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4 protocols using plenti vector

1

Generation of ADAR1 Catalytic Mutant

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To generate the editing deficient ADAR1 construct, site-directed mutagenesis was performed using the pLenti-ADAR1 construct (purchased by Origene) to integrate the point mutation at aa912 which leads to the substitution of glutamate (E, GAA) with alanine (A, GCA), previously shown to inactivate the catalytic activity of ADAR1 [28 (link),29 (link)]. HUVECs at 80–90% confluency were transfected with 5 μg of either pLenti-ADAR1, pLenti-ADAR1 E/A (generated editing deficient mutant) or an empty pLenti vector (control, purchased also by Origene). Transient plasmid transfection was performed with Lipofectamine 2000 (Invitrogen) according to the manufacturers protocol. After 48 h of incubation at 37 °C, 5% CO2 cells were harvested for RNA expression studies, as described below.
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2

Characterization of ERCC6 and ERCC4 Deficient Cell Lines

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ERCC6 (GM16095)- and ERCC4 (GM08437)-deficient immortalized fibroblast cell lines (Coriell Cell Repository) were cultured in DMEM (Invitrogen), supplemented with 10% FBS, 1% Penicillin Streptomycin and L-glutamine. ERCC6-deficient line was complemented with either wild-type or mutant N-terminal Flag-tagged ERCC6, cloned in a pOZ vector. The ERCC4-deficient line was complemented with C-terminal Myc-tagged wild-type or mutant ERCC4, cloned in a pLenti vector (Origene).
For Western blotting, whole cell extracts were prepared by lysing cells in RIPA with complete protease inhibitor. Lysates were resolved on a polyacrylamide gel, transferred to a PVDF membrane, and incubated with primary antibodies [BRCA2 (ab-1; Calbiochem), BRCA1 (ab-1; Calbiochem), ERCC4 (D3G8C; Cell Signaling Technology), ERCC6 (D-7; Santa Cruz Biotechnology), Flag (M2; Sigma), and β-actin (Cell Signaling Technology)]. Signal was detected using an ECL kit (Pierce) and visualized with a Fuji LAS-3000 luminescent image analyzer system.
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3

Lentiviral Transduction of Nasal Organoids

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The FLAG-tagged spike genes of WT, B.1.1.529, and BA.5 were inserted into a pLenti vector (Origene, PS100069). Lenti-X 293T cells seeded in a 6-well plate were cotransfected with three plasmids, including 12 μg pLenti-spike, 6 μg pspax2, and 6 μg pmd2g, using Lipofectamine 3000 (ThermoFisher). The culture media containing lentivirus particles were harvested 48 h posttransfection. After concentration with Amicon Ultra-15 Centrifugal Filter Unit (Millipore, UFC910008), we titrated the lentiviruses using a Lenti-X GoStix Plus kit (Takara Bio, 631280). Nasal organoid monolayers were transduced with lentiviruses at 5 MOI with 10 μg/mL polybrene. The transduced nasal organoids were fixed with 4% PFA at 48 h posttransduction and applied to immunostaining using an anti-FLAG (Sigma, F7425), followed by confocal imaging as described above (36 (link)).
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4

Overexpressing EIF3F in Human Cell Lines

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A549, HeLa, H460, and H1975 human cells were obtained from ATCC (Bethesda, MD, USA). Cell culture was performed in DMEM 5 mM glucose (Gibco), supplemented with 10% FBS (Gibco) and penicillin–streptomycin 1× (100×; Gibco). The lentiviral vector used for human EIF3F overexpression was constructed by inserting EIF3F cDNA into pLenti vector, which contains a FLAG tag and a gene for puromycin resistance (OriGene). Lentiviral particles were produced by transient transfection of 293T cells using a calcium phosphate transfection technique. Prior to infection the medium was removed and 5 × 105 cells were incubated with viral supernatants for 48 h at 37 °C in the presence of 8 μg/ml of protamine sulfate. EIF3F overexpressing cells were selected using promycin treatment (1 µg/mL) in culture medium.
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