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This volume aims at providing a selection of the most effective and widely employed protocols used in the Ewing sarcoma field. Chapters are divided into five sections detailing the molecular biology techniques used to analyze Ewing sarcoma including tissue preservation and methods used in morpho-molecular diagnostics and routine immune-histological analysis. Additional wet-lab protocols comprise in vitro techniques including re-expression and functional analyses of target genes together with in vivo tools and models such as patient-derived xenografts (PDX) and orthotopic xenografts for metastasis assessment in Ewing sarcoma. A full section on bioinformatic approaches to Ewing sarcoma covering ChIPseq, epigenetic and systems biology analyses finalizes this volume. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Cutting-edge and clearly written, Ewing sarcoma: Methods and Protocols aims to provide methods to further the study of Ewing sarcoma and bring researchers one step forward in the quest to fight this devastating disease.
List of contents
Germline Variation and Somatic Alterations in Ewing Sarcoma.- Western Blot Analysis in Ewing Sarcoma.- Tissue Preservation and FFPE Samples: Optimized Nucleic Acids Isolation in Ewing Sarcoma.- Liquid Biopsies in Ewing Sarcoma.- (Immuno-)histological Analysis of Ewing Sarcoma.- Molecular Approaches to Diagnosis In Ewing Sarcoma: Fluorescence in situ hybridization (FISH).- Molecular Approaches to Diagnosis in Ewing Sarcoma: RT-PCR.- Molecular Approaches to Diagnosis in Ewing Sarcoma: Targeted RNA Sequencing.- Ewing-specific (re)expression Models.- Analysis of Regulatory Sequences by Dual-luciferase Reporter Assays in Ewing Sarcoma.- Proliferation Assessment by Trypan Blue Exclusion in Ewing Sarcoma.- Drug Screening by Resazurin Colorimetry in Ewing Sarcoma.- Analysis of Migration and Invasion in Ewing Sarcoma.- Genetically Engineered Mouse Model in Ewing Sarcoma.- Tumor Growth Analysis of Ewing Sarcoma CellLines Using Subcutaneous Xenografts in Mice.- Metastasis Assessment in Ewing Sarcoma Using Orthotopic Xenografts.- Orthotopic Implants in Mice.- Ewing Sarcoma PDX Models.- Using Zebrafish Larvae as a Xenotransplantation Model to Study Ewing Sarcoma.- Main Repositories and Databases used in Ewing Sarcoma Research.- Chromatin Immunoprecipitation Followed by Next-Generation Sequencing (ChIP-seq) Analysis in Ewing Sarcoma.- Epigenetic Analysis in Ewing Sarcoma.- Systems Biology Analysis for Ewing Sarcoma.
