rdf-syntax-grammar
mods:
  schema location: http://www.loc.gov/mods/v3 http://www.loc.gov/standards/mods/v3/mods-3-2.xsd
  title info:
    title: High-density sequencing applications in microbial molecular genetics
  name:
    name part: Carpousis, Agamemnon J.
    role:
      role term: editor.
  name:
    name part: ScienceDirect (Online service)
  type of resource: text
  genre: bibliography
  genre: Electronic books.
  genre: Internet Resources.
  genre: Index not Present.
  origin info:
    place:
      place term: mau
    date issued: 2018
    issuance: monographic
  language:
    language term: eng
  physical description:
    form: remote
    extent: 1 online resource
  abstract: High-Density Sequencing Applications in Microbial Molecular Genetics, Volume 612 in the Methods of Enzymology series provides the latest on the high-density sequencing of DNA and cDNA libraries and how they have revolutionized contemporary research in biology. Methods permitting tens of millions of sequence reads in a single experiment have paved the way to genome-wide studies that are contributing to our understanding of the complexity of living systems. Chapters in this updated volume include Characterizing the role of exoribonucleases in the control of microbial gene expression: Differential RNA seq., Conformational studies of bacterial chromosomes by high-throughput sequencing methods, Measuring mRNA degradation, and more. Addition sections cover Global recognition patterns of bacterial RNA-binding proteins, High-resolution profiling of NMD targets, and the Generation of a metagenomic 3C/Hi-C library of human gut microbiota, Genome-wide mapping of yeast retrotransposons integration target sites, Measuring protein synthesis rates, Finding unsuspected partners of small RNAs with new screening approaches, Use of multiplexed transcriptomics to define the relationship between promoter sequence and transcription output, RNA-based control of quorum sensing in Vibrio cholerae, amongst other highly regarded topics. Detail methods used in research articles that were recently published in leading journals Provides the latest on the high-density sequencing of DNA and cDNA libraries and how they have revolutionized contemporary research in biology.
  table of contents: 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
  table of contents: 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
  table of contents: 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
  table of contents: 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
  table of contents: 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
  note: edited by Agamemnon J. Carpousis.
  note: Includes bibliographical references.
  subject:
    topic: Molecular genetics
  subject:
    topic: Microbial genetics
  subject:
    topic: High-Throughput Nucleotide Sequencing
    topic: methods
  subject:
    topic: Sequence Analysis, RNA
  subject:
    topic: Genetics, Microbial
  subject:
    topic: Metagenomics
    topic: methods
  subject:
    topic: Molecular Biology
  subject:
    topic: Génétique moléculaire
  subject:
    topic: Génétique microbienne
  subject:
    topic: SCIENCE
    topic: Life Sciences
    topic: Evolution
  subject:
    topic: Microbial genetics
  subject:
    topic: Molecular genetics
  classification: QH430
  classification: 572.8
  classification: W1 ME9615K v.612 2018
  classification: QU 550.5.S4
  related item:
    name:
      name part: High-density sequencing applications in microbial molecular genetics.
    origin info:
      publisher: Cambridge, MA : Academic Press, an imprint of Elsevier, 2018
      edition: First edition.
    identifier: (OCoLC)1035514436
  related item:
    title info:
      title: Methods in enzymology ; v. 612
  identifier: 9780128159941
  identifier: 0128159944
  identifier: 9780128159934
  identifier: 0128159936
  identifier: 9780128159941 Ingram Content Group
  identifier: http://proxy.library.tamu.edu/login
  record info:
    record content source: N$T
    record creation date: 181203
    record change date: 20260327154234.8
    record identifier: in00005764282
    language of cataloging:
      language term: eng