Plant Functional Genomics : Methods and Protocols / edited by Jose M. Alonso, Anna N. Stepanova.

Format:

Book

Contributor:

Alonso, Jose M., editor.

Stepanova, Anna N., editor.

SpringerLink (Online service)

Series:

Methods in molecular biology 1064-3745 ; 1284.

Springer Protocols (Springer-12345)

Methods in Molecular Biology, 1064-3745 ; 1284

Language:

English

Subjects (All):

Life sciences.

Botany.

Life Sciences.

Plant Sciences.

Local Subjects:

Life Sciences.

Plant Sciences.

Physical Description:

1 online resource (XV, 532 pages) : 85 illustrations, 64 illustrations in color.

Edition:

Second edition 2015.

Contained In:

Springer eBooks

Place of Publication:

New York, NY : Springer New York : Imprint: Humana Press, 2015.

System Details:

text file PDF

Summary:

This second edition volume discusses the revolutionary development of faster and less expensive DNA sequencing technologies from the past 10 years and focuses on general technologies that can be utilized by a wide array of plant biologists to address specific questions in their favorite model systems. This book is organized into five parts. Part I examines the tools and methods required for identifying epigenetic and conformational changes at the whole-genome level. Part II presents approaches used to determine key aspects of a gene's function, such as techniques used to identify and characterize gene regulatory networks. This is followed by a discussion of tools used to analyze the levels of mRNA, mRNA translation rates, and metabolites. Part III features a compilation of forward and reverse genetic approaches that include recent implementation of high-throughput sequencing in classical methodologies such as QTL mapping. The final two parts explore strategies to facilitate and accelerate the generation and testing of functional DNA elements, and basic computational tools used to facilitate the use of systems biology approached by a broad spectrum of plant researchers. Written in the highly successful Methods of 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 key tips on troubleshooting and avoiding known pitfalls. Practical and timely, Plant Functional Genomics: Methods and Protocols, Second Edition highlights the latest developments in DNA sequencing technologies that are likely to continue shaping the future of functional genomics.

Contents:

Epigenome Profiling of Specific Plant Cell Types Using a Streamlined INTACT Protocol and ChIP-seq

Whole-Genome DNA Methylation Profiling with Nucleotide Resolution

High-Throughput Nuclease-Mediated Probing of RNA Secondary Structure in Plant Transcriptomes

Genome-Wide Mapping of DNase I Hypersensitive Sites in Plants

Characterization of in-vivo DNA-Binding Events of Plant Transcription Factors by ChIP-seq: Experimental Protocol and Computational Analysis

Identification of Direct Targets of Plant Transcription Factors Using the GR Fusion Technique

Ribosome Profiling: A Tool for Quantitative Evaluation of Dynamics in mRNA Translation

Tissue-Specific Gene Expression Profiling by Cell Sorting

Translating Ribosome Affinity Purification (TRAP) Followed by RNA Sequencing Technology (TRAP-SEQ) for Quantitative Assessment of Plant Translatomes

Rapid Immunopurification of Ribonucleoprotein Complexes of Plants

Metabolomic Profiling of Plant Tissues

Targeted Plant Genome Editing via the CRISPR/Cas9 Technology

QTL Mapping Using High-Throughput Sequencing

Quantitating Plant MicroRNA-Mediated Target Repression Using a Dual-Luciferase Transient Expression System

Persistent Virus-Induced Gene Silencing in Asymptomatic Accessions of Arabidopsis

A User's Guide to the Arabidopsis T-DNA Insertion Mutant Collections

Genome-Wide Association Mapping in Plants Exemplified for Root Growth in Arabidopsis thaliana

Tilling By Sequencing

SHOREmap v3.0: Fast and Accurate Identification of Causal Mutations from Forward Genetic Screens

Software-Assisted Stacking of Gene Modules Using GoldenBraid 2.0 DNA-Assembly Framework

Ligation Independent Cloning for Plant Research

Gene Functional Analysis Using Protoplast Transient Assays

Descriptive vs. Mechanistic Network Models in Plant Development in the Post-Genomic Era

Analysis and Visualization of RNA-Seq Expression Data Using RStudio, Bioconductor, and Integrated Genome Browser

Constructing Simple Biological Networks for Understanding Complex High-Throughput Data in Plants.

Other Format:

Printed edition:

ISBN:

9781493924448

Access Restriction:

Restricted for use by site license.