High-density sequencing applications in microbial molecular genetics /

• Άλλοι συγγραφείς: Carpousis, Agamemnon J. (Επιμελητής έκδοσης)
• Μορφή: Ηλ. βιβλίο
• Γλώσσα: English
• Έκδοση: Cambridge, MA : Academic Press, 2018.
• Σειρά: Methods in enzymology ; v. 612.
• Θέματα: Molecular genetics.; High-Throughput Nucleotide Sequencing > methods.; Sequence Analysis, RNA.; Genetics, Microbial.; Metagenomics > methods.; Molecular Biology.; SCIENCE > Life Sciences > Evolution.; Electronic books.

Πίνακας περιεχομένων:

• Front Cover; High-Density Sequencing Applications in Microbial Molecular Genetics; Copyright; Contents; Contributors; Preface; Chapter One: Characterizing the Role of Exoribonucleases in the Control of Microbial Gene Expression: Differential RNA-Seq; 1. Overview of Exoribonucleases; 2. Overview of Differential RNA-Seq; 3. RNA Extraction; 4. Bioinformatics Analysis; 4.1. Mapping of Reads; 4.2. Transcript Expression Quantification; 4.3. Differential Expression Analysis; 4.4. Functional Annotation Analysis; 5. Experimental Validation; 5.1. qPCR; 5.2. Motility Assays; 6. Conclusion
• AcknowledgmentsReferences; Chapter Two: Conformational Studies of Bacterial Chromosomes by High-Throughput Sequencing Methods; 1. Introduction; 1.1. Chromosome Conformation; 1.2. DNA-Protein Interactions; 1.3. Combining NGS to 3C and ChIP Approaches; 2. 3C-Seq: The Protocol; 2.1. Buffers and Reagents; 2.2. Cross-Linking of Cell Cultures; 2.3. 3C Library Preparation; 2.3.1. Cell Lysis; 2.3.2. RE Digestion; 2.3.3. Ligation; 2.3.4. DNA Purification; 2.4. Notes; 3. ChIP-Seq: The Protocol; 3.1. Buffers and Reagents; 3.2. Cross-Linking of Cell Cultures; 3.3. Cell Lysis
• 3.4. Batch Immunoprecipitation of FLAG Fusions Proteins3.5. Elution of the Immunoprecipitated Protein; 3.6. Purification of the Coimmunoprecipitated DNA; 3.7. Notes; 4. Data Processing and Analysis; 4.1. Analysis of 3C-Seq Data; 4.2. Analysis of ChIP-Seq Data; 5. Conclusion; Acknowledgments; References; Chapter Three: Large-Scale Measurement of mRNA Degradation in Escherichia coli: To Delay or Not to Delay; 1. Introduction; 2. Measuring mRNA Degradation Rates; 2.1. Methods; 2.2. Rifampicin; 2.3. Practical Considerations; 3. Genome-Wide mRNA Quantification
• 3.1. mRNA Extraction and Quantification3.2. Normalization; 4. mRNA Half-Life Estimation; 4.1. Decay Models; 4.2. Accuracy Criteria of the Estimation; 5. Effect of the Delay Before the Onset of Exponential Decay on mRNA Half-Life Estimation; 5.1. Datasets of mRNA Levels Over the Time; 5.2. Estimations of the Delay Before the Onset of the mRNA Exponential Decay; 5.3. Comparison of mRNA Half-Lives Estimated With and Without a Delay; 5.4. Correlation Between mRNA Half-Lives Estimated With and Without a Delay; 5.5. Influence of the Delay Extent
• 5.6. Validation on RT-qPCR mRNA Quantification Datasets6. Concluding Remarks; Acknowledgments; References; Chapter Four: FASTBAC-Seq: Functional AnalysiS of Toxin-Antitoxin Systems in BACteria by Deep Sequencing; 1. Introduction; 2. Materials; 2.1. Molecular Biology Equipment; 2.2. General Equipment for Bacterial Cultures; 2.3. E. coli-Specific Equipment; 2.4. H. pylori-Specific Equipment; 2.5. Molecular Biology Reagents; 2.6. E. coli Strains and Cell Culture; 2.7. H. pylori Strains and Cell Culture