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3 protocols using ta150032

1

Immunoblotting Analysis of TRK Signaling

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Transfected HEK293T and patient-derived cell lines were treated with the indicated concentrations of inhibitors for 4 h. Following treatment, cells were pelleted, washed once in ice-cold PBS, and lysed in cell lysis buffer supplemented with 0.25% deoxycholate, 0.05% SDS, and protease and phosphatase inhibitors. Protein concentrations were determined using the Pierce BCA Protein Assay (ThermoFisher Scientific). Protein was extracted with NuPAGE LDS Sample Buffer (4×) (ThermoFisher Scientific) sample buffer, supplemented with β-mercaptoethanol, for 10 min at 75°C. An amount of 10–25 µg of extracted lysate protein was run on 4%–12% Bis-Tris (Invitrogen; ThermoFisher Scientific) and transferred to nitrocellulose membranes (Prometheus). Blots were probed with antibodies specific for phospho-TRK (CST; 4621; 1:1000), pan-TRK (CST; 3266; 1:1000), phospho-p44/42 MAPK (CST; 9101; 1:1000), total ERK2 (Santa Cruz; sc-1647;1:1000), phospho-S6 (CST; 4858; 1:1000), total S6 (CST; 2216; 1:1000), GFP (Origene; TA150032; 1:5000), phospho-RAF1 (CST; 9421; 1:1000), and GAPDH (Origene; OTI2D9; 1:5000). We used the Bio-Rad Chemidoc imaging station or LI-COR Odyssey imaging system and followed manufacturer's recommendations for immunoblot detection with use of HRP-conjugated or IR dye secondary antibodies, respectively.
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2

Immunostaining of Lung Tissue Sections

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The following antibodies were used to immunostain FFPE sections: goat Spc (1:100; sc7706; Santa Cruz Biotechnology); rabbit Spc (1:500; ab3786; Millipore); rabbit Pdpn (1:100; sc134483; Santa Cruz Biotechnology); rabbit 53BP1 (1:3500; NB100-304; Novus Biologicals); goat CD34 (1:100; Santa Cruz Biotechnology); rabbit eGFP (1:1000; TA150032; Origene); mouse αSMA (1:3000; A2547; Sigma Aldrich); rabbit ΔNp63 (1:100; 619001; Biolegend); donkey anti-goat Alexa 568 (1:2000; A11057; Thermo Fisher Scientific); goat anti-rabbit Alexa 647 (1:2000, A21244; Thermo Fisher Scientific); donkey anti-mouse (1:2000; A31571; Thermo Fisher Scientific). All sections were counterstained with DAPI. Whole slide immunofluorescence imaging was performed in the Digital Histology Shared Resource at Vanderbilt University Medical Center using a Leica Apiro Versa whole slide scanner that provides high resolution wide field images of ranging from 0.05x to 40x. Entire lung sections were first inspected at a low magnification. Following the initial inspection each entire lung section was then inspected at 20 to 40x. Images were captured as jpeg files. Confocal images of immunofluorescence staining were acquired using an Olympus FV-1000 inverted confocal microscope using a 60x/1.45 Plan-Apochromat oil immersion objective lens. Images were captured as jpeg files.
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3

Immunofluorescence Staining of Transfected HEK293T Cells

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Transfected HEK293T cells were fixed for 40 minutes in phosphate-buffered saline (PBS)-4% paraformaldehyde, washed 3 times in ice-cold PBS, and permeabilized in PBS-0.1% Triton for 20 minutes. The fixed cells were blocked with PBS-4% bovine serum albumin-Tween 0.05% for 1 hour and incubated with rabbit primary antibody at 4 °C for 12 hours (GFP, 1:2500, Origene TA150032). After washing, cells were incubated with secondary antibody for 1 hour (Rabbit Alexa 488, 1:1000, Thermo Fisher Scientific A-11094). After counterstaining with 3 μL DAPI, cells were visualized using confocal microscopy (Zeiss LSM170 Airyscan).
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