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29 protocols using x tremegene hp

1

Pancreatic and Melanoma Cell Transfection

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Panc1 and MiaPaca2 pancreatic adenocarcinoma cells and RPMI-7951 melanoma cells were obtained from American Type Culture Collection. HPNE cells (hTERT-immortalized human pancreatic epithelial nestin-expressing stably transfected with mutant KRAS g12V and p16 shRNA) (22 ) were a gift from Paul Chiao, MD Anderson Cancer Center. All cell culture media were from Corning. All cells were cultured in 5% CO2 at 37 °C. Panc1 were cultured in DMEM with 10% heat-inactivated fetal bovine serum (FBS, SAFC BioScience), RPMI-7951 cells in EMEM/10% FBS, and HSFs in DMEM/10% FBS plus 1:100 Penicillin-Streptomycin (Thermo). Cell lines in normal growth media (8 × 105 in 10 cm culture dishes) were transiently transfected utilizing XtremeGene HP (MilliporeSigma) using a ratio of 1 μg plasmid DNA/3 μl XtremeGene HP/ml of growth medium. CDK4 and CDK6 depletion was performed using Dharmafect1 reagent (Dharmacon) according to manufacturer's instructions with siCDK4 and siCDK6 ONTARGETplus SMARTpools, siRNAs (Dharmacon), and Allstar Neg. control siRNA (catalog # 1027281, Qiagen).
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2

Inducible Deup1 Overexpression in DLD-1 Cells

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The full-length mouse Deup1 ORF or Deup1 exons 8–12 were cloned into a pcDNA5/FRT/TO vector. A Myc tag was inserted on the 3’ end of the cDNA sequence. DEUP1 transgenes were inserted into a single genomic locus in the Flp-in TRex-DLD-1 cells using FLP-mediated recombination. DLD-1 cells were seeded at 2 × 105 cells per well in a 6-well plate. The next day a transfection mixture of 100 uL Opti-MEM (Thermo Fisher Scientific; Cat. # 31985070), 3 uL of X-tremeGene HP (Sigma-Aldrich, cat. no. 6366236001), 100 ng of pcDNA5 plasmid and 900 ng of POG44 (Flp recominase) was prepared and incubated at room temperature for 30 minutes and then added drop-wise to each well. Two days later, cells were selected with 50 ug/mL of Hygromycin B (ThermoFisher, cat. no. 10687010). HEK293FT were transfected using PEI reagent as previously described42 .
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3

Retroviral Transduction of CD25 in Cells

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Human full length CD25 was cloned into retroviral vector pMSCV-IRES-YFP (gift from Dr. Melissa McCracken, Stanford University). Retrovirus was packaged in HEK293T cells as described[29 (link)]. Briefly, HEK293T cells were plated the day before transfection. Cells were transfected with pMSCV-CD25-IRES-YFP and pCL-10A packaging vector using X-tremeGENE HP (Sigma-Aldrich). The supernatant was collected, filtered using sterile 0.45 um filter.
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4

Podoplanin and CLEC-2 Interaction Protocol

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Protein A beads (KANEKA KanCapA) were from Wako Chemicals (Osaka, Japan). X-tremeGENE HP was purchased from Sigma (St Louis, MO, USA). Sepasol was purchased from Nacalai Tesque (Kyoto, Japan). The anti-podoplanin antibody (NZ-1, rat IgG) was purchased from Angio Bio Co. (Del Mar, CA, USA) and the anti-CLEC-2 antibody (AF1718, goat IgG) was from Novus Biologicals (Littleton, CO, USA). Horseradish peroxidase (HRP)-labeled anti-human IgG Fab2 antibody (709–1317) was purchased from Rockland Immunochemicals Inc. (Limerick, PA, USA), anti-goat IgG-HRP (P0160) from Dako (Glostrup, Denmark) and anti-Rat IgG-HRP (7077S) from Cell Signaling Tech (Danvers, MA, USA). A set of plasmids for constructing a lentivirus expression vector system, including human immunodeficiency virus type 1 (HIV-1)-based CSII-MCS-Venus, pCAG-HIVgp, and pCMV-VSV-G-RSV-Rev, were obtained from RIKEN (Wako, Osaka, Japan). The Fc-fusion protein expression plasmid containing human IgG1 (pFUSEN-hG1Fc) was purchased from InVIVOGen (San Diego, CA, USA). Hematoporphyrin was from MedChemExpress (Monmouth Junction, NJ, USA). 2CP was synthesized as reported previously [10 (link)].
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5

Localization of PAPS Synthase Variants

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PAPS synthase protein variants with preferred nuclear or cytoplasmic localization have been described previously (18 (link)). Mutating K9A,K10A in PAPSS1 or K6A,K8A in PAPSS2 disrupts a conserved nuclear localization signal and results in preferential cytoplasmic localization. Changing R111A,R112A in PAPSS1 or R101A,R102A in PAPSS2, on the other hand, inactivates a motif with nuclear export signal activity, resulting in pronounced nuclear accumulation (18 (link)). Coding sequences for all these protein variants without stop codons were NheI/BamHI inserted in the eukaryotic expression vector pEGFP-N1 with a C-terminal EGFP fusion. HEK293 cells were transiently co-transfected with these plasmids and a SULT2A1 expression vector (14 (link)) using XtremeGene HP (Sigma) according to the manufacturer's protocol.
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6

Lentiviral Transduction of NSCs

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NFIA and SOX9 were cloned from cDNA from hPSC-derived astroglial progenitors (d90). FUW-tetO-GFP (Addgene 30130) was digested with EcoRI to remove the GFP fragment and NFIA or SOX9 was inserted using traditional ligation cloning. Plasmids containing NFIA, SOX9, FUCCI-O or M2-rtTA (Addgene 20342), the psPAX2 (Addgene 12260) packaging vector and the pMD2.G (Addgene 12259) envelope was transfected into 293T cells using X-tremeGene HP (Sigma) in a 1:2:1 molar ratio, respectively. Virus was harvested at 48 and 72 hours post transfection and concentrated using AMICON Ultra-15 Centrifugal Filter Units (Millipore). NSCs were plated at 3.5×105 cells/cm2 on PO/Lam/FN dishes. The cells were incubated with viral particles generated (described above) for 16–20 hours. The media is then switched to NSC media with 1–2μg/ml of doxycycline with daily media changes for a minimum of 5 days. Cells were then detached using 0.05% Trypsin and washed several times in preparation for CD44 labeling.
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7

Knockdown of Mouse MYO10 Using Lentiviral shRNA

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mCherry-Lifeact was purchased from Addgene (#54491; Cambridge, MA), and pEGFP-Myo10 was previously described5 (link). To knockdown mouse MYO10 expression, we used the pLKO.1-TRC lentiviral vector (MISSION shRNA, Sigma-Aldrich) containing shRNA against mouse MYO10 (shRNA-1;TRCN0000110606, shRNA-2;TRCN0000110608, and shRNA-3;TRCN0000379126). A non-target shRNA vector (SHC016; Sigma-Aldrich) was used as a control for the shRNA experiments. For lentiviral packaging, psPAX2 and pMD2.G vectors (Addgene plasmids #12260, #12259) were co-transfected with the pLKO.1 into HEK293T cells with X-tremeGENE HP (Sigma-Aldrich) according to the manufacturer’s instructions. Virus-containing medium was harvested 72 hrs after transfection and filtered with 0.45 μm filters (EMD Millipore, Billerica, MA). Melb-a or B16F1 cells were infected with culture supernatants from HEK293T cells at a 1:6 dilution in complete culture medium. Cells were passed after 24 hrs and selected with 4 μg/ml puromycin for 14 days.
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8

Generation of CYP4F3A Expression Vector

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The expression vector of human CY4F3A was developed by inserting Flag‐tagged and Myc‐tagged CYP4F3A cDNA (NM_000896.3) into the pCMV6 vector using KpnI and SacII restriction sites. Vector sequence can be found in supplementary methods. Next, the C1123 > G point mutation was inserted using QuikChange site‐directed mutagenesis (Agilent, Santa Clara, USA). HEK293T cells were kindly provided by the Laboratory of Protein Phosphorylation and Proteomics, KU Leuven and were transfected using X‐tremeGene HP (Sigma‐Aldrich, St Louis, USA).
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9

Inducible Deup1 Overexpression in DLD-1 Cells

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The full-length mouse Deup1 ORF or Deup1 exons 8–12 were cloned into a pcDNA5/FRT/TO vector. A Myc tag was inserted on the 3’ end of the cDNA sequence. DEUP1 transgenes were inserted into a single genomic locus in the Flp-in TRex-DLD-1 cells using FLP-mediated recombination. DLD-1 cells were seeded at 2 × 105 cells per well in a 6-well plate. The next day a transfection mixture of 100 uL Opti-MEM (Thermo Fisher Scientific; Cat. # 31985070), 3 uL of X-tremeGene HP (Sigma-Aldrich, cat. no. 6366236001), 100 ng of pcDNA5 plasmid and 900 ng of POG44 (Flp recominase) was prepared and incubated at room temperature for 30 minutes and then added drop-wise to each well. Two days later, cells were selected with 50 ug/mL of Hygromycin B (ThermoFisher, cat. no. 10687010). HEK293FT were transfected using PEI reagent as previously described42 .
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10

Establishing Cell Lines for Reelin Research

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HeLa cells and HEK293 cells were grown in Dulbecco’s Modified Eagle Medium (DMEM; Thermo Fisher) supplemented with 10% Fetal Bovine Serum and 1% Penicillin-Streptomycin. All cell cultures were maintained at 37°C at 5% CO2. Stable HEK293 wild-type (WT) Reelin-expressing cells were the kind gift of Dr. Eckart Förster (Zelluläre Neurobiologie, Hamburg) (Forster et al. 2002 (link)). Stable cell lines of HEK293 cells secreting full-length R2290C or R2290H Reelin were generated in the same manner. Transfections were performed using X-tremeGENE HP following the manufacturer’s protocols (Sigma). Cortical neuronal cultures were isolated from embryonic (E) day 15 or 16 and grown in neurobasal media supplemented with 2% B27 (Invitrogen) and 1% Pen-Strep. Cells were plated at a density of 3×105/cm2 on poly-L-lysine coated polystyrene dishes. One quarter of culture media was replaced every 2-3 days.
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