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54 protocols using ganciclovir

1

HCMV Virus Production and Titration

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Human cytomegalovirus (HCMV, strain AD169) was prepared as described previously [15 (link)]. For virus production and measurement of viral genomic DNA, HFF were grown to a confluent monolayer and infected with HCMV at a multiplicity of infection (MOI) of 0.01 to 0.05. After 1.5 h, the viral inoculum was replaced by fresh growth medium. The viral supernatant was harvested upon visibility of a total cytopathic effect, usually 8–10 days post infection, and stored at −80 xB0;C. After thawing, cellular material was removed by centrifugation at 3000× g for 20 min. Infectivity of the viral inoculum was then measured using a plaque assay [16 (link)]. HCMV strain TS15-rN (kindly provided by Sallie R. Permar) was used to infect ARPE-19 cells.
For infection of cell cultures with HCMV AD169, cells were seeded into 6-well plates overnight, and inoculated at MOI 1 (if not indicated otherwise) for 1 h at 37 °C. After viral adsorption, the cell layer was rinsed and fresh growth medium including 10% FBS was added to the cells. In LL-37 treatment experiments (see below), growth medium containing 2% FBS was resupplied after inoculation. For ganciclovir-treated control wells, ganciclovir (Merck Millipore, Burlington, MA, USA) was added to the growth media at a concentration of 10 μg/mL after removal of the inoculum.
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2

Targeted Genome Editing of TBX20 in iPSCs

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TALEN pair vectors were designed and constructed using the rapid TALEN assembly system as previously described54 (link). 500 bp fragments of wild-type TBX20 exon 7 and adjacent intronic sequences were synthesized as GeneArt String DNA fragments (Life Technologies) to make left and right homologous arms, and cloned into PB-MV1Puro-TK vector (Transposagen), as previously described55 (link). Four silent mutations in homologous arms were inserted in order to create an artificial TTAA site and to avoid re-cleavage of the genomic sequence. Both TALEN pair and targeting vectors were delivered into LVNC iPSCs by nucleofection using P3 Primary Cell 4D-Nucleofector X Kit (Lonza). Afterwards, cells with correct targeting vector integration were selected by puromycin (Life Technologies) and genotyped. To excise the selection cassette, the transient expression of piggyBac transposase was performed by nucleofection of excision-only piggyBac transposase plasmid, PBx (Transposagen). After negative selection using ganciclovir (Sigma Aldrich), the established clones were genotyped by PCR and bidirectional direct sequencing.
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3

Pharmacological Inhibition of TNKS, PARP, and Wnt

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XAV939, an inhibitor of TNKS activity, Salinomycin, an inhibitor of the Wnt pathway that decreases the phosphorylation of low-density lipoprotein receptor-related protein 6, and ABT-888, PARP1 and PARP2 inhibitor, were obtained from Sigma-Aldrich (St. Louis, MO, USA) and dissolved in water or DMSO. A stock of 10 mM was stored at −80 °C. The 50% inhibitory concentration (IC50) of XAV939 for TNKS1 and 2 is 10 and 4 nM, respectively and for PARP1and 2–2.2 and 0.1 μM. Therefore, XAV939 was used at concentrations of 0.1 and 1 μM, which are specific for inhibition of TNKS1 and 2. The IC50 of ABT88 towards PARP1 and TNK1 is 5.2 nM, and 15 μM; therefore, it was used at 0.1 μM. Cycloheximide (Sigma-Aldrich) was dissolved in DMSO and used at 100 μg/mL. Ganciclovir (Sigma-Aldrich) was dissolved in PBS and used at 5 μM.
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4

Cell Viability and Proliferation Assays

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Cell viability was analyzed using the AlamarBlue cell viability reagent (Thermo Fisher) or CellTiter-Glow (Promega) according to the manual. Fluorescence emission was recorded with a SpectraMax iD3 Multi-Mode Microplate Reader (Molecular Devices). To determine whether introduced mutations into the HBEGF locus affect the proliferative capacity, we evaluated cell growth of HEK293 wild-type cells and the produced HBEGF-mutant sublines. To monitor proliferation curves, 2000 cells were seeded per well of a 96-well plate and cell confluence was recorded every 24 h for 7 days, using the Incucyte S3 live-cell analysis system (Essen BioScience). For the experiments with the HSV-TK safety switch in hiPSCs, ganciclovir (Sigma, SML2346) was included in the cell culture media at 0.1, 1, and 10 µM concentration for 3 days, followed by a 3-day recovery.
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5

Depletion of lymphocyte populations

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Depletion of CD8+ T cells and other lymphocyte populations was achieved by intraperitoneal injection of the following purified antibodies: αCD4 (GK1.5 clone, BioXcell, 200 μg/mouse), αCD8 (2.43 clone, BioXcell, 100 μg/mouse), or isotype control (LTF-2 clone, BioXcell, 100 μg/mouse) one day prior to infection. For experiments in which mice received antiviral treatment, mice were treated with daily doses of the nucleoside analog Ganciclovir (Sigma, catalog number 1288306) from day 3 PI to day 7 PI at 20 mg/kg per mouse, dissolved in warm in PBS. For experiments in which mice received polyinosinic:polycytidylic acid (poly I:C) treatment, mice were treated with daily doses of poly I:C (Invivogen) from day 4 PI to day 7 PI at 2.5 mg/kg per mouse.
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6

Pin1 Inhibitor Evaluation in Cell Culture

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The drugs used in the present study were obtained from various sources: Pin1 inhibitor B (PiB; Sigma-Aldrich), juglone (Merck Millipore), ganciclovir (GCV; Sigma-Aldrich), staurosporine (Calbiochem), and maribavir (MBV; Shanghai PI Chemicals Ltd). Due to high target specificity and low cytotoxicity [59 (link)], PiB was used to block Pin1 activity in cell culture experiments. The potent but rather toxic Pin1 inhibitor juglone [60 (link)] was used only to block Pin1 activity in vitro in NMR experiments.
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7

Stable Cell Line Generation Protocol

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Stable cell line generation was performed exactly as described previously (Grill et al., 2018 (link)). Briefly, HeLa-EM2-11ht cells were co-transfected with 1 μg each of the p3X-FLAG-TPP1-F3 (TPP1-L or TPP1-M87A) and Flp recombinase-expressing plasmid (that also codes for puromycin resistance). Cells were selected for one day using puromycin (5 μg/ml; Sigma-Aldrich), and then fresh medium with ganciclovir (50 μM; Sigma-Aldrich) was added for 10 days of negative selection. Individual clones were picked and expanded, and positive clones were selected based on western blot analysis of FLAG-TPP1 signal after overnight induction with doxycycline (200 ng/ml). Generation of the stable cell lines expressing vector, TPP1-S, and TPP1ΔNOB constructs used in this study have been described previously (Grill et al., 2018 (link); Nandakumar et al., 2012 (link))
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8

Conditional T Cell Ablation Assay

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T cells expressing TK were evaluated for conditional ablation using ganciclovir (GCV; Sigma-Aldrich, St. Louis, MO, USA). 4 × 105 T cells were co-cultured in triplicate with 8 × 105 γ-irradiated aAPC in a 24-well plate in the absence or presence of graded doses of GCV (0.01–10.00 μM) in a volume of 2 ml/well of complete RPMI medium (HyClone) containing 50 U/ml soluble recombinant human IL-2 and 30 ng/ml soluble recombinant human IL-21. On day 7, viable T cells were counted based on Trypan blue exclusion using Cellometer (Nexcelom Bioscience, Lawrence, MA, USA). The results are expressed as mean percentages of the final cell numbers relative to starting counts derived from triplicate wells.
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9

Preparation of Common Research Compounds

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Doxycycline hyclate was purchased from Sigma-Aldrich (Fluka; cat# 44577-5G) and stock solution of 10 mg/ml was prepared in deionized water. Erythromycin was purchased from Sigma-Aldrich (Sigma; cat# E5389-1G) and stock solution of 10mg/ml was prepared in 100% ethanol. Ganciclovir was purchased from Sigma-Aldrich (Sigma; cat# G2536) and stock solution of 2.6 mg/ml (10 mM) was prepared in 2mMHCl solution in deionized water. Tamoxifen ((Z)-4-Hydroxytamoxifen) was purchased from Sigma-Aldrich (Sigma; cat# H7904-5MG) and Stock solution of 0.39 mg/ml was prepared in 100% ethanol. Calcein AM was purchased from Life Technologies (cat# C3100MP) and tubes with 50 μg were resuspended in 50 μl of 100% DMSO (1 mM solution).
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10

Stable Cell Line Construction for BioID

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For the construction of stable cell lines (Cdc25C/14-3-3ɛ constructs for split-BioID, and BirA*-Ago2 and BirA*-control proteins for Ago2 and control BioID, the control proteins were Rab11a, Lamp1, TGN38, GRASP65, RHD4 and Sec61β), HeLa 11ht cells that harbour a stably integrated Hygromycin-TK cassette flanked by flippase recognition target (FRT) sites were used. The split-BioID constructs were designed with the pSF3 backbone51 (link), which also harbours the same FRT sites and are therefore compatible with Flp-recombinase-mediated cassette exchange in HeLa 11ht cells. Cells were seeded at a concentration of 1 × 105 cells per well of a six-well plate on the day before transfection, which was done using Lipofectamine 3000 (LifeTechnologies) following the manufacturer's protocol (cotransfection of BirA* construct and Flp coding plasmid pPGKFLPobpA (addgene 13793)). Cells were transferred to a 10 cm dish 24 h after transfection and 50 μM ganciclovir (Sigma) was added 72 h after transfection to start the selection procedure. Approximately one week later, colonies had formed and could be picked and propagated. Cells were in total treated for at least 3 weeks with ganciclovir.
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