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34 protocols using x tremegene transfection reagent

1

Transfection of HEK293T Cells

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HEK293T cells were transfected with the vector or HOXB13-GFP-tagged constructs using the X-tremeGENE transfection reagent (Millipore Sigma, Darmstadt, Germany). GFP Expression was confirmed by fluorescence microscopy. Transfected cells were processed for experiments as described in the study.
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2

SEMA7A Knockdown and Overexpression

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For knockdown studies, SEMA7A-targeting shRNA plasmids (shSEMA7A KD1 and KD2) or a scrambled control (Scr; SA Biosciences, Frederik, MD, and the Functional Genomics Facility at the CU Anschutz Medical Campus) were transfected using X-tremeGENE transfection reagent (Millipore Sigma, St. Louis, MO) as described by the manufacturer. SEMA7A overexpression in MCF7 cells was achieved using a SEMA7A-Fc plasmid (generous gift from R. Medzhitov, Yale University, New Haven, CT). A pcDNA3.1 empty vector control plasmid was obtained from H. Ford (CU Anschutz Medical Campus). All other plasmids were obtained from the Functional Genomics Core at the University of Colorado Anschutz Medical Campus. Knockdown and overexpression were confirmed via qPCR and Western blot analysis.
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Production of MLL-AF9 Transduced Human CD34+ Cells

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Production of MLL-AF9 transduced human CD34+ cells has been described.78 Human CD34+ cells were isolated from human cord blood (New York Blood Center) using the EasySep™ Human Cord Blood CD34 Positive Selection Kit II (Stemcell Technologies). For pre-enrichment, Lymphoprep (Stemcell Technologies) and SepMate™ columns (Stemcell Technologies) were used. Viral supernatants were generated by co-transfection of HEK293-T cells with retroviral (pMSCV-MLL-AF9-IRES-GFP)78 expression vector with packaging and envelope vectors (Human Retro: pUMVC and VSV-G) and X-tremeGene transfection reagent (Millipore). The viral supernatant was filtered through 0.45μm and was concentrated using Amicon Ultra centrifugal filters (Millipore). Human CD34+ cells were plated on retronectin-coated plates (Takara) and were spin infected at a 1:1 dilution of virus:media at 800g at 37°C for 1.5h. The cells were dissociated from the plates using enzyme-free dissociation buffer (Gibco) and were plated in fresh media. Cells were maintained in IMDM with 20% FBS, 1x penicillin/streptomycin (Gibco), 1xß-mercaptoethanol (Gibco), 6 μg/mL hIL3, 10 μg/mL hIL6, 10 μg/mL hSCF, 10 μg/mL TPO, and 10 μg/mL FLT3 (Stemcell Technologies) at 37°C and 5% CO2. Two days after transduction, GFP positive cells were sorted using FACSAria cell sorter (BD Bioscience).
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4

Production of MLL-AF9 Transduced Human CD34+ Cells

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Production of MLL-AF9 transduced human CD34+ cells has been described.78 Human CD34+ cells were isolated from human cord blood (New York Blood Center) using the EasySep™ Human Cord Blood CD34 Positive Selection Kit II (Stemcell Technologies). For pre-enrichment, Lymphoprep (Stemcell Technologies) and SepMate™ columns (Stemcell Technologies) were used. Viral supernatants were generated by co-transfection of HEK293-T cells with retroviral (pMSCV-MLL-AF9-IRES-GFP)78 expression vector with packaging and envelope vectors (Human Retro: pUMVC and VSV-G) and X-tremeGene transfection reagent (Millipore). The viral supernatant was filtered through 0.45μm and was concentrated using Amicon Ultra centrifugal filters (Millipore). Human CD34+ cells were plated on retronectin-coated plates (Takara) and were spin infected at a 1:1 dilution of virus:media at 800g at 37°C for 1.5h. The cells were dissociated from the plates using enzyme-free dissociation buffer (Gibco) and were plated in fresh media. Cells were maintained in IMDM with 20% FBS, 1x penicillin/streptomycin (Gibco), 1xß-mercaptoethanol (Gibco), 6 μg/mL hIL3, 10 μg/mL hIL6, 10 μg/mL hSCF, 10 μg/mL TPO, and 10 μg/mL FLT3 (Stemcell Technologies) at 37°C and 5% CO2. Two days after transduction, GFP positive cells were sorted using FACSAria cell sorter (BD Bioscience).
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5

Retroviral Transduction of Murine LSK and Human CD45+ Cells

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Viral supernatants were generated by co-transfection of HEK293-T cells with retroviral (MSCV-MLL::AF9-IRES-GFP or MSCV-MLL::AF9-HA-FKBP12F36V-IRES-GFP) expression vectors with packaging and envelope vectors (Human Retro: pUMVC and VSV-G; Mouse Retro: pCL-Eco) and X-tremeGene transfection reagent (Millipore). The viral supernatant was filtered through 0.45μm and was concentrated using Amicon Ultra centrifugal filters (Millipore). The murine LSK cells were spin infected at a 1:1 dilution of virus:media and 0.8μg/ml polybrene (Millipore) at 2000rpm at 37°C for 1.5h and the supernatant was replaced with fresh medium immediately after the spin infection. The human CD45+ cells were plated on retronectin-coated plates (Takara) and were spin infected at a 1:1 dilution of virus:media at 2000rpm at 37°C for 1.5h. The cells were dissociated from the plates using enzyme-free dissociation buffer (Gibco) and were plated in fresh media.
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6

THY1 Restoration via Lentiviral Transduction

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HONE1, HK1, and NPC43 cells with low THY1 expression were used as recipient cells for THY1 restoration with stable expression of THY1, mediated by the pLVX expression vector [20 (link)]. The packaging vectors psPAX2 and pMD2.G were obtained from Addgene. The pLVX-EF1α-THY1-expressing vector was constructed. Lentivirus packaging was performed using 293T cells and X-tremeGENE transfection reagent (Millipore, Burlington, MA, USA, #6366236001). The cells were incubated for the production of lentivirus-containing medium for 2 days. Subsequently, the medium was harvested and stored at −80 °C until usage. For infection, NPC cells were trypsinized and then mixed with the lentivirus-containing medium at a ratio of 1:1 in a culture flask, with the addition of polybrene (Santa Cruz, Santa Cruz, CA, USA, #sc-134220). After 12 h, the medium was replaced with fresh, complete medium. Puromycin (Invitogen, Waltham, MA, USA, #ant-pr-1) was used for selection of successfully infected cells.
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7

Prostate Cancer Cell Line Generation

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To generate stable prostate cancer cell lines expressing Vector (Vec), WT and Mut-ATP5F1A or RWPE-1 cell line stably expressing Vector (Vec), TNK2/ACK1 and kd-TNK2/ACK1, respective retrovirus constructs were subcloned into pMSCV vector and transfected in 293 T cells with a packaging plasmid (pCMV-VSV-G and pUMVC3-gag pol) using X-tremeGENE transfection reagent (Sigma-Aldrich, 4,476,093,001). Prostate cancer cell lines or RWPE-1 cells were infected for 12 h with viral supernatants containing 8 μg/mL polybrene (Santa Cruz Biotechnology, sc-134,220). The transfected cells were selected in the presence of 2 μg/mL puromycin (Thermo Fisher Scientific, A1113802). WT and Mut-ATP5F1A cells were cultured in media with 1% serum for 12 h prior experiments or specifically mentioned in experiments.
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8

Ack1 Knockdown in Jurkat Cells

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Jurkat cells were transfected with Ack1-specific siRNA (Dharmacon RNA Technologies, Lafayette, CO) or control siRNA by using X-tremeGENE transfection reagent (Sigma-Aldrich). Cells were allowed to culture for 48 hr and then harvested for immunoblotting experiments.
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9

PEG10 Knockdown and Overexpression Assays

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For the knockdown assays, both cell lines were transfected with siRNA targeting PEG10 (Applied Biosystems, Cat#4392420) or control siRNA (Applied Biosystems, Cat#4390847) for 18hrs and plated as required for the assay. For the gain of function assay, cells were transfected with PEG10 plasmid (OriGene, Cat#RC208683) or control plasmid for 18hrs using the XtremeGENE Transfection Reagent (SigmaAldrich, Cat#06365779001). At 48hrs post-transfection, qPCR was performed to confirm that PEG10 gene expression was decreased for the knockdown assays in both cell lines and increased for the gain of function assay in the HT-29 cell line (Supplement 3).
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10

Production and Purification of HIV-1 gp120 Core

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Plasmids encoding the layer mutant gp120 extended core (coree) proteins, HIV-193TH057 gp120 coree LM+HS and LM+HT, were transfected into GnT1 cells using Xtremegene transfection reagent (Sigma-Aldrich) per the manufacturer’s instructions. Following 7 days of culture growth at 37°C and 8% CO2, cells were pelleted by centrifugation and cell supernatant was filtered. Expressed gp120 was purified by passage over a 17b affinity column made by cross-linking MAb 17b to protein A (Pierce protein A IgG plus orientation kit; Thermo Fisher). gp120 was eluted with 0.1 M glycine (pH 3.0) into tubes containing 1/10 the final volume of 1 M Tris-HCl (pH 8.5) to raise the pH. The protein was then deglycosylated with 10 units/μg of Endo Hf (New England Biolabs) overnight at 37°C in a mixture of deglycosylation buffer, 50 mM sodium acetate (pH 6.0), and 350 mM sodium chloride. Endo Hf was removed by passage over an amylose resin column, and the protein was further purified by gel filtration chromatography on a Superdex 200 16/60 column (GE Healthcare, Piscataway, NJ) equilibrated with 5 mM Tris-HCl (pH 7.2) and 150 mM sodium chloride. The protein was concentrated to approximately 5 mg/ml for use in crystallization trials.
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