltenyi Biotec | #130-042-201 |
| OctoMACS™ Separator | Miltenyi Biotec | #130-042-109 |
| OneView camera | Gatan | CMOS 4K camera |
| Open-Top Thinwall Polypropylene Konical Tube, 31.5 mL, 25 ´ 89 mm | Beckman Coulter, Inc. | #358126 |
| OPTILUX Petri dish - 100 × 20 mm | Dutscher | #353003 |
| Plate reader | Biorad | PR3100 TSC |
| Pre-Separation Filter 30 μm | Miltenyi Biotec | #130-041-407 |
| Precision cover glasses 12 mm Æ thickness No. 1.5H | Marienfeld | #0117520 |
| QuadroMACS™ Separator | Miltenyi Biotec | #130-090-976 |
| Refrigerated benchtop centrifuge | Eppendorf | Centrifuge 5415 R |
| Rotor for LE-80K | Beckman Coulter, Inc. | SW32Ti |
| Star-Frost slides 76 × 26 mm | Dutscher | #100204 |
| Stericup Quick Release-HV Sterile Vacuum Filtration System 0.45 μm | Millipore | #S2HVU05RE |
| Thermocycler | Eppendorf | Mastercycler® nexus |
| Thermocycler (qPCR) | Eppendorf | Mastercycler® realplex2 |
| Ultracentrifuge | Beckman Coulter, Inc. | Optima™ LE-80K |
| Cryo-Ultramicrotome | Leica | Leica EM UC7 FC7 |