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3 protocols using xylene

1

Deparaffinization and Hydration Protocol

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Slides were deparaffinised in xylene (Electron Microscopy Sciences, Hatfield, PA, USA) and hydrated in 100, 95, and 70% ethanol gradient followed by water.
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2

Paraffin Embedding and H&E Staining of Tissue Samples

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After the explantation, formalin-fixed grafts were dehydrated in isopropanol during 30 h at 4°C, rinsed in distilled water, embedded in paraffin (Electron Microscopy Sciences), sectioned (5 μm), and finally mounted on glass microscope slides. For a deparaffinization, paraffin-embedded tissue sections were heated in dry oven at 60°C for 20 min, immersed in the following reagents: 3x xylene (Electron Microscopy Sciences) for 10 min, 100, 95, 70, 50, 30% ethanol for 1 min each, physiological saline for 2 min, PBS for 2 min, and finally rinsed with tap water. For hematoxylin and eosin (H&E) staining, the sections were immersed in Harris Hematoxylin solution (Electron Microscopy Sciences) for 1 min, rinsed with tap water, immersed in 1% aqueous Eosin Y solution (Electron Microscopy Sciences) for 1 min, rinsed with tap water, dehydrated in ascending ethanol solutions (50, 70, 80, 2x 95%, and 2x 100%), and then cleared 2x with xylene. Coverslips were mounted onto a labeled glass slide with Permount (Electron Microscopy Sciences). After the staining, sections were evaluated by light microscopy (Axio Imager A1, Carl Zeiss) in a blinded fashion; three sections per stain were assessed from each rat.
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3

Chromatin Immunoprecipitation and Myogenesis Assays

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Antibodies were purchased from ABclonal Technology, USA (anti-PBRM1, A9878) and Santa Cruz Biotech, USA (anti-BRG1, sc-17796; anti-BrdU, sc-32323; anti-Cyclin A, sc-596; anti-Cyclin E, sc-198; anti-Vinculin, sc-25336; anti-LaminB1, sc-56144; anti-β-tubulin, sc-166729). Anti-acetyl histone H3 (06–599) and anti-acetyl histone H4 (06–598) were purchased from Miilipore Sigma, USA. Myosin Heavy Chain (MHC) (#MF20) and Myogenin (#F5D) antibodies were purchased from the Developmental Studies Hybridoma Bank, University of Iowa, USA. BRM and Myod antisera were described previously (25 (link),58 (link)). PFI-3 was purchased from Cayman Chemicals, USA. Lysis buffers for ChIP assays were purchased from Cell Signaling Technology, USA (SimpleChIP® Enzymatic Cell Lysis Buffers A & B, 14282; SimpleChIP® Chromatin IP Buffers, 14231). Dulbecco's modified Eagle's medium (DMEM) was purchased from ThermoFisher Scientific (#11965118). Vectastain elite ABC (PK-6200) and HRP DAB substrate (SK-4100) kits were purchased from Vector Laboratories, USA. Corn Oil, Mayer's hematoxylin, Eosin Y and lithium carbonate were purchased from Millipore Sigma, USA. Cardiotoxin was purchased from Laxtoxan, France. Xylene was purchased from Electron Microscopy sciences, USA and Optimal Cutting Temperature (OCT) compound was from Fisher Healthcare, USA.
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