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65 protocols using c myc

1

Western Blot Analysis of Crude Protein

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Western blot analysis of crude protein extracts was performed according to Waschbüsch et al. (2009) (link). Briefly, cells were harvested and lysed in lysis buffer (R0278; Sigma) supplemented with protease and phosphatase inhibitors (P8340, P0044, P5726; Sigma) for 30 min at 4°C. Protein extracts were heat inactivated, separated using 4–20% SDS–PAGE gels (Bio-Rad, Hercules, CA) and blotted to polyvinylidene difluoride (PVDF) membranes (Bio-Rad). Primary antibodies against tubulin (MAB1864; Merck, Darmstadt, Germany), paxillin (AH00492; Invitrogen, Carlsbad, CA), talin (sc-15336; Santa Cruz Biotechnology, Dallas, TX), α-catenin (C2081; Sigma), c-Myc (M5546; Sigma) and E-cadherin (610182; BD Bioscience, Franklin Lakes, NJ) were used and detected by alkaline phosphatase (ALP)-coupled secondary antibodies directed against rat, rabbit, and mouse (Sigma), respectively.
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2

Evaluating Epithelial-Mesenchymal Transition Markers

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Trypsinized l.t.EMT+RGM1, l.t.EMTRGM1, and RGM1 cells were seeded at 8 × 106 cells per well and cultured for 96 h in Hp-AGF and GF supernatants enriched with TGFβR1 kinase activity inhibitor SB-431542 (10 μM/L) (Sigma-Aldrich, Saint Louis, MO, USA) and in DMEM + 10% FBS, respectively. After incubation period, total cellular RNA was isolated and RT-PCR was carried out (see above). Specific primers for Ki67, Cyclin D1, Bax, Bcl2, c-Myc, Oct4, Sox2, Klf4, and 18S RNA (the verification of the RNA integrity) were used (Sigma-Aldrich, Saint Louis, MO,USA) (Table 1).
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3

Reciprocal Co-Immunoprecipitation of Proteins

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Reciprocal co-immunoprecipitation experiments were done as before (Johnson et al., 2013 (link)) using adenoviral vectors. All experiments were performed on polarized MDCK monolayers grown on Transwell filters (Corning, Corning, NY, USA). Cells were infected at confluence at a MOI of 30 and, 48 hrs later, filters were harvested for immunoprecipitation. Cells were immunoprecipitated using rabbit, polyclonal antibodies specific to either YFP (Clontech, Mountain View, CA, USA) or c-myc (Sigma-Aldrich, St. Louis, MO, USA). Western blotting was then performed using a mouse, monoclonal antibody specific to the opposite tag, either cmyc (9E10; Invitrogen, Grand Island, NY, USA) or YFP (JL-8; Clontech, Mountain View, CA, USA). For the immunoprecipitation and blotting of WT Best1-YFP compared to the four truncation mutants, MDCK cells were immunoprecipitated for YFP using a rabbit, polyclonal antibody (Clontech, Mountain View, CA, USA) and western blotted back using a mouse, monoclonal antibody specific to YFP (JL-8; Clontech, Mountain View, CA, USA).
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4

Lentiviral shRNA Knockdown in MCC Cells

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Lentivector directing expression of shRNA specific to p21 (TRCN0000040123), p27 (TRCN0000009856), p57 (TRCN0000010484) and c-Myc (TRCN0000039642) were purchased from Sigma-Aldrich and nontargeting PLKO.1 scramble shRNA (plasmid 1864) was purchased from Addgene. To generate lenti-virus media, 293T/17 cells were co-transfected with gene transfer vectors and virus packaging vectors ΔH8.2 and VSVG by TransIT-LT1 transfection reagent (Mirus). Two days following transfection, viral supernatants were collected and MCC cells were transduced with viral supernatant for 48 hours in fibronectin-coated 6-well plates in the presence of 8 ug/ml polybrene after spinocculation at 800 g, 32°C for 30 min. Cells were then selected in culture media containing 2 µg/mL puromycin for at least 48 hours.
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5

Comprehensive Molecular Profiling Protocol

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Lenalidomide, pomalidomide, palbociclib, melphalan, bortezomib and dexamethasone were obtained from SelleckChem. BSJ-03-123, YKL-06-102 and CST528 were synthesized according to Brand et al. 2019 and Steinebach et al. 2020.
Primary antibodies used for Western blotting from Cell Signaling (Danvers, USA) include CDK6 (clone DCS83, #3136, RRID:AB_2229289, 1:2000), CDK4 (clone D9G3E, #12790, RRID:AB_2631166, 1:1000), Rb (clone 4H1, #9309, RRID:AB_823629, 1:1000), Phospho-Rb (Ser807/811) (#9308, RRID:AB_331472, 1:1000), IKZF3 (clone D1C1E, #15103, RRID:AB_2744524, 1:1000), IKZF1 (clone D6N9Y, #14859, RRID:AB_2744523, 1:1000), IRF4 (clone D43H10, #4299, RRID:AB_10547141, 1:1000), c-Myc (clone D84C12, #5605, RRID:AB_1903938, 1:1000), RRM1 (clone D12F12, #8637, RRID:AB_11217623, 1:1000), RRM2 (clone E7Y9J, #65939, 1:1000), anti-rabbit IgG HRP-linked antibody (#7074, 1:5000), anti-mouse IgG HRP-linked antibody (#7076, 1:5000); antibodies from Sigma-Aldrich (St. Louis, USA) include anti-α-Tubulin (#T5168, RRID:AB_477579, 1:7000); antibodies from Santa Cruz Biotechnology (Dallas, USA) include CDK6 (clone B-10, sc-7961, 1:1000), TRIP13 (clone A-7, sc-514285, 1:1000); antibodies from Abcam (Cambridge, UK) include anti-β-actin (ab20272, 1:10,000).
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6

Antibody Validation for Alzheimer's Research

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The mouse-specific membralin antibody used in this study was previously custom-made and now is available from Millipore (ABN1661, 1:1000). The PS1-NTF antibody used in this study was described previously (Rabbit polyclonal antibody, 1:1000)35 (link). Other antibodies were acquired from commercial sources as follows: c-Myc (Sigma, C2956, 1:1000), HA (Cell Signaling Technology, 3724 s, 1:1000), EMC3 (Santa Cruz, sc-365903, 1:1000), SYVN1 (Sigma, H7790, 1:500), SYVN1 (Santa Cruz biotechnology, sc-293484, 1:1000), AMFR (Cell Signaling Technology, 9590 s, 1:1000), AMFR (Santa Cruz Biotechnology, sc-166358, 1:1000), VCP (Thermo Fisher Scientific, MA3-004, 1:1000), VCP (Cell Signaling Technology, 2648 s, 1:1000), PS1-CTF (Millipore, 5232, 1:2000), human membralin (Sigma, HPA042669, 1:500), nicastrin (Cell Signaling Technology, 9447 s, 1:1000), nicastrin (Millipore, MAB5556, 1:1000), β-actin (Sigma, 5441, 1:10000), NICD (Cell Signaling Technology, 4147 s, 1:1000), PEN2 (Cell Signaling Technology, 8598 s, 1:1000), PSD95 (Cell Signaling Technology, 3450 s, 1:1000), active (cleaved) caspase3 (Cell Signaling Technology, 9662 s, 1:100), MOAB2 (Aβ40/42, Biosensis, M-1586-100, 1:500), rabbit IgG control (Cell Signaling Technology, 2729, 1 μg used as IP control).
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7

Comprehensive TBX3 Protein Analysis Protocol

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Tbx3 (Frank et al., 2012 (link), 2013 (link)), TBX3 (SC-17871,MAB10089,A303-098A), CAPERα (A300-291A), GST (SC-33613), LaminB1 (SC-56144), C-Myc (SC-40), R-IgG (SC-2027), m-IgG (SC-2025), Anti-Flag (Sigma, F3165), H3K9me3 (Cell Signaling, 9754), H3K4me3 (Cell Signaling, 9751), H3K27me3 (Cell Signaling, 9733), H3K9ace (Cell Signaling, 9649), H4K5ace (Cell Signaling, 9672), H3K14ace (Cell Signaling, 4353), p-RB -Ser 810--811 (SC-16670), p-RB -Ser 795 (SC-7986), p-RB -Ser 780 (SC-12901), Rb1 (SC-73598), H3S10P (SC-8656), H2A K119ub (8240S), p21 (SC-756), p53 (Invitrogen 134100), Cyclin D1 (SC-753), Cyclin D2 (SC-754), Cyclin D3 (SC-755), Cyclin E (SC-20648), CDK2 (SC-6248), CDK4 (SC-601) CDK6 (SC-177), hnRNP K (SC-53620), hnRNP C1/C2 (SC-32308), hnRNP H (SC-10042), hnRNP U (SC-32315), hnRNP A2/B1 (SC-53531), hn RNP A1 (SC-32301), and hnRNP D1 (AB-61193).
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8

Cholangiocyte Isolation and Characterization

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Normal Rat Cholangiocytes (NRC) were isolated and established in culture as described [13 (link)]. Human CCA cell lines (KWCH, KWBC-1, Mz-ChA-1) and normal human cholangiocyte H69 cells were gifted from Dr. Gregory Gores. Cells were cultured in DMEM with 10% FBS. PPAR agonist GW501516, Akt inhibitor LY294002, fatty acid-free BSA, c-myc, Flag, GST and other chemicals were from Sigma (St. Louis, MO). All cell-culture reagents were from Invitrogen (Carlsbad, CA). PPAR, Akt, p-AKT, CDK2, NM23-H2 and -actin monoclonal antibodies were purchased from Santa Cruz (Santa Cruz, CA). All of the secondary antibodies were from Cell Signaling Technology (Danvers, MA).
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9

Targeted siRNA Knockdown of Key Regulators

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siRNAs specific to Numb (SASI_Hs01_00245423, 5′GAUAGUGUUGGUGCAUCA, 3′UGAUGAACCAACGACUAUC), SRPK1, SRPK2, c-Myc, Oct4, Rbfox1, Rbfox2, Rbfox3, Hsp90 and negative control siRNA were purchased from Sigma-Aldrich. Transfection was performed using Lipofectamine RNAiMAX (Invitrogen), according to the manufacturer’s instructions. A final concentration of 20 nM siRNA duplex was used for each transfection.
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10

Western Blot Analysis of Protein Expression

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Cell monolayers were lysed in Laemmli´s sample buffer (62.5 mM Tris-HCl [pH 6.8], 2% sodium dodecyl sulfate [SDS], 0.01% bromophenol blue, 10% glycerol and 5% β-mercaptoethanol). Protein samples were subjected to 12% SDS-polyacrylamide gel electrophoresis (PAGE) and transferred to nitrocellulose membranes (BioRad). Membranes were blocked for 30 min at room temperature in Tris-buffered saline supplemented with 0.05% Tween 20 (TBS-T) containing 5% non-fat dry milk, and later incubated with primary antibodies diluted in the same buffer at 4 °C overnight. Antibodies used in this study were β-actin (Santa Cruz Biotechnology SC-47778), c-Myc (Sigma PLA0001 or Roche 11667149001), Histone 3 (Sigma H0164), and Flag (Sigma B3111). Then, membranes were washed with TBS-T and incubated with goat anti-mouse IgG-peroxidase conjugate (Sigma DC02L) for 1 h at room temperature and washed again. All antibodies were used at a 1:10,000 dilution in TBS-T with 5% non-fat dry milk. Detection of immunoreactive proteins was carried out using the enhanced chemiluminescence (ECL) reaction (SuperSignal ThermoScientific) and detected by the ChemiDoc Touch Imaging System (BioRad).
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