E-grāmata: Plant Gene Regulatory Networks: Methods and Protocols

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 CRISPRAct3.0 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 DNA methylation method that captures both
transient and stable TF-DNA interactions genome-wide 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.- Immunoprecipitation-mass spectrometry (IP-MS) of protein-protein
interactions of nucleus-localized plant proteins.- Mapping active gene
modules by ChIA-PET in rice.- Building high-confidence gene regulatory
networks by integrating validated TF-target gene interactions using
ConnecTF.- The ChIP-hub resource: towards plantEncode.- A practical guide to
inferring multi-omics networks in plant systems.- Gene regulatory network
modelling 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 gene across
species.