Plant Functional Genomics

Chapter 1 Epigenome Profiling of Specific Plant Cell Types Using a Streamlined INTACT Protocol and ChIP-seq.

Chapter 2 Whole-genome DNA methylation profiling with nucleotide resolution.

Chapter 3 High-Throughput Nuclease-Mediated Probing of RNA Secondary Structure in Plant Transcriptomes

Chapter 5 Characterization of In Vivo DNA-Binding Events of Plant Transcription Factors by ChIP-seq: Experimental Protocol and Computational Analysis.

Chapter 6 Identification of Direct Targets of Plant Transcription Factors Using the GR Fusion Technique.

Chapter 7 Ribosome profiling: a tool for quantitative evaluation of dynamics in mRNA translation.

Chapter 8 Tissue-Specific Gene Expression Profiling by Cell Sorting

Chapter 9 Translating Ribosome Affinity Purification (TRAP) Followed by RNA Sequencing Technology (TRAP-SEQ) for Quantitative Assessment of Plant Translatomes.

Chapter 10 Rapid Immunopurification of Ribonucleoprotein Complexes of Plants

Chapter 11 Metabolomic profiling of plant tissues.

Chapter 12 Targeted Plant Genome Editing via the CRISPR/Cas9 Technology.

Chapter 13 QTL Mapping Using High-Throughput Sequencing

Chapter 14 Quantitating Plant MicroRNA-Mediated Target Repression Using a Dual-Luciferase Transient Expression System.

Chapter 15 Persistent virus-induced gene silencing in asymptomatic accessions of Arabidopsis.

Chapter 16 A User’s Guide to the Arabidopsis T-DNA Insertion Mutant Collections

Chapter 17 Genome-Wide Association Mapping in Plants Exemplified for Root Growth in Arabidopsis thaliana

Chapter 18 Tilling by sequencing.

Chapter 19 SHOREmap v3.0: Fast and Accurate Identification of Causal Mutations from Forward Genetic Screens

Chapter 20 Software-Assisted Stacking of Gene Modules Using GoldenBraid 2.0 DNA-Assembly Framework.

Chapter 21 Ligation-Independent Cloning for Plant Research

Chapter 22 Gene Functional Analysis Using Protoplast Transient Assays

Chapter 23 Descriptive vs. Mechanistic Network Models in Plant Development in the Post-Genomic Era.

Chapter 24 Analysis and visualization of RNA-Seq expression data using RStudio, Bioconductor, and Integrated Genome Browser

Chapter 25 Constructing simple biological networks for understanding complex high-throughput data in plants.