Avian and Reptilian Developmental Biology: Methods and Protocols

Preface...
Table of Contents...
Contributing Authors...

Commentary

1 Some Thoughts on Experimental Design
Claudio D. Stern

Part I Genomics and Transcriptomics

2 Comparative Genomics as a Foundation for Evo-Devo Studies in Birds
Phil Grayson, Simon Y.W. Sin, Timothy B. Sackton, and Scott V. Edwards

3 A Step-by-Step Guide to Assemble a Reptilian Genome
Asier Ullate-Agote, Yingguang Frank Chan, Michel C. Milinkovitch, and Athanasia C. Tzika

4 Genomic and Transcriptomic Analyses of Avian Sex Chromosomes and Sex-Linked Genes
Jilin Zhang, Jing Li, and Qi Zhou

5 Systems Biology Analyses in Chicken: Workflow for Transcriptome and ChIP-Seq Analyses using the Chicken Skin Paradigm
Yung-Chih Lai, Randall B. Widelitz and, and Cheng-Ming Chuong

6 Application of a CAGE Meth

od to an Avian Development Study
Ruslan Deviatiiarov, Marina Lizio, and Oleg Gusev

Part II Genetic Manipulation

7 CRISPR/Cas9 in the Chicken Embryo
Val?rie Morin, Nad?ge V?ron, and Christophe Marcelle

8 Fluorescent Quail: A Transgenic Model System for the Dynamic Study of Avian Development
David Huss and Rusty Lansford

9 Lentiviral-Mediated Transgenesis in Songbirds
Wan-chun Liu, Marian Hruska-Plochan, and Atsushi Miyanohara

10 In Ovo Electroporation Methods in Chick Embryos
Hidekiyo Harada, Minoru Omi, and Harukazu Nakamura

11 Genetic Manipulation of the Avian Urogenital System using In Ovo Electroporation
Claire E. Hirst, Olivier Serralbo, Katie L. Ayers, Kelly N. Roeszler and Craig A. Smith

12 Enhancer Analyses using Chicken Embryo Electroporation
Masanori Uchikawa, Naoko Nishim

ura, Makiko Iwafuchi-Doi, and Hisato Kondoh

13 Transgene Introduction into the Chick Limb Bud by Electroporation
Shogo Ueda, Takayuki Suzuki, and Mikiko Tanaka

Part III Stem Cells

14 Chicken Induced Pluripotent Stem Cells: Establishment and Characterization
Aurelie Fuet and Bertrand Pain

15 Isolation and Characterization of Chicken Primordial Germ Cells and their Application in Transgenesis
Jae Yong Han and Bo Ram Lee

16 Handling of Gametes for In Vitro Insemination in Birds
Shusei Mizushima, Mei Matsuzaki, and Tomohiro Sasanami

17 In Vitro and Ex Ovo Culture of Reptilian and Avian Neural Progenitor Cells
Wataru Yamashita, Toyo Shimizu and Tadashi Nomura

Part IV New Model Systems
18 Lifting the Veil on Reptile Embryology: The Veiled Chameleon (Chamaeleo calyptratus) as a Model System to Study Reptilian Development
Rau

l E. Diaz, Jr., Federica Bertocchini, and Paul A. Trainor

19 Model Clades versus Model Species: Anolis Lizards as an Integrative Model of Anatomical Evolution
Thomas J. Sanger and Bonnie K. Kircher

20 The Feather Model for Chemo- and Radiation Therapy-Induced Tissue Damage
Zhicao Yue and Benhua Xu

21 An Early Chick Embryo Culture Device for Extended Continuous Observation
Hans-Georg Sydow, Tobias Pieper, Christoph Viebahn, and Nikoloz Tsikolia

22 A Sensitive and Versatile In Situ Hybridization Protocol for Gene Expression Analysis in Developing Amniote Brains
Pei-Shan Hou, Takuma Kumamoto, and Carina Hanashima

23 Somitogenesis and Axial Development in Reptiles
Cindy Xu, Mariana B. Grizante, and Kenro Kusumi

24 Micro-CT Imaging on Living Alligator Teeth Reveals Natural Tooth Cycling
Randall B. Widelitz, Alaa Abdelh