Plant Functional Genomics

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.