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8 protocols using pegip

1

Lentiviral Upregulation of SDF-1α

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The SDF-1α upregulation plasmid was created by Dr. Oskar Laur at the Emory University Custom Cloning Core Facility. The human SDF-1α gene was obtained from Addgene (plasmid #12270) and sub-cloned under the human elongation factor 1α (EF1α) promoter in the plasmid, pEGIP (Addgene, plasmid #26777). The SDF-1α upregulation plasmids were created with the backbone, pEGIP which has GFP reporter gene and puromycin resistance for selection. The SDF-1α plasmid was created with the 2A expression system. Control plasmids were empty vectors without the SDF-1α gene and GFP expressed under the IRES system inherent to the pEGIP backbone. The empty plasmid (control) and the SDF-1α plasmid were packaged into lentiviruses.
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2

Generating RARE-GFP Organoids

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To generate organoids expressing retinoic acid response elements (RAREs) tagged with green fluorescent protein (GFP), we infected wild-type C57BL/6 organoids with in-house-produced pGreenFire 1–RARE viral particles (System Biosciences, catalogue number TR037PA-1) or, as a control, with pEGIP (Addgene, plasmid number 26777) at 0 h. For a detailed explanation of single guide RNA (sgRNA) design in CRISPR–Cas9-mediated gene-knockout experiments and the production of lentiviral particles, see Supplementary Methods.
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3

Generating RARE-GFP Organoids

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To generate organoids expressing retinoic acid response elements (RAREs) tagged with green fluorescent protein (GFP), we infected wild-type C57BL/6 organoids with in-house-produced pGreenFire 1–RARE viral particles (System Biosciences, catalogue number TR037PA-1) or, as a control, with pEGIP (Addgene, plasmid number 26777) at 0 h. For a detailed explanation of single guide RNA (sgRNA) design in CRISPR–Cas9-mediated gene-knockout experiments and the production of lentiviral particles, see Supplementary Methods.
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4

Wnt5a Lentiviral Transduction of MSCs

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MSCs were transfected with lentiviral particles containing the Wnt5a gene and empty vectors. The lentiviral system consisted of three vectors: the packaging plasmids psPAX2 (Addgene, USA), the envelope plasmids pMD2.G (Addgene, USA), and the expression vector pEGIP (Addgene, USA). To generate the Wnt5a expression vector, the cDNA encoding mouse Wnt5a (NM_009524.4) was amplified by RT-PCR using specific primers, digested with restriction enzymes, and subcloned into the expression vector plasmid pEGIP. The recombinant lentivirus was produced by co-transfecting psPAX2, pMD2.G, and the expression vector containing Wnt5a or empty vector into HEK 293 T cells using calcium phosphate transfection. The supernatant containing the virus was collected 48 h after transfection, centrifuged at 1,500 rpm for 5 min to remove debris, and then filtered through a 0.45 μm pore-size filter. For lentiviral transduction, MSCs were incubated with lentiviral solution and 10 μg/mL polybrene (Sigma-Aldrich, USA, H9268) in complete medium for 9 h. Subsequently, the culture medium was changed, and MSCs were selected in complete medium containing 1.6 μg/mL of puromycin (Genechem, China) for 72 h. Finally, the MSCWnt5a and MSCVector cell lines were obtained and expanded for subsequent experiments.
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5

Stable and Transient Knockdown of EP4 and P-selectin

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For stable knockdown of EP4 gene, HEK293T cells were transfected with pLKO.1 lentiviral vector TRCN0000000204 or TRCN0000000205 (Thermo Scientific) encoding shRNAs targeting human EP4. Lentiviral supernatants were collected, and used either separately or in combination to transduce ACHN and SN12C. Lentiviral vector targeting GFP was used to establish control cells. Cells were selected with 2 μg/ml puromycin (Sigma-Aldrich) commencing 48 h after transduction to establish stable lines. Stable knockdown cells were maintained in complete medium containing 1 μg/ml puromycin. For transient knockdown of EP4 or P-selectin gene, 50 nM SMARTpool ON-TARGETplus siRNA (Dharmacon) were transfected into ACHN and SN12C cells with DharmaFECT 2 reagent (Dharmacon). To rescue CD24 expression, EP4 stable knockdown cells were transfected with pCMV6-Entry-CD24 (RC209542, Origene) or control pCMV6-Entry (PS100001, Origene) plasmid. To label cells, wild type ACHN and SN12C were transfected with GFP expressing lentiviral vector pEGIP (Addgene). Stable expressing cells were selected with 2 μg/ml puromycin.
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6

Generation of SARS2-PsV for Signaling Assays

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For generation of lentivirus-based SARS2-PsV used in the PS externalization and [Ca2+]i measurements, HEK 293T cells were plated in a 6-well plate and transfected the next day when they were approximately 80% confluent with a combination of the following plasmids: 1 μg of pEGIP (Addgene #26777), 0.75 μg of psPAX2, and 2.25 μg of pcDNA3.1-SARS2-Spike (Addgene #145032). The TransIT-X2 Dynamic Delivery System (#MIR6006; Mirus Bio LLC, Madison, WI, US) was used for transfection, following the manufacturer’s protocol. The next day, the transfection medium was replaced with fresh culture medium and cells were cultured for 48 h. The pseudotyped virus-containing culture medium was collected 48 h post transfection, centrifuged at 500 ×g for 5 min, and stored at −80°C.
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7

Flag-tagged Protein Expression in ESCs

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Flag-tagged CNBP/HNRNPF/SFRS9 cassette was cloned into pEGIP (Addgene #26777). Lentiviral production and ESC infection were performed using protocols from the RNAi Consortium (Broad Institute).
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8

Lentiviral Transduction of Foxa2 and Hnf4a

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A 2nd-generation lentiviral system was used, and non-replicative lentiviral particles were produced by transient transfection of HEK293FT cells with psPAX2 (Addgene #12260), pMD2.G (Addgene #12259), and expression vector, at a 2:1:3 ratio, as previously described [9 (link)]. Three expression vectors were constructed: pFOXA2IP, pFHIG, and pCWFOXA2. Foxa2 was amplified from pGCDNsam_Foxa2 (Addgene #33004) with the primers mmFoxa2_BamHI_F and mmFoxa2_BsrGI_R and subcloned between BamHI and BsrGI sites in pEGIP (Addgene #26777). For dox-inducible expression studies, Foxa2 was amplified with mmFoxa2_NheI_F and mmFoxa2_BamHI_R primers and subcloned into the pCW-cas9 (Addgene # 50661) Tet-on expression vector in the NheI/BamHI flanked region. Hnf4a was amplified from pGCDNsam_HNF4α (Addgene #33002) with primers mmHnf4a_XbaI_F and mmHnf4a_BamHI_R and subcloned into pFUWOSKM (Addgene #20328) vector in the XbaI/BamHI flanked region, while IRES-GFP sequence was subcloned in frame, within BamHI/AscI restriction sites, after amplification from MSCVPIG (Addgene #18751) using IRES-GFP_BamHI_F and IRES-GFP_AscI_R primers. Primer sequences are listed in Table S1.
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