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81 protocols using anti rabbit

1

Extraction and Analysis of Brain Tissue Proteins

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To obtain samples for Western Blots, brain tissue surrounding the wound (70–90 mg) as well as an equal part of the contralateral, un-operated cortex were dissected out and immediately frozen at −80 °C until use. To prepare lysates, frozen brain tissues were minced with eye scissors in ice. The samples were then homogenized in lysis buffer (1% NP-40, 50 mmol/L Tris, pH 7.5, 5 mmol/L EDTA, 1% SDS, 1% sodium deoxycholate, 1% Triton X-100, 1 mmol/L PMSF, 10 mg/mL aprotinin, and 1 mg/mL leupeptin) and clarified by centrifuging for 20 min in a micro centrifuge at 4 °C. After determination of its protein concentration with the Bradford assay (Bio-Rad, Hercules, CA, USA), the resulting supernatant (50 μg of protein) was subjected to SDS-polyacrylamide gel electrophoresis. The separated proteins were transferred to a polyvinylidine difluoridemembrane (Millipore, Boston, MA, USA) by a transfer apparatus at 350 mA for 2.5 h. The membrane was then blocked with 5% nonfat milk and incubated with primary antibody against PHB2 (Anti-Rabbit, 1:500; Santa Cruz, CA, USA) or GAPDH (Anti-Rabbit, 1:1000; Santa Cruz, CA, USA). After incubation with an Anti-Rabbit or anti-mouse horseradish peroxidase-conjugated secondary antibody, protein was visualized using an enhanced chemiluminescence system (ECL, Pierce Company, Rockford, IL, USA).
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2

Testicular Protein Expression Analysis

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Protein extraction was performed on frozen testicular tissue by the Trizol precipitation method. Protein concentrations were evaluated using the Bradford’s test (Bio-Rad; USA). Equal amounts of each protein (30 μg) were loaded onto 12% SDS polyacrylamide gels (PAGE) which were then transferred to PVDF membrane (Bio-Rad; USA). Blocking solutions were prepared separately for each antibody. Nrf2 (1/500, Anti-rabbit, Abcam, USA), Slc7a11 (1/500, Anti-rabbit, Abcam, USA), Gpx-4(1/1000, Anti-rabbit, Abcam, USA), p-Jnk (1/1000, Anti-mouse, Abcam, USA) and β-Actin (1/500, Anti-rabbit, Santacruz, USA) were used as primary antibodies. Polyclonal IgG-HRP goat Anti-mouse (1/5000, Dako, Denmark) and IgG-HRP goat Anti-rabbit (1/16000, Santacruz, USA) were then used as secondary antibodies. Detection was performed using the GE Amersham ECL and Western Blotting kits (Amersham; GE Health care) and autoradiography [19 (link)]. Signal quantification was performed using Image J software.
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3

GPX7 Overexpression Modulates Cancer Cell Signaling

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AGS and MKN45 cancer cells were infected with control (Ad-Ctrl) and GPX7 (Ad-GPX7) adenovirus particles (5 MOI) for 48 hours, then cells were lysed in the presence of proteinase inhibitor cocktail and phosphatase inhibitor (Santa Cruz Biotechnology, Dallas, TX USA). The protein concentration was determined by a Pierce BCA Protein Assay (Thermo Scientific, Rockford, IL USA) using a FLUOstar OPTIMA microplate reader (BMG Labtech, Cary, NC USA). Equal amount of proteins were loaded and separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis and transferred to nitrocellulose membranes, and Western blot analysis was performed using standard protocols. The primary antibodies were: anti-GPX7 antibody (rabbit, 1:1000, Proteintech Group, Chicago, IL USA), and anti-PARP and cleaved PARP (Cell Signaling). A mouse monoclonal antibody against beta-actin (Sigma) was used as a loading control. Horseradish peroxidase-conjugated anti-mouse (1:10,000 dilution) and anti-rabbit (1:10,000 dilution) secondary antibodies were purchased from Santa Cruz and Cell Signaling, respectively. Immunoreactive protein bands were documented using a Bio-Rad ChemiDoc XRST image system (Bio-Rad).
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4

Western Blot Analysis of Signaling Proteins

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For protein isolation, the cells were lysed after treatment by homogenization in 100 μL IP Lysing Buffer (Pierce, Thermo Scientific) and 1 μL of Halt Protease and Phosphatase inhibitor cocktail (Thermo Scientific). Protein concentration was measured by BCA protein assay (Pierce, Thermo Scientific). Equal amounts (20 μg) of protein were subjected to SDS-PAGE, transferred to nitrocellulose membranes, blocked in TBST-T containing 5% skim milk and probed with anti-beta-catenin (dilution: 1:1000; #610154, BD Biosciences), anti-TCF (dilution: 1:1000, #sc-101170; Santa Cruz Biotechnology), anti-STAR (dilution: 1:200, #sc-25806; Santa Cruz Biotechnology) and anti-CYP11B2 (dilution: 1:500, provided by Dr. Celso Gomez-Sanchez, University of Mississipi Medical Center [40 (link)]). Anti-GAPDH (dilution: 1:1000, #sc-47724; Santa Cruz Biotechnology) was used as endogenous/loading control. Complexes were visualized with HRP-conjugated anti-mouse (dilution: 1:3000; #sc-2005; Santa Cruz Biotechnology) and anti-rabbit (dilution: 1:2000; #sc-; Santa Cruz Biotechnology) secondary antibodies and developed by enhanced chemiluminescence (Immun-Star™ WesternC™ Chemiluminescence Kit) on a ChemiDoc XRS+ System (Bio-Rad™, Hercules, CA, USA). Acquired bands were analyzed using the Image Lab™ software (Bio-Rad).
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5

Neutrophil Signaling Pathway Analysis

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The N-fMLP peptide was synthesized and HPLC-purified by PRIMM (Milan, Italy). SDS-PAGE reagents were purchased from Bio-Rad (Hercules, CA, USA). Protein A/G Plus, anti-Flk1, anti-p-Flk1 (Tyr951), anti-p-Flk1 (Tyr996), anti-p-Flk1 (Tyr1175), anti-p-Flk1 (Tyr1214), anti-p-Tyr, anti-p47phox, anti-p22phox, anti-p-PLCγ1 (Y783), anti-PLCγ1, anti-PKCα, anti-PKCβII, anti-PKCζ, anti-PKCδ, anti-tubulin, anti-mouse, and anti-rabbit were from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Anti-p-PI3K (p85) and anti-p-Akt (Ser473) were from Cell Signaling Technology (Danvers, MA, USA). Anti-p-Ser, p22phox siRNA (SI03078523), and scramble control siRNA (SI03650318) were from Qiagen (Hiden, Germany). FPR1 siRNA (L-005140-00) and scramble control (D-001810-10) were purchased from Dharmacon (Lafayette, CO, USA). Protein A-horseradish peroxidase was from Amersham Pharmacia Biotech (Little Chalfont, Buckinghamshire, UK). Pertussis toxin (PTX), apocynin, wortmannin, and LY294002 were from Sigma (St. Louis, MO, USA).
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6

Protein Analysis via SDS-PAGE and Western Blotting

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Cells were lysed, and protein levels were determined by SDS-PAGE coupled to Western blotting. Additional details for this protocol are provided in the Supplementary Materials. Antibodies were obtained commercially and included GATA4 (1:1000, Cell Signaling Technology, Danvers, MA, USA) and COL1α1 (1:1000, Aviva Systems Biology, San Diego, CA, USA). The secondary antibody was anti-rabbit (1:10,000, Santa Cruz Biotechnology Inc., Dallas, TX, USA). Image analysis was performed using Image Lab 6.0 software from Bio-Rad (Berkeley, CA, USA).
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7

Antibody Panel for Pluripotency Marker Detection

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Antibodies used in this research are as follows: anti-OCT4 (sc-9081), anti-KLF4 (sc-20691), anti-GLIS1 (sc-67584), anti-c-MYC (sc-42), TRA-1-60 (sc-21705), SSEA1 (sc-21702), SSEA4 (sc-21704), anti-mouse (sc-2005), anti-rabbit (sc-2004) and anti-goat (sc-2020) from Santa Cruz; anti-SOX2 (AF2018) and anti-NANOG (AF1997) from R&D Systems; anti-LIN28A (#46020) from Abcam; anti-TRA-1-81 (09–0011) from Stemgent; Alexa Fluor 488 anti-mouse (A11029), Alexa Fluor 488 anti-rabbit (A11034) and Alexa Fluor 488 anti-goat (A11055) for immunostaining of iPS clones from Life Technologies. IRDye800 anti-mouse (610-132-121) for Odyssey imaging of iPSC colonies from Rockland.
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8

Quantifying Protein Expression in Spinal Cord

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Spinal cord samples were homogenized in a standard homogenizing buffer (50 mM Tris-HCl, pH 7.4; 5 mM EGTA; 1 mM phenylmethylsulfonyl fluoride) on ice plus protease inhibitor as described (Haque et al., 2007 (link); Haque et al., 2002 (link); O’Donnell et al., 2004 ). Equal protein concentrations from designated samples were separated on a 4–12% Bis/Tris NuPage gel (Invitrogen, Grand Island, NY) (God et al., 2015 ; Haque et al., 2017a (link); Hathaway-Schrader et al., 2018 (link)). Proteins were transferred onto a nitrocellulose membrane (Pierce, Rockford IL), and probed with caspase-1 (1:500, Santa Cruz, sc-622), NeuN (1:100, Proteintech, Catalog # 26975–1-AP), and MBP (1:1000, Millipore, MAB384) antibodies. The secondary antibodies used were horseradish peroxidase conjugated anti-mouse (1:2000, Santa Cruz, sc-2005), and anti-rabbit (1:4000, Santa Cruz, sc-2004). Monoclonal antibody for β-actin (1:1000, Santa Cruz, sc-81178) was used as a protein loading control. Relative protein expression was assessed using Image J software (National Institutes of Health, Bethesda, MD) and expressed as relative density for each sample (Goldstein et al., 2008 (link); Radwan et al., 2012 (link); Zhao et al., 2011 (link)).
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9

Molecular Profiling of Cellular Signaling

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Antibodies against NF-κB (p-65) (Cat# 8242S), p-NF-κB (p65) (Cat# 3033S), IκBα (Cat# 9242S), p62 (Cat# 5114S), Atg3 (Cat# 3415P), Atg7 (Cat# 2631P), Atg12 (Cat# 4180P), and cleaved caspase 3 (Cat# 9664S), and 7 (Cat# 8438S) were purchased from Cell Signaling Technology (Danvers, MA). Lipocalin-2 (Cat# AF1857) was from R&D Systems. Bcl-2 (Cat# MA5-11757), Bax (Cat# MA5-14003), and fluorescently tagged secondary antibodies, anti-rabbit (Alexa Fluor 488, Cat# A-11008 and Alexa Fluor 594, Cat# A-11012), anti-mouse (Alexa Fluor 488, Cat# A-11001 and Alexa Fluor 594, Cat# A-11005) were purchased from Invitrogen (Carlsbad, CA). LC3-I/II (Cat# ab58610), KIM-1/TIM-1 (Cat# ab47635) were purchased from Abcam (Cambridge, MA), and Beclin 1 (Cat# NB500-249), TLR4 (Cat# NB100-56566) was from Novus Biologicals (Centennial, CO). GAPDH (Cat# sc-365062 HRP), Tubulin (Cat# sc-5286 HRP) and HRP conjugated secondary antibodies, anti-rabbit (Cat# sc-2357), anti-mouse (Cat# sc-516102) were from Santa Cruz Biotechnology (Dallas, TX). We followed the manufacturer’s recommendation for all antibody dilutions. All other chemicals used in activity assays were purchased from Sigma Aldrich (St. Louis, MO).
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10

Immunohistochemistry of Tyrosine Hydroxylase in Hypertensive Mouse Kidneys

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We performed immunohistochemistry in the kidneys of our normotensive BPN/3J mice and hypertensive BPH/2J mice. Kidney tissues from both our BPN/3J and BPH/2J mice were sectioned at 5 μm onto positively charged microscope slides and de-waxed in xylene and rehydrated in ethanol. Antigen retrieval was performed on the slides by heating in EDTA buffer (pH 8.5; Sigma-Aldrich, Sydney, NSW, Australia). Slides were treated with 3% hydrogen peroxide and then blocked in 5% FCS in PBS/0.1% Tween-20. Tyrosine hydroxylase was detected with rabbit anti-tyrosine hydroxylase antibody (AB152; Merck Millipore, Melbourne, VIC, Australia). Antibody binding was detected with anti-rabbit (1:100, Santa Cruz Biotechnology, Sydney, NSW, Australia) secondary antibodies conjugated to HRP, followed by treatment with diaminobenzidine (DAB, Ventana, AZ, USA). Tissues were counterstained with haematoxylin before being dehydrated in ethanol and cleared in xylene and mounted with DPX (Sigma-Aldrich, Sydney, NSW, Australia). Photomicrographs were taken of stained kidneys from mice using a Nikon Eclipse Ti Microscope (Nikon Instruments Inc, Tokyo, Japan). Tyrosine hydroxylase positive nerves were counted in random fields of view.
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