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9 protocols using a2856

1

Protein Aggregation Analysis via Western Blot

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Western blot analysis was performed as previously described [6 ]. Regular Western blot analysis was performed using LV lysates that were prepared using RIPA buffer (50 mM Tris (pH 8.0), 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and a protein inhibitor mixture (Sigma-Aldrich)). In addition, Western blot analysis of protein aggregation was performed using LV detergent-soluble and -insoluble lysates. Briefly, detergent-soluble fractions of LV tissues were obtained using a 2% Triton X-100 lysis buffer (50 mM Tris (pH 8.0), 150 mM NaCl, 1 mM EDTA, 10% glycerol, 2% Triton X-100, and a protein inhibitor mixture (Sigma-Aldrich)). The insoluble fractions were further solubilized using the 2% Triton X-100 lysis buffer supplemented with 1% SDS. Primary antibodies included anti-LC3 (L7543, Sigma-Aldrich), anti-P62 (ab91526, abcam), anti-NQO1 (sc-376023, Santa Cruz Biotechnology, Inc.), Anti-ATG5 (A2859, Sigma-Aldrich), anti-ATG7 (A2856, Sigma-Aldrich), anti-LAMP1 (ab24170, Abcam), anticathepsin D (2284, CST), and anti-Ub (sc-8017, Santa Cruz Biotechnology, Inc.). Ubiquitinated proteins with molecular weights from the top to 35 kDa on the membranes of immunoblots were quantified
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2

Cardiac and Vascular Histomorphometry

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Femoral arteries and hearts were fixed in 4% formalin for 24 h and paraffin embedded. Transversal sections of the heart were stained with masson’s trichrome staining to determine cardiac fibrosis. Atg7 on femoral artery segments was assessed by immunohistochemistry using anti-Atg7 (Sigma-Aldrich, A2856) monoclonal antibody. Transversal sections of femoral artery segments were stained with hematoxylin-eosin (H&E) to calculate media thickness. Images were acquired with Universal Graph 6.1 software using an Olympus BX40 microscope and quantified with Image J software.
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3

Autophagy-Related Protein Analysis

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l‐arginine (A8094), the primary antibodies against Rep2 (029628), LC3 (L7543) and ATG7 (A2856), as well as horseradish peroxidase‐conjugated secondary antibodies (goat anti‐rabbit, (A0545); goat anti‐mouse, (A9044)) were purchased from Sigma. The primary antibodies against GAPDH (sc‐32233), NQO1 (sc‐32793), NRF2 (sc‐13032), RAB7 (sc‐376362) and phospho‐S6 (sc‐293144) were purchased from Santa Cruz. LAMP1 (9091), mTOR (2983), phospho‐mTOR (5536), S6K (9202), phospho‐S6K (9234), and S6 (2217) antibodies were all obtained from Cell Signaling. The primary antibody against SQSTM1/p62 (89‐015‐843) was obtained from Abnova, and the SNAP29 antibody from Proteintech (12704‐1‐AP). CHML Flexitube siRNA constructs were purchased from Qiagen. The A549, H1299, A375 and MDA‐231 cell lines were all purchased from the American Type Culture Collection (ATCC). Dulbecco’s modified Eagle’s medium (DMEM; MT10014CV) was purchased from Corning. DMEM low glucose without amino acids was purchased from US Biological Life Sciences (D9800‐13). (FBS; S11150H) was purchased from Atlanta Biologicals. l‐glutamine (25030081) and penicillin‐streptomycin (15140722) were obtained from Gibco.
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4

Western Blot Analysis of Autophagy Proteins

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Proteins were extracted by RIPA buffer and separated on 4–12% stacking SDS–PAGE gel. Proteins were then transferred to PVDF membrane (Biorad). Membranes were blocked with 5% non-fat dry and then incubation with the primary antibody overnight at 4°C. Following TBST washing, membranes were incubated with peroxidase-conjugated secondary antibody for 1_h and exposed on film using the enhanced chemiluminescence (ECL) detection system (Thermo Scientific). Antibodies used were: ATG5 (1:500, NB110-53818, Novus Biological), ATG7 (1:300, A2856, Sigma), LC3B (1:500, NB600-1384, Novus Biological), p53 (1:1000, FL-393, Santa Cruz Biotechnology) and β-Actin (1:3000, A2066, Sigma).
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5

Immunoblotting Antibody Panel Protocol

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The following antibodies were used for immunoblotting: anti-LC3 (L8918, Sigma-Aldrich), anti-paxillin (ab32084, Abcam), anti-Atg5 (#12994, Cell Signaling), anti-Atg7 (A2856, Sigma-Aldrich), anti-glyceraldehyde 3-phosphate dehydrogenase (GAPDH; ab181602, Abcam), anti-FAK-pY397 (44-624G, ThermoFisher Scientific), anti-FAK (610087, BD Transduction Laboratories), anti-Src-pY416 (#2101, Cell Signaling), anti-Src (#2109, Cell Signaling), anti-RhoA (ab187027, Abcam), and anti-β-actin (ab8227, Abcam).
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6

Protein Lysate Preparation and Immunoblotting

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Total protein was lysed from the cells using radio-immunoprecipitation assay (RIPA) buffer (50 mM Tris pH 8.0, 150 mM NaCl, 1% Triton, 0.1% sodium dodecyl sulphate [SDS], 1 mM ethylenediaminetetraacetic acid [EDTA], 1% sodium deoxycholic acid, 1 mM Na3VO4, and 10 mM NaF) with protease inhibitors and phenylmethylsulfonyl fluoride (PMSF). Equivalent amounts of total cellular lysates were separated using 10% SDS-polyacrylamide gel electrophoresis. Primary antibodies used for immunoblotting included anti-ATG7 (1:1000; A2856, Sigma), and antibodies to FTH1 (1:1000; A19544, ABclonal), β-actin (1:10000; AC004, ABclonal). Horseradish peroxidase-conjugated antimouse or antirabbit secondary antibodies (RGAR001 or RGAM001, Proteintech) were used, and signals were determined using Western ECL Substrate. Uncropped data were shown in supplementral material.
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7

Western Blot Analysis of Urea Cycle Enzymes

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Tissues and tumor samples were grounded in liquid nitrogen, lysed in Tris lysis buffer (50 mM Tris HCl, 150 mM NaCl, 1 mM EDTA, 0.1% NP40, 5 mM MgCl2, 10% glycerol), separated on 12.5% SDS-PAGE gel and then transferred on PVDF membrane (Millipore). Membranes were blocked with 5% non-fat milk for 1 hour and probed overnight at 4˚C with antibodies against ASS1 (1:1,000, Ab170952, Abcam), ASL (1:500, sc-374353, Santa Cruz), OTC (1:500, sc-515791, Santa Cruz), ARG1 (1:500, sc-271430, Santa Cruz), ATG7 (1:2,000, A2856, Sigma), transferrin (1:1,000, sc-22597, Santa Cruz), ATG5 (1:1,500, Ab108327, Abcam) and β-actin (1:5,000, A1978, Sigma). Immunoreactive bands were detected using peroxidase-conjugated antibody (GE Healthcare) and enhanced chemiluminescence detection reagents (NEL105001EA, Perkin Elmer) and were analyzed using the ChemiDoc XRS+ system (Biorad). Protein levels were quantified using the Image Lab v6.0.1 software. Antibodies were validated with the use of positive and negative control following manufacturer’s protocol.
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8

Biochemical Assays and Immunoblotting Protocol

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Fatty Acid Supplement (F7050), palmitic acid (P0050), palmitoleic acid (P9417), oleic acid (O1383), stearic acid (S4751), sulforaphane (S6317), MTT (M2003), rapamycin (R8781), and ferrostatin-1 (SML0583) were purchased from Sigma-Aldrich. The Amplite™ Colorimetric Aspartate Aminotransferase (AST) Assay Kit (13801) and Amplite™ Colorimetric Alanine Aminotransferase (ALT) Assay Kit (13803) were purchased from AAT Bioquest. Antibodies against NRF2 (1:1000, sc-13032), KEAP1 (1:1000, sc-15246), p62 (1:1000, sc-28359), GPX4 (1:1000, sc-166570), GAPDH (1:3000, sc-32233), as well as the mouse (1:3000, sc-2005), goat (1:3000, sc-2350), and rabbit (1:3000, sc-2004) secondary antibodies conjugated to horseradish peroxidase were purchased from Santa Cruz Biotechnology. The antibodies against SLC7A11 (1:3000, 12691S), AMPK (1:3000, 5831S), pAMPK (1:3000, 2535S), AKT (1:3000, 4691S), pAKT (1:3000, 4060S), mTOR (1:3000, 2983S), and pmTOR (1:3000, 5536S) were purchased from Cell Signaling. The antibodies against LC3 (1:3000, L8918) and ATG7 (1:3000, A2856) were purchased from Sigma. The antibody against 4-HNE (1:200, ab46545) was purchased from Abcam.
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9

Western Blot Analysis of Urea Cycle Enzymes

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Tissues and tumor samples were grounded in liquid nitrogen, lysed in Tris lysis buffer (50 mM Tris HCl, 150 mM NaCl, 1 mM EDTA, 0.1% NP40, 5 mM MgCl2, 10% glycerol), separated on 12.5% SDS-PAGE gel and then transferred on PVDF membrane (Millipore). Membranes were blocked with 5% non-fat milk for 1 hour and probed overnight at 4˚C with antibodies against ASS1 (1:1,000, Ab170952, Abcam), ASL (1:500, sc-374353, Santa Cruz), OTC (1:500, sc-515791, Santa Cruz), ARG1 (1:500, sc-271430, Santa Cruz), ATG7 (1:2,000, A2856, Sigma), transferrin (1:1,000, sc-22597, Santa Cruz), ATG5 (1:1,500, Ab108327, Abcam) and β-actin (1:5,000, A1978, Sigma). Immunoreactive bands were detected using peroxidase-conjugated antibody (GE Healthcare) and enhanced chemiluminescence detection reagents (NEL105001EA, Perkin Elmer) and were analyzed using the ChemiDoc XRS+ system (Biorad). Protein levels were quantified using the Image Lab v6.0.1 software. Antibodies were validated with the use of positive and negative control following manufacturer’s protocol.
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