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204 protocols using ab56416

1

Apoptosis and Autophagy Regulation in PBDE-47 Exposure

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The following antibodies were used: anti-PARP (Cell Signaling Technology, 9542), anti-caspase-3 (9661, Cell Signaling Technology, USA), anti-autophagy-related protein 7 (ATG7) (ab133528, Abcam, USA), anti-LC3 (14600-1-AP, Proteintech, USA), anti-p62 (ab56416, Abcam, USA), anti-GAPDH (60004-1-Ig, Proteintech, USA). The following chemical regents were used: PBDE-47 (purity 99.5%, GC/MS) (BDE-047N-3G, AccuStandard Corp, USA), Wortmannin (WM) (S2758, Selleck Chemicals, USA), Rapamycin (RAP) (R5000, Shanghai Haoran, China), Ac-DEVD-CHO (DEVD) (C1206-10 mM, Beyotime Institute of Biotechnology, China). All other chemical regents were analytical grade purchased from credible supplier or as described in the relevant methods.
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2

Western Blot Analysis for Oxidative Stress

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Cells were lysed in RIPA buffer that contained a protease/phosphatase inhibitor cocktail (Sigma-Aldrich) at 4 °C for 30 min and used for immunoblotting. The cytosolic fraction for cathepsin B detection was prepared as previously described45 (link). A total of 20 μg of protein was loaded per lane of an SDS-PAGE gel and separated by electrophoresis. Proteins were transferred onto nitrocellulose (GE Healthcare, IL, USA) or PVDF membranes (IPVH00010, Millipore, MA, USA). Membranes were subsequently probed with primary antibodies and incubated with either goat anti-mouse IgG (Cell Signalling, 7076, MA, USA) or goat anti-rabbit IgG (Cell Signaling,7074) secondary antibodies conjugated with horseradish peroxidase (HRP). Chemiluminescence was detected using an enhanced chemiluminescence (ECL) system (Translab). The following primary antibodies were used: GPX4 (ab125066, Abcam), SCL7A11 (Cell Signalling, 12,691), Nrf2 (ab62352, Abcam), Keap1 (Cell Signalling, 8047), HO-1 (Cell Signalling, 5853), p62 (ab56416, Abcam), LC3 (PM036, MBL), cathepsin B (Cell Signalling, 31,718) and β-actin (Santa Cruz Biotechnology, sc-47778). The result of gels images was cropped and full-length gels and blots are included in the Supplementary Data.
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3

Western Blot Analysis of Autophagy and Inflammatory Markers

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Western blot analysis was performed as described previously[9 (link)]. Briefly, cultured cells were homogenized in a lysis buffer containing a protease inhibitor cocktail. After SDS-PAGE, the proteins on the gel were transferred to a polyvinylidene membrane. Then, the membrane was stained with the desired antibodies. The membrane was visualized with ImmobilonWestern (Millipore, Hayward, CA), and the image was captured with ChemDoc XRS (Bio-Rad, Hercules, CA). Primary antibodies used for Western blotting: microtubule-associated protein 1 light chain 3 (LC3) rabbit polyclonal antibody (PM036; MBL, Nagoya, Japan), p62 mouse monoclonal antibody (ab56416; Abcam, Cambridge, UK), PARP1 rabbit polyclonal antibody (9542S; Cell Signaling Technology, Danvers, MA), phospho-NF-kB p65 rabbit monoclonal antibody (Ser536) (3033S; Cell Signaling Technology), NF-kB p65 rabbit polyclonal antibody (sc-372; Santa Cruz Biotech, Dallas, TX), phosphor-extracellular signal–regulated kinase (ERK) rabbit polyclonal antibody (9101S; Cell Signaling Technology), ERK rabbit monoclonal antibody (4695S; Cell Signaling Technology), tubulin rabbit monoclonal antibody (ab176560; Abcam). Goat anti-rabbit IgG-HRP (sc-2030; Santa Cruz) or goat anti-mouse IgG-HRP (sc-2005; Santa Cruz) were used as secondary antibodies.
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4

Immunohistochemistry of Mouse Brain Tissue

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Mouse brain tissue sections and cells were incubated with following specific antibodies: anti‐LC3B (PM036, MBL), anti‐Iba‐1 (019‐19741, Wako), anti‐NeuN (MAB377, Millipore), anti‐P62 (ab56416, Abcam), anti‐LAMP2 (sc‐18822), anti‐ki67 (ab15580, Abcam), anti‐MAP2 (ab11267, Abcam), anti‐MBP (ab62631, Abcam), and anti‐Iba1 (019‐19741, Wako Pure Chemical Industries, OSA) in a humidified container for 12 h at 4°C, followed by incubation with fluorescent conjugated secondary antibodies (Santa Cruz Biotechnology).
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5

Cellular Autophagy, Proliferation, and Apoptosis Analysis

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The autophagy, proliferation, and apoptosis of CCECs after treatment were analyzed by western blot as described previously [36 (link)]. Briefly, all the CCECs were harvested from each lower chamber, and proteins were extracted using RIPA lysis buffer (Cwbiotech, China) containing proteinase inhibitor cocktail (Cwbiotech) and phosphatase inhibitor cocktail (Cwbiotech). The primary antibodies included anti-PCNA (1 : 1000; 200947-2E1, ZenBio, China), anti-cleaved-caspase3 (1 : 1000; 9661, Cell Signaling Technology, USA), anti-LC3 A/B (1 : 1000; 4108, Cell Signaling Technology), anti-p62 (1 : 1000; ab56416, Abcam), anti-Beclin1 (1 : 2000; ab207612, Abcam), and anti-GAPDH (1 : 2000; Affinity Biosciences, USA) antibodies. PCNA is an indicator of cell proliferation and cleaved-caspase3 is an indicator of cell apoptosis. LC3, p62, and Beclin1 are autophagic markers. GAPDH was used as loading control.
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6

Endothelial Function Protein Expression

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The corpus cavernosum tissues were lysed, and western blot analysis was performed as described previously [36 (link)]. The primary antibodies included anti-CD31 (1 : 2000; ab222783, Abcam), anti-eNOS (1 : 500; ab76198, Abcam), anti-phosphor-eNOS (S1177) (1 : 1000; 9571, Cell Signaling Technology), anti-VEGFRA (1 : 200; ab1316, Abcam), anti-VEGFR2 (1 : 1000; 9698, Cell Signaling Technology), anti-LC3 A/B (1 : 1000; 4108, Cell Signaling Technology), anti-p62 (1 : 1000; ab56416, Abcam), anti-Beclin1 (1 : 2000; ab207612, Abcam), and anti-GAPDH (1 : 2000; Affinity Biosciences, USA) antibodies. CD31, eNOS, phosphor-eNOS (S1177), VEGFRA, and VEGFR2 are indicators of endothelial function.
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7

Western Blot Analysis of Autophagy and Apoptosis Markers

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The PR-M(+) cells were lysed in a lysis buffer containing proteinase and phosphatase inhibitor at 4°C for 30 min and centrifuged at 10,000 r/min for 15 min. The cell lysates were then separated using 10% PAGE followed by transfer onto a polyvinylidene fluoride (PVDF) membrane. Membrane was blocked using 5% skim milk for 1 h at room temperature, followed by incubation at 4°C overnight with Tris-buffer saline with Tween (TBST)-diluted primary antibodies: anti-p62 (1:1000, ab56416, Abcam), anti-LC3B (1:10000, L7543, Sigma–Aldrich, St. Louis, MO, U.S.A.), anti-Bcl-2 (1:1000, sc-7382, Santa Cruz), anti-Beclin1 (1:500, sc-48341, Santa Cruz), anti-β-actin (1:5000, sc-47778, Santa Cruz) as an internal control, anti-PR (A-2) (1:5000, sc-398898, Santa Cruz), anti-PR-M (C262; 1:1000, sc-53943, Santa Cruz), anti-PR-B (B-30; 1:2000, sc-811, Santa Cruz) and anti-caspase-3 (1:1000, ab2302, Abcam). The membrane was then incubated with the horseradish peroxidase (HRP)-conjugated secondary antibodies at room temperature for 1 h: goat anti-mouse IgG (1:5000, ab6789, Abcam) or anti-rabbit (1:5000, ab6721, Abcam). Finally, the membrane was washed six times with TSBT and developed using enhanced chemiluminescent (ECL), with the gray value of the protein bands quantified by ImageJ 1.48u software (Bio-Rad, Hercules, CA, U.S.A.). The experiments were repeated three times.
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8

Western Blot Analysis of Autophagy Markers

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Tissue samples and cultured cells were lysed with RIPA lysis buffer containing protease inhibitor. SDS-PAGE was used to detect the proteins of interest. Proteins were resolved on SDS gels and were electro-transferred to polyvinylidene fluoride membranes (Millipore, Boston, MA, USA). Then, the membranes were blocked with 5% non-fat milk and incubated overnight at 4°C with primary antibodies, including anti-LC3B (#ab48394, 1:500; Abcam), anti-p62 (#ab56416, 1:500; Abcam), anti-ATG5 (#ab108327, 1:500; Abcam), anti-BECLIN1 (#ab55877, 1:500; Abcam), and anti-β-ACTIN (#A8481, 1:4000; Sigma-Aldrich). After washing, the membranes were incubated with a secondary antibody and imaged with Odyssey SA (Gene Company Limited, Hong Kong, China).
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9

Western Blot Analysis of Autophagy and Apoptosis

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Western blot assay was performed following the standard protocol. In brief, after total protein was isolated and quantified, the proteins were separated by sodium dodecyl sulfonate-polyacrylamide gel (SDS-PAGE; Solarbio, Beijing, China) and then transferred onto polyvinylidene difluoride membranes (PVDF; Pall Corporation, New York, NYC, USA). Next, the membranes were blocked in slim milk for 2 h and then incubated with primary antibodies against ATG3 (ab108251; 1:2000; Abcam, Cambridge, MA, USA), LC3Ⅱ/LC3Ⅰ (ab128025; 1:200; Abcam), P62 (ab56416; 1:500; Abcam), B-cell lymphoma-2 (BCL-2; ab196495; 1:1000; Abcam), cleaved caspase-3 (ab49822; 1:500; Abcam), cleaved caspase-9 (ab2324; 1:2000; Abcam), BCL2-Associated X (Bax; ab182733; 1:2000; Abcam) or GAPDH (ab181602; 1:5000; Abcam) at 4°C overnight followed by incubation with HRP-conjugated secondary antibody (D110150; 1:5000; Sangon, Shanghai, China) for 2 h. The protein bands were analyzed using an enhanced chemiluminescence reagent (Beyotime).
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10

Western Blot Analysis of Podocyte Proteins

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Podocytes were lysed using RIPA buffer, and protein concentration was determined using the BCA protein assay kit. Approximately 30 μg of protein from each sample was separated using a 10% SDS-polyacrylamide gel and transferred to PVDF membranes. Membranes were blocked with 5% skim milk in TBST and incubated with primary antibodies overnight at 4°C. Membranes were then incubated with the corresponding secondary antibodies for 1 h at room temperature and washed in TBST. Proteins were detected using specific antibodies: HMOX1: Abcam, ab13248; Sirt1: Abcam,ab110304; LC3B:Abcam,ab63817; AMPK:Abcam,ab110036; p-AMPK: Abcam,ab194920; P62: Abcam,ab56416; beta-actin: Abcam: ab115777.
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