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462 protocols using sc 47778

1

Cell Lysis and Protein Quantification

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Prior to ELISA and western blot analysis, cells in both the 2D and 3D cell culture formats were lysed in ice-cold RIPA buffer (20 min, frequent agitation, 4 °C, 2 × 106 cells per mL of lysis buffer). The resulting lysates were clarified by centrifugation at 10,000 ×g at 4 °C for 10 min. For ELISA, ERα and HIF-1α concentrations were determined with commercial kits (R&D Systems, DYC-5715 and DYC1935); β-actin concentration was determined with a sandwich assay consisting of a β-actin capture antibody (R&D Systems, AF4000) and an HRP-linked detection antibody (SantaCruz Biotechnology, sc-47778).
For western blot analyses, clarified lysates were separated by SDS-PAGE and transferred to PVDF membranes. Membranes were probed with antibodies for ERα (1:500), HIF-1α (1:200), and β-actin (1: 500), detected with HRP-conjugated secondary antibodies (1: 1000 m-IgGº BP-HRP), and visualized with the Pierce ECL Plus Western blotting substrate. Antibodies for ERα (sc-8002), β-actin (sc-47778), and mIgGº BP-HRP (sc-516102) were purchased from Santa Cruz Biotechnology; the HIF-1α antibody (610958) was purchased from BD Transduction Laboratories.
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2

Western Blot Analysis of Autophagy Proteins

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Cell lysates collected in RIPA buffer (supplemented with 1 mM PMSF, 1× protease inhibitor) were separated by SDS–PAGE, transferred to a PVDF membrane (Immobilon-P, Merck Millipore Ltd), and incubated with primary antibodies (1:1000) at 4 °C overnight. After subsequent staining with HRP-conjugated secondary antibodies (1:10000 for anti-rabbit and 1:3000 for anti-mouse antibodies; 4 °C; overnight), the signal was developed using the ECL Star kit (Euroclone SpA, according to the instruction of the manufacturer using the BioRad ChemidocTM imaging system (Image LabTM touch software, BioRad). β2-actin was used as the loading control. Western blot experiments were performed with anti-ATG5, anti-PU.1, anti-Beclin1, anti-IRF1 (D5F5U; 9G7; D40C5; D5E4, Cell Signaling Technology), anti-LC3I/LCRII (MBL-PM036, MBL International), anti-CRLS1 (PA5–25338, Invitrogen), anti-LPCAT1, anti-PGS1 (PA5–26318; PA5–43247, Invitrogen) and anti-β2 actin (SC-47778, Santa Cruz) antibodies.
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3

Western Blot Analysis of Protein Targets

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RIPA lysis buffer was employed to lyse cells or tumor tissues, which were then separated on SDS-PAGE gels and transferred onto the polyvinylidene fluoride (PVDF) membrane. The primary or secondary antibodies were incubated together with membranes. Antibodies of anti-WDR76 (HPA039804, Sigma-Aldrich; 1:1,000 dilution), anti-β-actin (sc-47778, Santa Cruz Biotechnology; 1:1,000 dilution), anti-Flag (A8592, Sigma-Aldrich; 1:1000 dilution), anti-HRAS (2867S, Cell Signaling Technology; 1:500 dilution), anti-p-ERK (ab229912, ABCAM; 1:500 dilution) and anti-p-MEK (ab96379, ABCAM; 1:500 dilution) were used.
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4

Oxidative Stress Pathway Evaluation

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Sulfasalazine and BSO were from Santa Cruz Biotechnology, DYC was from Tokyo Chemical Industry and OXY was from Alfa Chemistry. For immunoblot analysis, human xCT was detected with rabbit monoclonal antibodies (#12691, 1:1000 dilution; Cell Signaling Technology), Nrf2 with rabbit monoclonal antibodies (ab62352, 1:500 dilution; Abcam) and β‐actin with mouse monoclonal antibodies (sc‐47778, 1:500; Santa Cruz Biotechnology). For immunocytofluorescence analysis, 4‐HNE was detected with mouse monoclonal antibodies (MAB3249, 1:100; R&D Systems). For immunohistochemical or immunohistofluorescence analysis, 4‐HNE was detected with mouse monoclonal antibodies (HNEJ‐2, 1:100; JaICA) and cyclooxygenase‐2 (COX‐2) was detected with rabbit polyclonal antibodies (HPA001335, 1:100; Atlas Antibodies).
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5

Western Blot Analysis of HIF1α, VHL, and DDAH1

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Cells were scraped and lysed using RIPA buffer (150mM NaCL, 5mM EDTA, 50mM Tris pH 8.0, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS). Lysate was spun in a microfuge at maximum speed and the soluble protein concentration was determined using Bradford reagent (Biorad). A total of 10–20 ug protein was subjected to SDS-PAGE. Proteins were transferred to a nitrocellulose membrane using a Trans-Blot Turbo (Biorad) for 45 minutes at 25V. Membranes were blocked with 1% non-fat dry milk for 1 hour and probed overnight with primary antibodies, β-actin at 1:7500 (sc-47778, Santa Cruz Biotech.), DDAH1 at 1:1000 (sc-514841, Santa Cruz Biotech.), VHL at 1:3000 (sc-17780, Santa Cruz Biotech.), and HIF1α at 1:3000 (ab179483, Abcam). Secondary HRP-conjugated antibodies, anti-mouse and anti-rabbit, were incubated at 1:1000 dilution for 1 hour at room temperature and chemiluminescence reactions were performed as per manufacturer’s instructions (GE Healthcare).
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Western Blot Analysis of Kidney Injury

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The cells or kidney tissues were lysed in RIPA lysis buffer (Servicebio, China), and protein concentration was detected by bicinchoninic acid assay kits (Beyotime, China). Proteins were separated using 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transferred onto polyvinylidene fluoride membranes (Millipore, USA). The membranes were then sealed with NcmBlot blocking buffer (NCM Biotech) for 15 min and incubated overnight at 4 ℃ with primary antibodies against Kidney Injury Molecule-1 (KIM-1, 1:1000, MA5-28211, Invitrogen), Collagen 1 (1:1000, sc-59,722, Santa Cruz), α-SMA (1:1000, sc-53,142, Santa Cruz), Tfam (1:1000, ab272885, Abcam), COX IV; (1:5000,11242-1-AP, Proteintech), Sirt1 (1:1000, ab110304, Abcam), PGC1α (1:5000, 66369-1-Ig, Proteintech), or β-actin (1:10000, sc-47,778, Santa Cruz). After incubation with horseradish peroxidase-conjugated goat anti-mouse or anti-rabbit IgG (1:3000, Cell Signaling, USA) for 1 h at room temperature, the blots were detected with the chemiluminescence advanced system (GE Healthcare).
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7

Western Blot Analysis of Brain Injury

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Brains were collected at 24 or 48 h after surgery for Western blotting. The tissues from the ipsilateral cortex were homogenized in RIPA buffer (Sigma-Aldrich, St. Louis, MO, USA) with protease inhibitor cocktail (ROCHE, Indianapolis, IN, USA) and then centrifuged at 10,000 g at 4 °C for 30 min. We collected the supernatants for protein quantification with the bicinchoninic acid assay. Equal amounts of each protein sample were separated by electrophoresis in 4–15% sodium dodecyl sulfate-polyacrylamide gels and transferred to polyvinylidene fluoride membranes. After being blocked, membranes were probed during overnight incubation at 4 °C with the following primary antibodies: mouse anti-β-actin (1:3000, sc-47778, Santa Cruz Biotechnology, Dallas, TX, USA), goat anti-sEH (1:50, sc-22344, Santa Cruz Biotechnology), rabbit anti-IL-1β (1:100, ab9722, Abcam, Cambridge, MA, USA), rabbit anti-IL-10 (1:500, ab9969, Abcam), and rabbit anti-TGF-β (1:500, ab66043, Abcam). We quantitatively analyzed the protein bands with Image J software to obtain the optical densities.
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8

Comprehensive Antibody Characterization for Cell Biology

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The mouse anti-CI-MPR antibody (Ab2733; Abcam) and rabbit anti-CI-MPR antibody (ab124767; Abcam) were used for immunofluorescence and Western blot, respectively. The antibodies for Giantin (924,302; Convance), HRS (ab155539; Abcam), GM130 (610,822; BD Biosciences) and EEA1 (610,456; BD Biosciences) were used for immunofluorescence. The antibodies for γ1 (610,386; BD Biosciences), γ2 (HPA004106; Sigma-Aldrich), μ1A (AB111135; Abcam), GAPDH (G9545; Sigma-Aldrich) and β-actin (sc-47778; Santa Cruz) were used for Western blot. The same antibodies for γ1 and γ2 were also used for immunofluorescence. The rabbit anti-Vps26 and anti-Snx2 anti-serum were kind gifts from Juan Bonifacino, and previously described (97 (link), 98 (link)). The rabbit anti-GFP antibody used for western-blot was a gift from R. Hegde (MRC). The mouse monoclonal anti-CD8 antibody used for flow cytometry and antibody uptake assays was a kind gift from Matthew Seaman (MRC) (9 (link)). Horseradish-peroxidase-conjugated donkey anti-mouse immunoglobulin G (IgG) and donkey anti-rabbit IgG were obtained from GE Healthcare. Secondary antibodies conjugated to Alexa fluorophores were purchased from Thermo Scientific.
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9

Western Blot Analysis of Protein Expression

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Briefly, total protein extracts were prepared from homogenized tissues or cultured cells with RIPA buffer containing protease inhibitors and a phosphatase inhibitor (cOmplete & PhosSTOP, Roche, Basel, Switzerland). Protein was quantified with an Enhanced BCA Protein Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA). Equal amounts of protein were separated by SDS-PAGE before wet transfer onto nitrocellulose membranes (GE Healthcare Life Sciences, Pittsburgh, PA, USA). The membranes were blocked with 5% nonfat milk for 2 h at room temperature. After blocking, the membranes were incubated at 4 °C overnight with primary antibodies against SKP2 (1:1000; ab183039, Abcam, Cambridge, UK), GLUT1 (1:1000; 66,290–1, Proteintech, Rosemont, IL, USA), or β-actin (1:5000; sc47778, Santa Cruz, AR, USA), the latter of which was used as an internal control. Protein complexes were developed and observed with a chemiluminescent detection system (Millipore, Waltham, MA, USA) and a G-Box Chemiluminescence image capture system (Syngene, Cambridge, UK). The resulting bands were analyzed using Gel-Pro Analyzer software (Media Cybernetics).
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10

Western Blot Analysis of Vascular Cells

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We lysed VICs in Laemmli lysis buffer and the cell lysate was resolved by SDS-PAGE (7.5%–10%). Proteins were blotted onto nitrocellulose membranes (Amersham, GE Healthcare, Chicago, IL, USA). Western blotting was performed with the use of primary antibodies listed in Table 2. Secondary antibodies—horseradish peroxidase linked rabbit (NA-934) and mouse IgG (NA-931) (Amersham)—were applied at a concentration of 0.5 µg/ml. Blots were developed with enhanced chemiluminescence system Clarity Western ECL (BioRad, Hercules, CA, USA). Chemiluminescent signals were either detected on an x-ray film or with a C-Digit Blot Scanner (LI-COR Biosciences, Lincoln, NE, USA). Following the development, all membranes were stripped and re-probed for β-actin using anti-β-actin antibody at a concentration of 0.5 µg/ml (sc-47778, Santa Cruz Biotechnology Inc., Dallas, TX, USA). We used the inbuilt software of the C-Digit Blot Scanner for quantification. Experiments were repeated three times.
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