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48 protocols using padvantage

1

Lentiviral Production and Transduction of Expi293 Cells

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cDNAs for soluble SARS-CoV-2 S and RBD (containing C-terminal His-tag) [11 (link)] were cloned into EcoRV-cut plenti-CMV-Puro-DEST (Addgene, #17452, gift from Eric Campeau & Paul Kaufman) using NEBuilder HiFi DNA Assembly Master Mix (NEB). Lentivirus was produced in HEK293FT by co-transfection of cDNA containing pLenti plasmids together with pCMV-dR8.2 dvpr (Addgene, #8455, gift from Bob Weinberg), pCMV-VSV-G (Addgene, #8454, gift from Bob Weinberg) and pAdVAntage (Promega) using FugeneHD (Promega). Supernatants were collected 48 hr post-transfection and filtered using a 0.45 μm syringe filter. For the transduction of Expi293 cells, five 6-well plates with 2 million cells per well were spin-infected with lentivirus diluted 1:2.5 in fresh Expi293 expression media under the following conditions: 2 hr, 33°C, 1,000 g. Cells were subsequently pooled together and cultured in 30 mL Expi293 expression media on a shaking incubator. 24 h post-transduction puromycin was added at 2 μg/mL and cells were selected for 7 days.
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2

HIV-1 Virus Production and Transduction

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NL4.3 WT or W757A was co-transfected with BlaM-Vpr (Addgene, Watertown, MA, USA) and pAdVAntage (Promega, Madison, WI, USA) into 293T cells to generate virions packaging BlaM-Vpr. Virus was concentrated by ultracentrifugation and quantified by SG-PERT. Next, 1011 pU RT of virus was used to infect target 106 Jurkat cells for 4 h by gravity infection, and the BlaM-Vpr assay was performed as described [37 (link)].
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3

Lentiviral Production Protocol

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To generate lentivirus, the human lentiCRISPRv2 plasmid library (Addgene 1000000048) was co-transfected with packaging plasmids pCAG-VSVG and psPAX2 (Addgene plasmids 35616 and 12260, respectively). Briefly, a T-75 flask of 80% confluent HEK293T cells was transfected in OptiMEM (Thermo Fisher Scientific) using 8 μg of the lentiCRISPRv2 plasmid library, 4 μg pCAG-VSVG, 8 μg psPAX2, 2.5 μg pAdVantage (Promega), 30 μl of P3000 Reagent (Thermo Fisher Scientific), and 30 μl of Lipofectamine 3000 (Thermo Fisher Scientific). Cells were incubated overnight, and then, the media were changed to DMEM (Sigma-Aldrich) with 10% BCS and 1× GlutaMAX (Thermo Fisher Scientific). After 48 h, viral supernatants were collected and centrifuged at 2000 rpm for 10 min to get rid of cell debris. The supernatant was filtered through a 0.45-μm ultra-low protein binding filter (Merck Millipore). Aliquots were stored at − 80 °C.
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4

Inducible Lentiviral Expression of PARP-7

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Cells were transduced with lentiviruses for Dox-inducible ectopic expression of PARP-7 (wild-type and mutant). We generated lentiviruses by transfection of the pINDUCER20 constructs described above, together with: (i) an expression vector for the VSV-G envelope protein (pCMV-VSV-G, Addgene 8454), (ii) an expression vector for GAG-Pol-Rev (psPAX2, 12260), and (iii) a vector to aid with translation initiation (pAdVAntage, Promega) into 293 T cells using Lipofectamine 3000 reagent (Invitrogen, L3000015) according to the manufacturer’s instructions. The resulting viruses were collected in the culture medium, concentrated by using a Lenti-X concentrator (Clontech, 631231), and used to infect OVCAR4 cells. Stably transduced cells were selected with G418 sulfate (Sigma, A1720; 1 mg/ml). The cells were treated with 1 µg/mL Dox for 24 hr to induce protein expression. Inducible ectopic expression of the cognate proteins was confirmed by western blotting.
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5

Lentiviral Packaging Protocol for HEK293 Cells

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HEK293 cells (American Type Culture Collection, 2.5 × 106 per well) were transfected on a 1% PEI (Sigma Aldrich; Cat #P3143) coated six-well plate in 2.5 mL DMEM (Invitrogen, Cat #11965118) with 10% FBS (Phoenix Scientific, Cat #PS-100-02-500) according to the Lipofectamine 3000 protocol (Thermo Fisher Scientific, Cat #L3000015). Briefly, psPAX (Addgene Cat #12260; 0.8 μg), pMD302 (Addgene Cat #12259; 0.3 μg), and pAdvantage (Promega Cat #E1711; 0.1 μg) viral packaging plasmids were added to P3000 reagent with 1.2 μg plasmid (MyoD – vector ID #VB200213-1024pkg or Tet3g – vector ID #VB200811-1097xwy) before adding dropwise to cells.
The next day, media was replaced on HEK cells with 3 mL fresh medium supplemented with 6 μL 500× ViralBoost reagent (ALSTEM, Cat #VB100). On day 4, virus was harvest by pooling supernatants and centrifuged for 10 min at 500×g. Clarified supernatant was transferred to a new tube and Lenti-X concentrator (Takara, Cat #631231) was added at a 1:3 ratio (concentrator:media). The supernatant was incubated at 4 °C for 45 min with Lenti-X concentrator and centrifuged at 1,500×g for 45 min at 4 °C. Supernatant was removed, and pellet resuspended in media at 1/10 original volume.
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6

Lentiviral Knockdown in 3T3-L1 Cells

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Lentiviruses were generated by transfecting the pLKO.1 vectors described in the Method Details, each containing a different shRNA sequence directed against its cognate target (Parp1 or Nmnat1), into 293T cells, together with the expression vectors for the VSV-G envelope protein (pCMV-VSV-G, Addgene plasmid no. 8454), the expression vector for GAG-Pol-Rev (psPAX2, Addgene plasmid no. 12260), and a vector to aid with translation initiation (pAdVAntage, Promega) using Lipofectamine 3000 transfection reagent (Thermo Fisher Scientific, L3000015) according to the manufacturer’s instructions. The viruses were collected in the culture medium, concentrated by using a Lenti-X concentrator (Clontech, 631231), and used to infect 3T3-L1 cells. The infected cells were selected with 2 μg/mL puromycin (Sigma, P9620), expanded, and frozen in aliquots for future use.
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7

Generation of Huh7.5.1 cells expressing hACE2

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Huh7.5.1-ACE2 cells were generated as described previously in (Wang, et al., 2020b (link)). Briefly, hACE2 (Addgene, #1786, gift from Hyeryun Choe) was amplified and cloned into EcoRV-cut plenti-CMV-Hygro-DEST (Addgene, #17454, gift from Eric Campeau & Paul Kaufman) using NEBuilder HiFi DNA Assembly Master Mix (NEB). Lentivirus was produced in HEK293FT by co-transfection of plenti-hACE2-Hygro together with pCMV-dR8.2 dvpr (Addgene, #8455, gift from Bob Weinberg), pCMV-VSV-G (Addgene, #8454, gift from Bob Weinberg) and pAdVAntage (Promega) using FugeneHD (Promega). Supernatant was collected 48 h post-transfection, filtered and added to Huh7.5.1 cells. Transduced cells were subsequently selected using Hygromycin for 7 days.
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8

Differentiation of Mouse Preadipocytes

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Mouse preadipocytes (derived from inguinal white adipocyte tissues, gift from Dr. Shingo Kajimura) were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS and penicillin/streptomycin. To differentiate into adipocytes, preadipocytes were cultured to ~95% confluence before a differentiation cocktail was added to the following concentrations: 5 μg/mL of insulin (Sigma, #I0516), 1 nM T3 (Sigma, #T2877), 125 mM indomethacin (Sigma, #I-7378), 5 μM dexamethasone (Sigma, #D1756), and 0.5 mM IBMX (Sigma, #I5879). After 2 days, the cells were switched to DMEM supplemented with 10% FBS, 5 μg/mL of insulin, and 1 nM T3. After another 2 days, fresh media of the same composition were supplied. Differentiated adipocytes were usually analyzed 6 days after the addition of the differentiation cocktail.
To generate cell lines expressing the GFP-GLUT4-HA reporter, lentiviruses were produced by transfecting 293T cells with a mixture of plasmids including GFP-GLUT4-HA,74 (link) pAdVAntage (Promega, #E1711), pCMV-VSVG, and psPax2. Lentiviral particles were collected 40 h after transfection and every 24 h thereafter for a total of four collections. Lentiviruses were pooled and concentrated by centrifugation in a Beckman SW28 rotor at 25 000 rpm for 1.5 h. The viral pellets were resuspended in PBS and were used to transduce preadipocytes.
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9

Generating stable HeLa CCL2 cells expressing YFP-CASP4

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We generated stable HeLa CCL2 cells expressing YFP-CASP4(C258S) (31 (link)) by lentiviral transduction. Lentivirus was produced in HEK293T by transient transfection with the lentiviral backbone pMX-CMV-YFP CASP4(C258S) and the three packaging plasmids pVSV-G (#138479, Addgene), pAdvantage (E1711, Promega), and pGag-Pol (#14887, Addgene). DNA, mixed with FuGENE 6 Transfection Reagent (Promega) in Opti-MEM (Gibco), was incubated at RT for 15 min, then added dropwise into HEK293T cells. After 48h, the supernatant containing the lentivirus was collected, filtered using a 0.45 μm membrane filter, and supplemented with polybrene (Sigma) at 8 μg/mL. Lentivirus was then transduced into HeLa CCL2 cells by centrifugation of the HEK293T supernatant for 2 h at 1000 × g at 30°C. Two days later, HeLa CCL2 containing YFP-CASP4(C258S) were selected and maintained with 2 μg/mL of puromycin.
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10

BlaM-Vpr-based Viral Fusion Assay

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The BlaM-Vpr-based viral fusion assay was performed as previously described (Cavrois et al., 2002 (link)). Briefly, viruses were generated by co-transfection of HEK293T cells with three plasmids: pNL4-3 proviral DNA, pCMV4-BlaM-Vpr (kindly provided by Dr. Warner C. Greene), and pAdVAntage (Promega) (in the ratio of 6:2:1). Supernatant was harvested at 48 hours post co-transfection, concentrated, and then used for infection of resting CD4 T cells. For infection of resting CD4 T cells, 400 ng (p24) of HIV-1 (BlaM-Vpr) was used for 2 million cells. As a control, cells were pretreated with 10 μM AMD3100 for 1 hour and then infected with HIV-1 (BlaM-Vpr) virus for 2 hours. Infected cells were washed with medium and resuspended in 100 μl CCF2-AM loading solution, and inculabted for 1 hour at room temperature at dark. Cells were washed with 200 μl of development medium, resuspended into 200 μl of development media and incubated at room temperature for 16 hours in dark, and then washed and resuspended in 200 μl 1.2% paraformaldehyde for flow cytometry using a Becton Dickinson LSR II (Becton Dickinson).
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