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3 protocols using blue bio film

1

Western Blot Analysis of Hypoxia Signaling

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Whole-cell extracts were prepared by lysing cells with RIPA lysis buffer supplemented with a protease inhibitor cocktail (Sigma-Aldrich, St Louis, MO, USA). Protein concentrations were estimated using the Bradford’s method (Bio-Rad, Hercules, CA). Equal amounts of total protein were resolved on a 7.5% SDS-PAGE gels and transferred to a nitrocellulose membrane (Bio-Rad). After blocking in 5% milk-TBST (TBS Tween), the membrane was separately probed with HIF-1α antibody (BD Biosciences San Jose, CA), HIF-2α antibody (Novus Biologicals, Littleton, CO) and COX-2 antibody (Cayman Chemical, Ann Arbor, MI). Anti-GAPDH antibody (Sigma-Aldrich) was used for equal loading assessment. Secondary antibodies were horseradish peroxidase conjugated anti-mouse, anti-rabbit (GE Healthcare, Chicago, IL), or anti-goat IgG (Novus Biologicals). The signal was visualized using ECL Plus reagents (Thermo Scientific, Rockford, IL) and developed on a Blue Bio film (Denville Scientific, Metuchen, NJ). The films were scanned and densitometric analysis was performed using the ImageJ (NIH, Bethesda, MD). Relative density changes against GAPDH were analyzed and in some cases normalized to the immunoreactive bands in control cells (HBSS treated), which was set to 1 using data from 2–3 cell lysates.
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2

Ubiquitin-Protease Assay and Reagents

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All chemicals and reagents were from Sigma Aldrich unless otherwise stated. Solvents (except DMSO) were from Fisher (Pittsburg, PA). Other reagents used in this study: PEITC (Acros Organics); Bortezomib (Millennium Pharmaceuticals); Mini-Complete and PhosSTOP inhibitory cocktails (Roche Applied Science); recombinant human K63-linked di-ubiquitin (UC-300), recombinant human His6-USP1/UAF1 complex (E-568; Boston Biochem.); DMEM, glutamax, penicillin/streptomycin (Gibco); trypsin (0.25%), DPBS (Hyclone); cell dissociation buffer (fisher); Bradford dye (Bio-rad); dithiothreitol (GoldBio Tech); PVDF hybond, Amersham ECL Prime WB detection reagent (GE Healthcare Life Sciences); Blue Biofilm (Denville Scientific); ML323 USP1 inhibitor (EMD Millipore); TransIT 2020 transfection reagent (Mirus bio); Pierce protein G magnetic beads (ThermoFisher Scientific); TAMRA-ubiquitin propargylamide (TAMRA-Ub-PA), Cy5-ubiquitin vinyl methyl ester (Cy5-Ub-VME), Biotin-Ahx-Ub-VME, Biotin-Ahx-Ub-PA and Ub-Rh110MP (UbiQ). HA-ubiquitin vinylsulfone (HA-Ub-VS) and HA-Ub-VME were synthesized using standard methods previously described [88 (link)]. The plasmid encoding the HA-Ub(1-75)-intein-chitin binding domain fusion protein was a gift from Prof H. Ploegh of the Whitehead Institute.
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3

Western Blot Analysis of Hypoxia Signaling

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Whole-cell extracts were prepared by lysing cells with RIPA lysis buffer supplemented with a protease inhibitor cocktail (Sigma-Aldrich, St Louis, MO, USA). Protein concentrations were estimated using the Bradford’s method (Bio-Rad, Hercules, CA). Equal amounts of total protein were resolved on a 7.5% SDS-PAGE gels and transferred to a nitrocellulose membrane (Bio-Rad). After blocking in 5% milk-TBST (TBS Tween), the membrane was separately probed with HIF-1α antibody (BD Biosciences San Jose, CA), HIF-2α antibody (Novus Biologicals, Littleton, CO) and COX-2 antibody (Cayman Chemical, Ann Arbor, MI). Anti-GAPDH antibody (Sigma-Aldrich) was used for equal loading assessment. Secondary antibodies were horseradish peroxidase conjugated anti-mouse, anti-rabbit (GE Healthcare, Chicago, IL), or anti-goat IgG (Novus Biologicals). The signal was visualized using ECL Plus reagents (Thermo Scientific, Rockford, IL) and developed on a Blue Bio film (Denville Scientific, Metuchen, NJ). The films were scanned and densitometric analysis was performed using the ImageJ (NIH, Bethesda, MD). Relative density changes against GAPDH were analyzed and in some cases normalized to the immunoreactive bands in control cells (HBSS treated), which was set to 1 using data from 2–3 cell lysates.
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