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293T cells are a widely used human embryonic kidney cell line. They are a commonly employed host cell for the production and propagation of various viral vectors, proteins, and other biological materials. 293T cells exhibit high transfection efficiency and are known for their ability to support the amplification of many types of viruses.

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910 protocols using 293t cell

1

Production and Purification of Anti-ALK2 and Anti-ALK3 Antibodies

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Anti-ALK2 and anti-ALK3 IgG1 and BsAbs were produced in CHO (Evitria AG) and 293T cells (ATCC® CRL-1573) For antibody production in 293T cells, the cells were cultured in 150 mm2 dishes to 70% confluence. A 1:1 mixture of 30 µg of plasmids I and II, and 240 µg of the transfection agent polyethylenimine (PolyScience) was maintained at room temperature (RT) for 10 min and subsequently added to the cells for 6 h at 37°C. Following incubation, the transfection medium was replaced with DMEM-F12 (Gibco; Thermo Fisher Scientific, Inc.) without FBS. After 5 days at 37°C, the supernatant was collected by centrifugation at 300 × g for 5 min at 4°C and diluted (1:1) with 40 mM sodium phosphate buffer, pH 8, filtered through a 0.22-µm filter and purified on a 1-ml protein A column for 24 h at 4°C. The antibodies were eluted with glycine, pH 3, and immediately stabilized with Tris buffer, pH 9. Amicon-ultra® filters (MiliporeSigma) with a cut-off of 50 kDa were used for antibody concentration in PBS; 200 ml cell culture provided ~1 mg of purified antibody.
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2

Production and Characterization of Reporter HIV-1

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EB-FLV (containing bcl2), pNL4-3-Δ6-drEGFP (reporter HIV-1), pHelper [54 (link)], and pMD2.G (VSV-g) (Addgene, Cat#12259) plasmids were purified with Plasmid Plus Maxi Kit (Qiagen, Cat# 12963). 293T cells (ATCC, CRL-3216; CVCL_0063) grown in DMEM media (Hyclone, Cat# SH30022_01) were transfected with Lipofectamine LTX with PLUS reagent (ThermoFisher, Cat# 15338100), and, after an additional 48 h, supernatants were harvested. We tested the functional infectivity of NL4-3-Δ6-drEGFP by transducing 293T cells (American Type Culture Collection, Cat# CRL-3216) with the viral particles. After 48 h, we measured GFP signals with flow cytometry. We determined virus titers by the HIV-1 p24 ELISA Assay (XpressBio, Cat# Cat#XB-1000). Virus-containing supernatant was concentrated with LentiXconcentrator (Clontech, Cat# 631231).
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3

Assessing MTHFR Variants' Enzymatic Activity

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To test whether variants had an effect on MTHFR activity, and whether these effects were altered by FAD or S-adenosylmethionine (SAM) supplementation, we used an in vitro assay as previously described;39 (link),40 (link) we used 293T cells (ATCC: CRL-3216) modified by genetic editing to harbor MTHFR knock-out (KO) or specific variants.41 (link) In MTHFR-KO 293T cells, specific activity was measured after transfection with empty vector (pcDNA-C-Flag-LIC), vector harboring WT MTHFR (corresponding to GenBank: NM_005957.5), or variant MTHFR constructs generated by site-directed mutagenesis.31 (link) The assay was performed in 50 mM potassium phosphate buffer (pH 6.6) under saturating substrate concentrations (100 μM methyleneTHF; 200 μM NADPH) in the absence or presence of 75 μM FAD (for FAD responsiveness studies) or in the presence of 75 μM FAD after preincubation for 5 min at 37°C with purified SAM42 (link) (for SAM inhibition studies). The Ki for SAM was estimated from a plot of inhibitor versus response and a four-parameter curve fit (GraphPad Prism v8.00). For heat-treatment studies, samples were incubated at 46°C for 5 min before the assay, either without FAD supplementation or with 75 μM FAD supplemented either before or after heat treatment, as described.40 (link)
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4

Generating NSCLC Cell Lines for Drug Resistance Research

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H1299 and A549 NSCLC cells were obtained from American Type Culture Collection
(ATCC, Manassas, USA) and cultivated in RPMI-1640 medium (Invitrogen) with 10%
fetal calf serum (FCS, Biosera, Boussens, France) as reported.18 (link) Human bronchial 16HBE cell line (Procell, Wuhan, China) was used as a
control of non-tumor cells and propagated using standard protocols provided by
Procell. 293 T cells (ATCC) were cultivated in maintain medium provided by ATCC
for dual-luciferase reporter assays.
DTX-resistant NSCLC cells (A549/DTX and H1299/DTX) were established in our
laboratory by treating A549 and H1299 cells with gradually increasing
concentrations of DTX (Sigma-Aldrich, Steinheim, Germany; starting from 20 ng/L
and progressively increasing the concentration up to 10 µg/L) more than 9 months
until they acquired the ability to grow in the presence of DTX at the same rate
as parental cells in the absence of the drug. To maintain the resistance
phenotype, additional 10 µg/L of DTX was used in the cell medium.
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5

AAV8 Vector Production and Purification

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Recombinant AAV8 vectors were generated as previously described45 (link) with several modifications.46 (link) Plasmids required for AAV packaging, adenoviral helper plasmid pAdDeltaF6 (PL-F-PVADF6), and AAV8 packaging plasmid pAAV2/8 (PL-T-PV0007) were obtained from the University of Pennsylvania Vector Core. Each AAV transgene construct was co-transfected with the packaging constructs into 293T cells (ATCC, CRL-3216) using polyethylenimine (PEI). Cell pellets were harvested and purified using a single cesium chloride density gradient centrifugation. Fractions containing AAV vector genomes were pooled and then dialyzed against PBS using a 100 kD Spectra-Por Float-A-Lyzer G2 dialysis device (Spectrum Labs, G235059) to remove the cesium chloride. Purified AAV were concentrated using a Sartorius Vivaspin Turbo 4 Ultrafiltration Unit (VS04T42) and stored at −80°C until use. AAV titers were calculated after DNase digestion using qPCR relative to a standard curve of the transgene plasmid. Primers used for titer are included in Table S3.
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6

Cell Culture Protocols for Glioblastoma Research

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U87 MG cells and A172 cells were purchased from ATCC. U87 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM):F12 media (1:1) (ThermoFisher Scientific) with 10% FBS and 1% Glutamax. A172 cells were cultured in DMEM high glucose media (ThermoFisher Scientific) with 10% fetal bovine serum (FBS) and 1% Glutamax. GBM-110 and GBM 511 FHTC primary pediatric cancer cell lines were purchased from Fred Hutchinson Cancer Research Center and grown in predefined serum-free neural stem cell medium, supplemented with epidermal growth factor and fibroblast growth factor, on laminin (ThermoFisher Scientific) coated plates. Tissue culture plates were coated with 1 mL laminin working solution prepared in phosphate-buffered saline (PBS) (10 μg/mL) and incubated at 37°C for a minimum of 1 h. Plates were washed once with PBS before seeding cells. Membrane-bound interleukin 15 (IL15) and 41BB ligand-expressing K562 cells were kindly provided by Dr. Dario Campana (St. Jude Children’s Research Hospital, Memphis, TN) and cultured in RPMI 1640 media (ThermoFisher Scientific) with 10% FBS and 1% Glutamax. We purchased 293T cells from ATCC and were grown in DMEM high glucose media with 10% FBS and 1% Glutamax. Samples were obtained under the guidelines of the Institutional Review Board at CNH - Pro0004033 and CR00000266.
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7

Culturing 293T Cells in DMEM

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293T cells (ATCC) were maintained in DMEM (GIBCO) supplemented with 10% FBS, 1% penicillin/streptomycin and 2 mM L-glutamine. Cells were cultured at 37°C and 5% CO2.
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8

Lentiviral Knockdown of Ezh2 and Eif4ebp1

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Lentiviruses bearing shRNA against Ezh2 and Eif4ebp1 were produced in 293T cells (ATCC) co-transfected with the vectors pMD2.G and psPAX2, gifts from Dr. Didier Trono (Addgene plasmids #12259 and #12260). Lipofectamine 3000 (Invitrogen, L3000075) was used for transfection according to the manufacturer’s instructions and virus-containing media was harvested and filtered through a 0.45 µm filter at 24 and 48 h post-transfection. MMTV-NIC cells were transduced in the presence of 10 µg/ml polybrene (Sigma, 107689). Transduced cell lines were selected and maintained in Complete Media with 2 μg/ml puromycin (BioShop, PUR333).
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9

Cell Culture and Metabolic Labeling

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U2OS cells (American Tissue and Cell Collection, HTB-96) were a kind gift of Dr. John Hogenesh (University of Pennsylvania) NIH-3T3 (CRL-1658), MDCK (CCL-34) and 293T cells (CRL-3216) were directly obtained from ATCC. All cell lines were cultured in 10% Dulbecco’s modified Eagle medium supplemented to 10% decomplemented fetal bovine serum at 37°C, 5% CO2, 21% O2 and 100% humidity unless otherwise indicated. For aminoacid depletion experiments, dialyzed FBS was used and L-glutamine was supplemented as indicated. Cell lines were maintained and passaged according to ATCC recommended procedures. Pharmacological agents was as follows: Purvalanol-A (Sigma P4484), Z-VAD-FMK (EMD Millipore 627610), actinomycin D (Sigma A9415), cycloheximide (Sigma C7698), NAC (Sigma A9165), Trolox (Santa Cruz Biotech sc-200810) and CCCP (Sigma C2759) were added to cell cultures 12 h after cell seeding at the concentrations indicated and maintained until analysis, changing the medium every 24 hours. Ethynyl-uridine (Life Technologies E10345) and homopropargyl-glycine (Life Technologies C10186) were added at 5 and 50 μM respectively, two hours prior to incorporation analysis using the Click-iT alkyne detection kit (Life Technologies C10330).
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10

Characterization of EGFR-mutant NSCLC Cell Lines

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EGFR mutant PC-9 and HCC827 (ΔE746-A750) and PC-9/ER, PC-9/ERC15, PC-9/ERC16, and HCC827/ER (ΔE746-A750; T790M) NSCLC cells were provided by Dr. William Pao (Vanderbilt University). erlotinib resistant cells were derived as described and characterized (27 ). AZD9291 resistant cells were derived as described and characterized (28 ). Cell lines were authenticated and sequenced for signature mutations (27 ). EGFR TKI resistant lines were maintained in the presence of 1μM erlotinib (Cell Signaling Technology) throughout the study (refreshed every 72 hours) although experiments were routinely conducted after a 72 hour drug holiday. ALW-II-41-27 and NG-25 were generously provided by Nathanael Gray (Dana-Farber Cancer Institute, Harvard Medical School). ALW-II-41-27 was determined to have >99.7% purity by LCMS analysis. 293T cells used for lentivirus production were purchased from ATCC.
All lung cancer cell lines were cultured in RPMI-1640 medium (Corning/Cellgro) supplemented with L-glutamine (2mM), 10% fetal bovine serum (FBS) (Thermo Scientific, HyClone Laboratories Inc.), penicillin (100U/mL), and streptomycin (100μg/mL). 293T cells were grown in DMEM (Corning/Cellgro) supplemented with L-glutamine (2mM), and 10% FBS. All cells were grown in a humidified incubator with 5% CO2 at 37°C.
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