Microbiome Analysis

  1. Nucleic Acid Extraction and Quality Assessment
    1. DNA Extraction Methodologies
      1. Cell Lysis Techniques
        1. Mechanical Disruption
          1. Bead Beating
            1. Sonication
              1. Homogenization
              2. Enzymatic Lysis
                1. Lysozyme Treatment
                  1. Proteinase K Digestion
                    1. Cellulase Application
                    2. Chemical Lysis
                      1. Detergent-Based Methods
                        1. Chaotropic Salt Solutions
                          1. Alkaline Lysis
                        2. DNA Purification Methods
                          1. Column-Based Purification
                            1. Magnetic Bead Separation
                              1. Phenol-Chloroform Extraction
                                1. Precipitation Methods
                                2. Commercial Kit Selection
                                  1. Kit Comparison Criteria
                                    1. Automation Compatibility
                                      1. Cost-Effectiveness Analysis
                                    2. RNA Extraction for Transcriptomics
                                      1. RNA Stabilization
                                        1. RNase Inhibition
                                          1. DNase Treatment
                                            1. RNA Purification
                                              1. Quality Assessment
                                              2. Extraction Challenges and Solutions
                                                1. Low Biomass Samples
                                                  1. Concentration Methods
                                                    1. Carrier Addition
                                                      1. Amplification Strategies
                                                      2. Inhibitor Removal
                                                        1. Humic Acid Removal
                                                          1. Polysaccharide Removal
                                                            1. Metal Ion Chelation
                                                            2. Sample-Specific Optimization
                                                            3. Quality Control and Quantification
                                                              1. Spectrophotometric Analysis
                                                                1. Absorbance Measurements
                                                                  1. Purity Ratios
                                                                    1. Concentration Determination
                                                                    2. Fluorometric Quantification
                                                                      1. Double-Stranded DNA Quantification
                                                                        1. Sensitivity Advantages
                                                                          1. Specificity Assessment
                                                                          2. Electrophoretic Analysis
                                                                            1. Agarose Gel Electrophoresis
                                                                              1. Fragment Size Distribution
                                                                                1. Integrity Assessment
                                                                                2. Advanced Quality Metrics
                                                                                  1. DNA Integrity Number
                                                                                    1. RNA Integrity Number
                                                                                      1. Degradation Assessment

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                                                                                  3. Sample Collection and Processing

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                                                                                  5. High-Throughput Sequencing Technologies