Gene Regulation

  1. Experimental Approaches to Gene Regulation
    1. Chromatin Analysis Techniques
      1. Chromatin Immunoprecipitation
        1. Cross-Linking Protocols
          1. Antibody Selection
            1. DNA Purification
              1. Target Validation
              2. ChIP-Sequencing
                1. Library Preparation
                  1. Sequencing Strategies
                    1. Peak Calling Algorithms
                      1. Motif Discovery
                      2. Chromatin Accessibility Assays
                        1. DNase-Seq
                          1. Hypersensitivity Mapping
                            1. Footprinting Analysis
                            2. ATAC-Seq
                              1. Transposase Accessibility
                                1. Single-Cell Applications
                                2. FAIRE-Seq
                                  1. Formaldehyde-Assisted Identification
                              2. Transcriptome Analysis
                                1. RNA Sequencing
                                  1. Library Preparation Methods
                                    1. Single-End versus Paired-End
                                      1. Strand-Specific Protocols
                                        1. Single-Cell RNA-Seq
                                        2. Quantitative PCR
                                          1. Primer Design
                                            1. Reference Gene Selection
                                              1. Relative Quantification
                                                1. Absolute Quantification
                                                2. In Situ Hybridization
                                                  1. Tissue Section Analysis
                                                    1. Whole-Mount Preparations
                                                      1. Fluorescent Detection
                                                    2. Protein-DNA Interaction Studies
                                                      1. Electrophoretic Mobility Shift Assays
                                                        1. Binding Reaction Optimization
                                                          1. Competition Assays
                                                            1. Supershift Analysis
                                                            2. DNA Footprinting
                                                              1. DNase I Protection
                                                                1. Hydroxyl Radical Footprinting
                                                                  1. Contact Point Identification
                                                                  2. Yeast One-Hybrid Assays
                                                                    1. Reporter Gene Systems
                                                                      1. Library Screening
                                                                        1. Interaction Validation
                                                                      2. Functional Analysis Methods
                                                                        1. Gene Perturbation Techniques
                                                                          1. RNA Interference
                                                                            1. siRNA Design
                                                                              1. shRNA Vectors
                                                                                1. Off-Target Assessment
                                                                                2. CRISPR-Cas Systems
                                                                                  1. Guide RNA Design
                                                                                    1. Delivery Methods
                                                                                      1. Knockout Validation
                                                                                        1. Base Editing Applications
                                                                                      2. Reporter Gene Assays
                                                                                        1. Luciferase Systems
                                                                                          1. Fluorescent Proteins
                                                                                            1. Regulatory Element Testing
                                                                                            2. Transgenic Approaches
                                                                                              1. Overexpression Studies
                                                                                                1. Tissue-Specific Expression
                                                                                                  1. Conditional Systems

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                                                                                              8. Gene Regulation in Development and Disease

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                                                                                              1. Introduction to Gene Regulation