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2 420 protocols using pmd2 g

1

Generation of Viral Expression Constructs

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pcDNA-3xFLAG-Vpr and pscAAV-mCherry-T2A-Vpr WT and mutant plasmids were generated as previously described (28 (link)). For rAAV production, pHelper and pAAV-2.5 capsid plasmids were used (Addgene and (28 (link)). For VLP production, psPAX2 and pmD2.G were used (Addgene). For HIV-1 ΔENV production, Bru-GFP ΔENV was generated as previously described (62 (link)) and pmD2.G (Addgene). For lentivirus stable knock-down of DCAF1, pLKO.1 (Addgene), psPAX2(Addgene) and pmD2.G (Addgene) were used.
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2

Viral Vector Cloning and Packaging

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Individual gRNAs were cloned into lentiCRISPR v2 (Addgene 52961) or lentiGuide-Puro (Addgene 52963)35 (link) and cDNAs were cloned in pLenti (Addgene 22255), pMSCV (Clontech), or pcDNA4TO (Addgene 60914). Drug resistance genes in lentiGuide, pLenti, and pMSCV were replaced by Neomycin, or Zeocin resistant genes. The resulting plasmid was verified by sequencing. pMD2.G (Addgene 12259) and psPAX2 (Addgene 12260) were used for lentiviral packaging. pMD2.G and gag/pol (Addgene 14887) were used for retroviral packaging.
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3

Viral Vector Cloning and Packaging

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Individual gRNAs were cloned into lentiCRISPR v2 (Addgene 52961) or lentiGuide-Puro (Addgene 52963)35 (link) and cDNAs were cloned in pLenti (Addgene 22255), pMSCV (Clontech), or pcDNA4TO (Addgene 60914). Drug resistance genes in lentiGuide, pLenti, and pMSCV were replaced by Neomycin, or Zeocin resistant genes. The resulting plasmid was verified by sequencing. pMD2.G (Addgene 12259) and psPAX2 (Addgene 12260) were used for lentiviral packaging. pMD2.G and gag/pol (Addgene 14887) were used for retroviral packaging.
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4

Lentivirus Production and Transduction Protocol

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Lentivirus stocks were produced as previously described with slight modifications. Human embryonic kidney 293FT cells (Invitrogen) were transfected using Lipofectamine 2000 (Thermo Fisher) with the expression of two helper plasmids: psPAX2 (Addgene #12260) and pMD2.G (Addgene #12259) Ten micrograms of the transfer vector, 5 µg psPAX2 and 5 µg pMD2.G of DNA were used per 10‐cm plate. Forty‐eight hours after transfection, the supernatants of four plates were pooled, centrifuged at 780 × g for 5 min, filtered through a 0.45‐µm pour size filter, and further centrifuged at 24 000 rpm for 2 h. The resulting pellet was re‐suspended in 100 µL of PBS. Lentivirus titration was performed on DIV5‐6 at titer range 107 IU/mL. In most experiments, cultures were infected overnight, rinsed twice with virus‐free medium the next morning and incubated in normal culturing medium for another 48–72 h prior assay.
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5

Overexpression and Knockdown of Lhx8 and Suv39h1 in DPSCs

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For the overexpression of Lhx8 or Suv39h1, the open reading frames of target genes were amplified and the amplicon was inserted into the lentivirus expression vector of pWPI (Plasmid #12254; Addgene). A lentivirus was produced through transfecting HEK293T cells with the lentivirus expression vector along with pMD2.G (Plasmid #12259, Addgene) and psPAX2 (Plasmid #12260, Addgene) (pWPI 6.25 μg, pMD2.G 0.625 μg and psPAX2 3.125 μg). Supernatants containing lentivirus particles were then collected after 48 hours and were stored at −80°C before use. DPSCs were infected with a lentivirus in 8 μg/mL polybrene (Santa Cruz Biotechnology). DPSCs were transfected with the lentivirus or the negative control according to Multiplicity of Infection (MOI) 50:1 for 2 days.
For shRNA knockdown of Lhx8 or Suv39h1 in DPSCs, lentiviral shRNAs were purchased from GenePharma. Five shRNAs were used for lentiviral treatment. DPSCs were transfected with the lentiviral‐mediated shRNA or the negative control according to Multiplicity of Infection (MOI) 50:1 for 2 days. Compared with the non‐silencing scramble virus, the shRNAs with the highest knockdown efficiencies were chosen for follow‐up experiments. The chosen sequences were listed in Supplemental Table S1.
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6

Retroviral and Lentiviral Particle Generation

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The pBabe, pBabe-myc-BirA*-LMP1, and pBabe-LMP1-BirA*-HA
retrovirus particles were generated by Jetprime transfection of HEK293T cells in
10 mm dishes with pBabe vectors and packaging plasmids pMD2.G (Addgene, 12259)
and pSPAX2 (Addgene, 12260). Five μg of each construct DNA were used per
plate with 30 μL of Jetprime and 500 μL of JetPrime buffer
(Polyplus) was mixed and incubated at room temperature for 25 minutes. The
DNA-Liposome complexes were then added dropwise to each place. Media was
collected and replaced with fresh DMEM at 48, 72, and 96 hours
post-transfection, centrifuged at 1,000 × g for 10 minutes, filtered
through a 0.45 μM filter into sterile tubes, and frozen at
−80°C until use. To make shRNA lentiviral stocks, HEK293-T cells
were transfected with expression plasmids (pLenti X1 Syntenin-1 shRNA, pLenti X1
ALIX shRNA, or pLenti X1 scramble shRNA) and the packaging plasmids pMD2.G
(Addgene; #12259), pMDLgpRRE (Addgene; #12251), and pRSVRev
(Addgene; #12253) to produce retroviral particles for transduction.
Media was collected and stored as described for pBabe viruses. All packaging
plasmids were gifts from Didier Trono.
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7

Generating Gene Knockout Cell Lines

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To generate the gene knockouts, tetracycline induced cas9 vector (Addgene # 50661) was stably expressed in prostate cancer lines. sgRNAs against target genes given in were cloned in pLXsgRNA vector (Addgene# 50662), and lentiviral particles for sgRNA were produced in HEK293T cells by co-transfecting pLXsgRNA plasmid with pMD2.G (Addgene# 12259) and psPAX2 (Addgene #12260). (Supplementary Table S1A) Viruses were harvested after 48h, and cells were infected with lentiviral particles. Transduced cells were treated with 1 μg/mL doxycycline to induce cas9 before selection with 10 μg/mL blasticidin. Following selection, cells were transferred in 96-well plates to select individual clones. Knockouts were verified by western blots, and confirmed clones were expanded and cryopreserved for future experiments.
For NCOA4 knockdown in LNCaP cells, MISSION shRNA constructs (TRCN0000236184, TRCN0000236186, TRCN0000236187, TRCN0000236188 and TRCN000019724) were purchased from Sigma, and lentiviral particles were generated in HEK293T cells by co-transfecting shRNA plasmid construct with pMD2.G (Addgene#12259) and psPAX2 (Addgene#12260). LNCaP cells were infected with NCOA4 lentivirus and were selected with 1.0 μg/mL puromycin. The level of NCOA4 knockdown was measured by western blots, and confirmed cells were expanded, cryopreserved, and used for the experiments.
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8

Isolation of Extracellular Vesicles and Viral-Like Particles

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EVs isolated from thirty ml of conditioned medium were collected from cells cultured at 70% confluency in two 100 mm plates after 72 h (seeding density 2.2 × 106 cells/plate). The conditioned media was centrifuged at 300 × g for 10 min to remove intact cells, dead cells, and cell debris. The medium was then concentrated using a centrifugal concentrator with a 100,000 molecular-weight cutoff (Amicon®Ultra-15 Centrifugal filters), yielding about 0.5 ml concentrate (two spins of 10 ml at 6000 × g for 10 min). This concentrate was resolved by passing through IZON qEV original size exclusion columns (SEC) followed by 15 ml of double filtered (0.2 μm) PBS. Five-hundred-microliter fractions were collected. High particle/low protein fractions (from 7 to 11) were pooled and concentrated using Amicon®Ultra-0.5 Centrifugal filters to a final volume of 200 µL at 10,000 × g for 30 min. The typical yield of an EV isolation was approximately 7.1 × 107 ± 3.2 × 107 particles/ml. This method was adapted to isolate EVs, LVVs (transgene plasmid, psPAX2 (Addgene #12260) and pMD2.G (#12259), VSV G-VLPs (pMD2.G (Addgene #12259), and GAG-VLPs (psPAX2 (Addgene #12260)) before being exposed to scProteins (see below). LVVs purified from media of 2.5 million HEK293Tcells transfected with psPAX2 (Addgene #12260) and pMD2.G (Addgene #12259) were isolated with SEC.
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9

Lentiviral Packaging and Titration

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Lentivirus particles were packaged in fresh HEK 293T culture (passaged ≤ 15 times) as previously described13 (link). Briefly, 2 × 106 cells were replated in T25 flasks one day before transfection. At the day of transfection, media was refreshed without antibiotics. pLenti-dCas9-KRAB-BSD (Addgene # 89567) was co-transfected with pMD2.G (Addgene #12259) and psPAX2 (Addgene #12260) at a 4:2:3 molar ratio; other viral vectors including FUW-M2rtTA (Addgene # 20342), pTet-O-Ngn2-puro (Addgene # 52047), CROPseq-Guide-Puro gRNA (Addgene # 86708), and pTet-O-Ngn2-hygro were co-transfected with pMDLg/pRRE (Addgene #12251), pMD2.G (Addgene #12259), and pRSV-Rev (Addgene #12253) at 1:1:1:1 molar ratio. Transfection was performed using FuGENE HD (Promega) following the vendor’s instructions. 24 hrs post transfection, media was refreshed with Neurobasal Medium supplemented with 1× Glutamax/B27. 48 hrs post transfection, the supernatant was collected and centrifuged at 500 × g for 5 min to remove debris. The virus-containing media was aliquoted into 1.5 ml low protein binding tubes and stored at -80°C until use. Viral RNA was extracted and the titer (MOI) was measured using the Lenti-X qRT-PCR titration kit from Takara (Cat. #: 631235) following vendor’s instructions.
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10

Lentiviral Particle Production in HEK293T

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Transduction retrovirus particles were collected from HEK293T cells following Lipofectamine 3000 transfection of expression plasmids (pLenti CMV TetR BLAST and pLenti X1 shRNA plasmids) and packaging plasmids pMD2.G (Addgene; number 12259; a gift from Didier Trono) and PSPAX2 (Addgene; number 12260; a gift from Didier Trono) according to the manufacturer’s instructions (Invitrogen; L3000015). The overexpression pCT-CD9-RFP (SBI; CYTO123-PA-1) and pCT-CD63-GFP (SBI; CYTO120-PA-1) plasmids were transfected in HEK293T cells with the packaging plasmids pMD2.G (Addgene; number 12259; a gift from Didier Trono), pMDLgpRRE (Addgene; number 12251; a gift from Didier Trono), and pRSVRev (Addgene; 12253; a gift from Didier Trono) according to the manufacturer’s instructions (Invitrogen; L3000015). Medium was collected and reapplied at 48, 72, and 96 h following transfection, centrifuged for 10 min at 1,000 rcf, filtered through a 0.45-μm filter, and frozen at −80°C until use.
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