Kaufmann Kerstin, Vandepoele Klaas (eds.) Plant Gene Regulatory Networks: Methods and Protocols

2nd edition. — Humana Press, 2023. — 380 p. — (Methods in Molecular Biology 2698). — ISBN 978-1-0716-3353-3.This second edition details protocols that analyze and explore gene regulatory networks (GRNs). Chapters guide readers through experimental techniques used to study genes and their regulatory interactions in plants, and computational approaches used for the integration of experimental data and bioinformatics-based predictions of regulatory interactions. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.Authoritative and cutting-edge, Plant Gene Regulatory Networks: Methods and Protocols, Second Edition aims to be a useful and practical guide to new researchers and experts looking to expand their knowledge.Characterization​ of Gene Regulatory Networks in Plants Using New Methods and Data Types
Inducible, Tissue-Specific Gene Expression in Arabidopsis Using GR-LhG4-Mediated Trans-Activation
Targeted Activation of Arabidopsis Genes by a Potent CRISPR–Act3.0 System
Single Cell RNA-Sequencing in Arabidopsis Root Tissues
Analysis of Chromatin Accessibility, Histone Modifications, and Transcriptional States in Specific Cell Types Using Flow Cytometry
Untargeted Proteomics and Metabolomics Analysis of Plant Organ Development
DamID-seq:​ A Genome-Wide DNA Methylation Method that Captures Both Transient and Stable TF-DNA Interactions in Plant Cells
CUT&​Tag for Mapping In Vivo Protein-DNA Interactions in Plants
Identification of Plant Transcription Factor DNA-Binding Sites Using seq-DAP-seq
Estimating DNA-Binding Specificities of Transcription Factors Using SELEX-Seq
Immunoprecipitat​ion-Mass Spectrometry (IP-MS) of Protein-Protein Interactions of Nuclear-Localized Plant Proteins
Mapping Active Gene-Associated Chromatin Loops by ChIA-PET in Rice
Building High-Confidence Gene Regulatory Networks by Integrating Validated TF–Target Gene Interactions Using ConnecTF
The ChIP-Hub Resource:​ Toward plantEncode
A Practical Guide to Inferring Multi-Omics Networks in Plant Systems
Gene Regulatory Network Modeling Using Single-Cell Multi-Omics in Plants
Methodology for Constructing a Knowledgebase for Plant Gene Regulation Information
Predicting Gene Regulatory Interactions Using Natural Genetic Variation
Prediction of Transcription Factor Regulators and Gene Regulatory Networks in Tomato Using Binding Site Information
AGENT for Exploring and Analyzing Gene Regulatory Networks from Arabidopsis
A Transferable Machine Learning Framework for Predicting Transcriptional Responses of Genes Across Species