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Part I: Protocols for Establishment of Dental Cells Lines and Animal Models 1. Micro-dissection and Isolation of Mouse Dental Epithelial Cells of Continuously Growing Mouse Incisors Hidemitsu Harada and Keishi Otsu 2. Establishment of an Immortalized Mouse Bmp2 Knock–Out Dental Papilla Mesenchymal Cell Line Wen’an Xu and Shuo Chen 3. Establishment of Stable Cell Lines from Primary Human Dental Pulp Stem Cells Elizabeth Guirado, Youbin Zhang, and Anne George 4. Isolation of Dental Stem Cell Enriched Populations from Continuously Growing Mouse Incisors Anamaria Balic 5. Application of Cell Lineage Tracing Combined with Immunofluorescence in the Study of Dentogenesis Yan Jing, Chaoyuan Li, and Jian Q. Feng 6. Tissue Recombination and Kidney Capsule Transplantation Assays for the Study of Epithelial-mesenchymal Interactions Lucia Jimenez-Rojo and Thimios Mitsiadis 7. Dental Mesenchymal Stem Cells: Dental Pulp Stem Cells, Periodontal Ligament Stem Cells, Apical Papilla Stem Cells, Primary Teeth Stem Cells: Isolation, Characterization and Expansion for Tissue Engineering Mey Al-Habib and George T.-J. Huang Part II: Protocols for Dental Stem Cells and Tissue Regeneration 8. Phenotypic Identification of Dental Pulp Mesenchymal Stem/Stromal Cells Subpopulations with Multiparametric Flow Cytometry Maxime Ducret, Jean-Christophe Farges, Marielle Pasdeloup, Emeline Perrier-Groult, Andreas Mueller, Frdric Mallein-Gerin, and Hugo Fabre 9. Dental Pulp Stem Cells: Isolation, Characterization, Expansion and Odontoblast Differentiation for Tissue Engineering Qing, Dong; Wang, Yuanyuan; Mohabatpour, Fatemeh; Zheng, Li; Papagerakis, Silvana; Chen, Daniel; and Papagerakis, Petros 10. In vitro Analysis of Intramolecular Signaling Events in PDLSCs using Confocal and TIRF Microscopy Annette Merkel and Anne George 11. A Mouse Model to Study Reparative Dentinogenesis Babb RC, Chandrasekaran D, Zaugg LK, and Sharpe PT 12. Multiwalled Carbon Nanotubes for Dental Applications Petros Kechagioglou;Eleftherios Andriotis; Petros Papagerakis; and Silvana Papagerakis 13. Peptide-mediated Biomimetic Regrowth of Human Enamel in situ Kaushik Mukherjee, Qichao Ruan, and Janet Moradian-Oldak 14. Bioengineering Tooth Bud Constructs using GelMA Hydrogel Elizabeth E. Smith and Pamela C. Yelick 15. Whole-mount In Situ Hybridization of Mouse Embryos Using DIG-labeled RNA Probes Jingyi Wu and Xiaofang Wang Part III: Protocols for Studying Gene and Protein Expression 16. In Situ Hybridization on Mouse Paraffin Sections Using DIG-labeled RNA Probes Jingyi Wu, Jian Q. Feng, and Xiaofang Wang 17. Methods for in situ Proteins Visualization in Dental Mineralized Tissues D. Hotton, A. Berdal, and A. Bolanos 18. In Situ Hibridization in Mineralized Tissues: The Added Value of LNA Probes for RNA Detection Lignon G, Hotton D, Berdal A, and Bolanos A 19. Immunofluorescence Procedure for Developing Enamel Tissues Xu Yang and Elia Beniash 20. Silver-albumin Tissue Staining Protocol to Visualize Odontogenesis in Whole Embryos Julia C. Boughner and David M. L. Cooper 21. Isolation of SIBLING Proteins from Bone and Dentin Matrix Jingyi Wu and Xiaofang Wang 22. Immunohistochemical Co-localization of Amelogenin and Ameloblastin in Developing Enamel Matrix Rucha Arun Bapat and Janet Moradian-Oldak 23. The Expression and Purification of Recombinant Mouse Ameloblastin in e-coli Jingtan Su, Rucha Bapat, and Janet Moradian-Oldak Part IV: Protocols for Biochemistry and Imaging 24. Protocols for Studying Formation and Mineralization of Dental Tissues in vivo Extraction Protocol for Isolating Dentin Matrix Proteins from Developing Teeth Yasuo Yamakoshi, Jan C-C Hu, Mari M. Saito, and James P. Simmer 25. Purification of Developing Enamel Matrix Proteins using Preparative SDS PAGE Steven J. Brookes and Claire M. Gabe 26. Using ImageJ (FIJI) to Analyse and Present X Ray CT Images of Enamel Steven J. Brookes 27. Scanning Electron Microscopy (SEM) Methods for Dental Enamel Steinar Risnes, Muhammad Saeed, and Amer Sehic 28. Microcomputed Tomography Imaging in Odontogenesis Studies Kostas Verdelis and Phil Salmon 29. Transmission Electron Microscopy (TEM) and Scanning Electron Microscopy (SEM) for the Examination of Dental Hard Tissues Victor E. Arana-Chavez and Leticia S. Castro-Filice 30. Rodent Dental Fluorosis Model–Extraction of Enamel Organ from Rat Incisors M. Suzuki and J. D. Bartlett Part V: Protocols to Study Dental Diseases 31. Three Dimensional Assessment of Crown Size and Eruption Space for Developing Third Molars: Data Collection Techniques Based on Cone-beam Computed Tomography (CBCT) D.F. Marchiori, G.V. Packota, and J.C. Boughner 32. Protocols to Study Dental Caries In Vitro: Microbial Caries Models Bennett T. Amaechi, Livia M. A. Tenuta, Antonio P. Ricomini Filho, and Jaime A. Cury 33. In vitro Caries Models for the Assessment of Novel Restorative Materials Sulaiman Ghandourah, Basma; Lefkelidou, Anna;Said, Raed; Chatzistavrou, Xanthippi; Flannagan, Susan; Gonzles-Cabezas, Carlos; Fenno, Christopher J.; Zheng, Li;Papagerakis, Silvana; and Papagerakis, Petros 34. Protocols to Study Dental Caries In Vitro: pH Cycling Models Bennett T. Amaechi 35. In Vivo Rodent Models for Studying Dental Caries and Pulp Disease Hsiao, June; Wang, Yuanyuan;Liu, Ruirui; Zheng, Li; Said; Raed; Hadjiyski, Lubomir; Cha, Heekon; Botero, Tatiana; Chatzistavrou, Xanthippi; Qing, Dong;Papagerakis, Silvana; Papagerakis, Petros 36. Protocol GenoDENT: Implementation of a New NGS Panel for Molecular Diagnosis of Genetic Disorders with Orodental Involvement Tristan Rey, Julien Tarabeux, Bndicte Gerard, Marion Delbarre, Antony Le Bchec Corinne Stoetzel, Megana Prasad, Virginie Laugel-Haushalter, Marzena Kawczynski, Jean Muller, Jamel Chelly, Hlne Dollfus, Marie-Ccile Manire, and Agns Bloch-Zupan Part VI: Protocols for Genetic, Epigenetic and Clinical Studies 37. Protocols for Genetic and Epigenetic Studies of Rare Diseases Affecting Dental Tissues Bruna Rabelo Amorim, Pollyanna Almeida Costa dos Santos, Caroline Loureno de Lima, Denise Carleto Andia, Juliana Forte Mazzeu, and Ana Carolina Acevedo 38. Protocols, Methods, and Tools for Genome-wide Association Studies (GWAS) of Dental Traits Cary S. Agler, Dmitry Shungin, Andrea G. Ferreira Zandon, Paige Schmadeke,Patricia V. Basta, Jason Luo, John Cantrell,Thomas D. Pahel Jr., Beau Meyer, John R. Shaffer, Arne S. Schefer, Kari E. North, and Kimon Divaris 39. Measurement of Early Childhood Oral Health for Research Purposes: Dental Caries Experience and Developmental Defects of the Enamel in the Primary Dentition Jeannie Ginnis, Andrea G. Ferreira Zandon, Gary D. Slade, John Cantrell, Mikafui E. Antonio,Bhavna T. Pahel, Beau D. Meyer, and Kimon Divaris 40. The Supragingival Biofilm in Early Childhood Caries: Clinical and Laboratory Protocols and Bioinformatics Pipelines Supporting Oral Metagenomics, Metatranscriptomics and Metabolomics Studies of the Oral Microbiome Kimon Divaris, Dmitry Shungin,Adaris Rodrguez-Corts, Patricia V. Basta, Jeff Roach,Andrea G. Ferreira Zandon, Jeannie Ginnis, Sivapriya Ramamoorthy,Jakub Kwintkiewicz, Natasha Butz, and M. Andrea Azcarate-Peril 41. Saliva and Gingival Crevicular Fluid (GCF) Collection for Biomarkers Screening Petros Papagerakis,Raed Said, Doohak Kim, Amber A. Ehlert, Kevin K. M. Chung, and Silvana Papagerakis
