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8 protocols using secondary fluorescent antibodies

1

Hippo Signaling Pathway Characterization

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Trp53 (1C12), YAP (D8H1X), GAPDH antibodies, and Hippo Signaling Antibody Sampler Kit were purchased from Cell Signaling Technology. Antibody against Rb1 was purchased from Santa Cruz Biotechnology. The secondary fluorescent antibodies and H&E staining kit were from Abcam. DAB Substrate Kit was ordered from Vector Laboratories Inc. Plasmids pRL-TK, 8xGTIIC-luciferase, and shYAP1/2 were obtained from Addgene. The transfection reagents (FuGENE® HD) were obtained from Promega Corporation.
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2

Antibody and Plasmid Utilization Protocol

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Antibodies against Smad2/3 and pSmad2/3 antibodies were obtained from Cell Signaling Technology (CST, USA). Antibodies against TEAD1, TβRII, GFP, flag, Ub, GAPDH, c-Cbl siRNA, and TEAD1 siRNA were ordered from Santa Cruz Biotechnology. The secondary fluorescent antibodies and H&E staining kit were ordered from Abcam. Calcein labeling, osmium tetroxide, and lipofectamine 3000 were purchased from Fisher Scientific. Dexamethasone, L-ascorbic acid, and β-glycerophosphate were ordered from Sigma. Plasmids pcDNA3.1-flag and pcDNA3.1-flag-TβRII, GFP-IFT20, HA-Ub were obtained from Addgene.
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3

Dissecting YAP/TEAD Signaling Pathway

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Antibodies against p127YAP (D9W2I), YAP (D8H1X), MST1, pMST (E7UD1), LATS1 (C66B5), pLATS1, Lamin B1 (D9V6H) and GAPDH were from CST. Antibodies of Ezrin, GNA12, GNA13, RhoA, flag, TEAD1, GST and GFP were from Santa Cruz Biotechnology. RGS12 antibody (ab1) was from Sigma. The secondary fluorescent antibodies were from Abcam. PDZ domain peptides of RGS12 were purchased from GenScript. GPCR activator LPA, GPCR inhibitor Ki6425, Rho GTPases inhibitor C3 and Rock inhibitor ‎Y2763 were obtained from Sigma. Doxorubicin hydrochloride (DOX), methotrexate 4-Amino-10-methylfolic acid hydrate (MTX) and EDTA-free cocktail inhibitor tablets were all obtained from Fisher Scientific. TEAD1 siRNA and controls were from Santa Cruz Biotechnology. FuGENE® HD Transfection Reagent was purchased from Promega Corporation. The primers used for the quantification are listed in Supplementary Table 1.
The following plasmids: pRL-TK was generously provided by Dr. Zhen Zhang (University of Pennsylvania, Philadelphia, PA, USA); pcDNA3.1, shYAP1/2, pcDNA3.1-GFP-YAP, PET-GST-YAP and pcDNA3.1-RhoA were obtained from Addgene. Three human shRGS12 lentivectors (shRGS12–1, shRGS12–2 and shRGS12–3; Catalog # i019000) were ordered from ABM. pcDNA3.1-flag-RGS12 (flag-RGS12) and the pcDNA3.1-flag-RGS12 mutant with the deletion of the PDZ domain vectors (flag-RGS12ΔPDZ) were constructed in our lab.
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4

Dissecting YAP/TEAD Signaling Pathway

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Antibodies against p127YAP (D9W2I), YAP (D8H1X), MST1, pMST (E7UD1), LATS1 (C66B5), pLATS1, Lamin B1 (D9V6H) and GAPDH were from CST. Antibodies of Ezrin, GNA12, GNA13, RhoA, flag, TEAD1, GST and GFP were from Santa Cruz Biotechnology. RGS12 antibody (ab1) was from Sigma. The secondary fluorescent antibodies were from Abcam. PDZ domain peptides of RGS12 were purchased from GenScript. GPCR activator LPA, GPCR inhibitor Ki6425, Rho GTPases inhibitor C3 and Rock inhibitor ‎Y2763 were obtained from Sigma. Doxorubicin hydrochloride (DOX), methotrexate 4-Amino-10-methylfolic acid hydrate (MTX) and EDTA-free cocktail inhibitor tablets were all obtained from Fisher Scientific. TEAD1 siRNA and controls were from Santa Cruz Biotechnology. FuGENE® HD Transfection Reagent was purchased from Promega Corporation. The primers used for the quantification are listed in Supplementary Table 1.
The following plasmids: pRL-TK was generously provided by Dr. Zhen Zhang (University of Pennsylvania, Philadelphia, PA, USA); pcDNA3.1, shYAP1/2, pcDNA3.1-GFP-YAP, PET-GST-YAP and pcDNA3.1-RhoA were obtained from Addgene. Three human shRGS12 lentivectors (shRGS12–1, shRGS12–2 and shRGS12–3; Catalog # i019000) were ordered from ABM. pcDNA3.1-flag-RGS12 (flag-RGS12) and the pcDNA3.1-flag-RGS12 mutant with the deletion of the PDZ domain vectors (flag-RGS12ΔPDZ) were constructed in our lab.
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5

Multimodal Analysis of Cellular Metabolism

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Antibodies against Glut1 (#SAB4502803), TRAP staining kits and 2-Deoxy-d-glucose (2-DG) were ordered from Sigma. Antibodies against MMP13 (sc-515284), BrdU (sc-32323), ColX (sc-59954), actin (sc-47778), Lamin (sc-377000) and Smad2/3 (sc-133098) were obtained from Santa Cruz Biotechnology. The secondary fluorescent antibodies and H&E staining kit were from Abcam. The fluorescent glucose analog 2-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl) amino)-2-deoxyglucose (2-NBDG) was purchased from Cayman Chemical Company. BrdU labeling, calcein labeling reagents and pSmad2/3 (#PA5-99378) were purchased from Fisher Scientific™. The plasmids pcDNA3.1-Myc and pcDNA3.1-Myc-IFT20 were obtained from Addgene. The transfection reagents (FuGENE® HD) were from Promega Corporation.
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6

Quantification of Dystrophin and Utrophin in mdx Mice

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Another cohort of 15-month WBPA-treated (N = 3) and untreated (N = 3) dystrophin-deficient mdx mice were euthanized using CO2. Ventricular tissues were dissected, minced, and homogenized in modified radioimmunoassay precipitation assay (RIPA) buffer as described before (Altamirano et al., 2014 (link)). Protein concentration was determined using the Pierce BCA Protein Assay Kit (Thermo Fisher Scientific, MA, United States). Proteins were separated on SDS gel, transferred to a nitrocellulose membrane, and incubated with primary. Equal amounts of total protein were separated on 4–12% NuPAGE Novex Bis-Tris SDS-PAGE Gels (Invitrogen Corporation, Carlsbad, CA, United States) and transferred to Immobilon-FL PVDF membrane (Millipore Corporation, Billerica, MA, United States). The following primary antibodies were used; dystrophin and utrophin and then secondary fluorescent antibodies (Abcam, MA, United States). Glyceraldehyde 3-phosphate dehydrogenase (Abcam, Cambridge, MA, United States) was used as protein loading controls. Blots were visualized by Enhanced Chemifluorescence (ECF) (GE Healthcare Bio-Sciences Corporation, Piscataway, NJ, United States) on Storm 860 Imaging System (GE Healthcare Bio-Sciences Corporation, Piscataway, NJ, United States).
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7

Quantification of Muscle Nitric Oxide Synthases

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Another cohort of WT and db/db mice treated with and without pGz was anesthetized (100 mg/kg of ketamine and 5 mg/kg of xylazine) and sacrificed by cervical dislocation. Gastrocnemius muscles were dissected, minced, and homogenized using a total protein extraction kit (Sigma Millipore, Saint Louis, MA, USA). Total protein concentrations were determined using the bicinchoninic acid (BCA) method (Thermo-Scientific, Waltham, MA, USA). Denatured, SDS-gel separated, and membrane-immobilized proteins were incubated overnight at 4 °C with primary antibodies: anti-eNOS, dilution 1:2500 (ab300072; Abcam, Waltham, MA, USA); anti-p-eNOS, dilution 1:2500 (ab230158, Abcam, MA, USA); anti-nNOS, dilution 1:2000 (ab76067, Abcam, MA, USA); anti-iNOS, dilution 1:2500 (ab283655, Abcam, MA, USA); anti-GAPDH, dilution of 1:5000 (SC47724; Santa Cruz, CA, USA); and secondary fluorescent antibodies (Abcam, MA, USA). The resolved bands were detected with a Storm 860 Imaging System (GE Bio-Sciences, Piscataway, NJ, USA). Protein levels were quantified using myImageAnalysis software V1.0 (Thermo-Fisher Scientific, Waltham, MA, USA) and normalized to glyceraldehyde-3-phosphate dehydrogenase (GAPDH).
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8

Immunohistochemistry and Immunofluorescence Staining

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Immunohistochemistry (IHC) was performed on 4‐μm sections from FFPE tissues using a Ventana Discovery XT automated system (Ventana Medical Systems) as previously reported.31 Slides were dewaxed using the automated system and then subjected to heat‐induced antigen retrieval. After nonspecific blocking (goat serum, ZSGB‐BIO), slides were incubated with specific antibody overnight at 4°C. Detailed information regarding the antibodies used in this study is provided in Table S1. After incubation with secondary antibodies (ZSGB‐BIO), slides were detected with DAB staining, and counterstained with hematoxylin. For double‐color IHC, primary antibodies were co–incubated, and then processed with a polymer dual‐stain kit (Mo/HRP + Rb/AP, DS‐0001; ZSGB‐BIO), according to the manufacturer’s instructions. Immunofluorescence (IF) was performed on FFPE as previously described.32 After incubation with primary rabbit anti–human HLA‐DR and mouse anti–human CD33, secondary fluorescent antibodies (Abcam) were used. Then sections were mounted with ProLong Diamond Antifade Mountant with DAPI (Invitrogen). A paraffin‐embedded human placenta section was used as a positive control for PD‐L1 and CD33 staining, human NK/T‐cell lymphoma for Granzyme B, and normal human tonsil for the other markers. The scoring methods of IHC and immunofluorescence are provided in Appendix S1.
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