Chapter title |
Comparative Genomics as a Foundation for Evo-Devo Studies in Birds
|
---|---|
Chapter number | 2 |
Book title |
Avian and Reptilian Developmental Biology
|
Published in |
Methods in molecular biology, January 2017
|
DOI | 10.1007/978-1-4939-7216-6_2 |
Pubmed ID | |
Book ISBNs |
978-1-4939-7215-9, 978-1-4939-7216-6
|
Authors |
Phil Grayson, Simon Y. W. Sin, Timothy B. Sackton, Scott V. Edwards |
Abstract |
Developmental genomics is a rapidly growing field, and high-quality genomes are a useful foundation for comparative developmental studies. A high-quality genome forms an essential reference onto which the data from numerous assays and experiments, including ChIP-seq, ATAC-seq, and RNA-seq, can be mapped. A genome also streamlines and simplifies the development of primers used to amplify putative regulatory regions for enhancer screens, cDNA probes for in situ hybridization, microRNAs (miRNAs) or short hairpin RNAs (shRNA) for RNA interference (RNAi) knockdowns, mRNAs for misexpression studies, and even guide RNAs (gRNAs) for CRISPR knockouts. Finally, much can be gleaned from comparative genomics alone, including the identification of highly conserved putative regulatory regions. This chapter provides an overview of laboratory and bioinformatics protocols for DNA extraction, library preparation, library quantification, and genome assembly, from fresh or frozen tissue to a draft avian genome. Generating a high-quality draft genome can provide a developmental research group with excellent resources for their study organism, opening the doors to many additional assays and experiments. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
Congo, The Democratic Republic of the | 1 | 20% |
Unknown | 4 | 80% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 3 | 60% |
Scientists | 2 | 40% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 21 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 7 | 33% |
Student > Bachelor | 4 | 19% |
Student > Master | 3 | 14% |
Researcher | 2 | 10% |
Unknown | 5 | 24% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 9 | 43% |
Biochemistry, Genetics and Molecular Biology | 3 | 14% |
Environmental Science | 1 | 5% |
Immunology and Microbiology | 1 | 5% |
Medicine and Dentistry | 1 | 5% |
Other | 1 | 5% |
Unknown | 5 | 24% |