Next-generation sequencing and sequence data analysis / by Kuo Ping Chiu. -- Sharjah : Bentham Science Publishers, 2015. – (58.17115/C543)

Contents

FOREWORD  i

PREFACE  ii

ACKNOWLEDGEMENTS  iv

PART 1  BACKGROUND INTRODUCTION

CHAPTER 1  THE ULTIMATE FRONTIER OF KNOWLEDGE: THE MYSTERIOUS GENOMES AND THE GENE EXPRESSION AND REGULATION IN THE UPSTREAM OF BIOLOGICAL INFORMATION FLOW  3

     INTRODUCTION  5

     MICROSCOPIC STRUCTURE AND ORGANIZATION OF INFORMATION MOLECULES  5

     THE STRUCTURE AND ORGANIZATION OF INFORMATION MOLECULES AT THE MOLECULAR LEVEL

    GENE EXPRESSION AND REGULATION IN THE EUKARYOTIC SYSTEM  11

     THE BOTTOM LINE  16

     REFERENCES  17

CHAPTER 2  EVOLUTION OF DNA SEQUENCING TECHNOLOGIES  19

     INTRODUCTION  20

     CHARACTERISTICS OF DNA SEQUENCING  20

     ADVANCES IN SEQUENCING TECHNOLOGIES  21

     MANUAL SANGER SEQUENCING  22

     AUTOMATED SANGER SEQUENCING  :  23

     KEY CHANGES FROM MANUAL TO AUTOMATED SANGER SEQUE-NCING  24

     THE NEXT-GENERATION SEQUENCING  25

     SINGLE MOLECULE SEQUENCING  26

     REFERENCES  27

CHAPTER 3  MECHANISMS OF NEXT-GENERATION SEQUENCING (NGS)  28

     INTRODUCTION  29

     REFERENCES  42

CHAPTER 4  GENOME ASSEMBLY, THE GENOMIC ERA AND THE RISE OF THE OMICS ERA  43

     INTRODUCTION  44

     PART I. REVIEW OF THE STRATEGIES EMPLOYED FOR GENOME ASSEMBLY  44

     PART II. THE GENOMIC ERA  47

     KEY EVENTS LEADING TO THE DEVELOPMENT OF THE GENOMIC ERA  49

     GENERAL PROCEDURE FOR RESEQUENCING  50

     ADVANTAGES OF DIRECT MAPPING AGAINST A REFERENCE (NORMAL) GENOME  50

     PART III. THE RISE OF THE OMICS ERA  51

     REFERENCES  52

CHAPTER 5  APPLICATION OF DNA SEQUENCING IN BIOLOGICAL INVESTIGATIONS LABORATORY SETUP AND FUNDAMENTAL WORKS  55

     INTRODUCTION  56

     I. WETLAB  58

     II. DRYLAB  60

     REFERENCES  62

CHAPTER 6  SEQUENCING LIBRARIES AND BASIC PROCEDURE FOR SEQUENCING LIBRARY CONSTRUCTION  63

     INTRODUCTION  63

     CLASSIFICATION OF SEQUENCING LIBRARIES  63

     GENERAL PROCEDURE FOR SEQUENCING LIBRARY CONSTRUCTION  65

     A. EMULSION PCR FOR 454 AND SOLID SEQUENCERS  67

     B. CLUSTER GENERATION  68

     REFERENCES  68

CHAPTER 7  PAIRED-END (PE), MATE PAIR (MP) AND PAIRED-END DITAG (PED) SEQUENCING

     INTRODUCTION  70

     PART I. PE SEQUENCING  71

     PART II. PAIRED-END DITAG (PED) SEQUENCING  74

    REFERENCES  84

 CHAPTER 8  GENOME SEQUENCING AND ASSEMBLY  87

     INTRODUCTION  87

     CLASSIFICATION OF GENOME ASSEMBLY  88

    WHAT SEQUENCING STRATEGIES TO TAKE?  89

     GENERAL PROCEDURE FOR DE NOVO GENOME SEQUENCING  89

     UCSC GENOME BROWSER  92

     REFERENCES

CHAPTER 9  EXOME SEQUENCING: GENOME SEQUENCING FOCUSING ON EXONIC REGIONS 96

    INTRODUCTION  96

     SEQUENCING LIBRARY CONSTRUCTION  98

     SEQUENCE DATA ANALYSIS  98

     SINGLE NUCLEOTIDE POLYMORPHISM  99

     REFERENCES  99

CHAPTER 10  TRANSCRIPTOME ANALYSIS  101

    INTRODUCTION  102

     IMPACT OF GENOME ASSEMBLY ON TRANSCRIPTOME ANALYSIS  103

     CONSTRUCTION OF TRANSCRIPTOMIC SEQUENCING LIBRARIES  104

     PAIRED-END  DITAG  SEQUENCING  VS  SHOTGUN  FRAGMENT  SEQUENCING  OF TRANSCRIPTOME LIBRARIES  104

    SEQUENCE DATA PROCESSING  104

     CALCULATION OF GENE EXPRESSION LEVEL  106

    DISPLAY OF TRANSCRIPTOMIC SEQUENCE DATA  106

     CATEGORIZATION OF UPREGULATED AND DOWNREGULATED GENES BY GENE ONTOLOGY ANALYSIS  108

    IDENTIFICATION OF MOST SIGNIFICANTLY UPREGULATED/DOWNREGULATED PATHWAYS  108

    REFERENCES  108

CHAPTER 11  SINGLE CELL SEQUENCING (SCS) AND SINGLE CELL TRANSCRIPTOME (SCT) SEQUENCING

     INTRODUCTION  111

     REFERENCES  118

CHAPTER 12  CHIP-TFBS ANALYSIS  120

     INTRODUCTION  120

     OBSERVATIONS AND DISCUSSION  124

     REFERENCES  127

CHAPTER 13  CHIP-EM LIBRARIES  128

     INTRODUCTION    128

     THE LAW OF UNCERTAINTY AT THE EPIGENETIC MODIFICATION LEVEL  129

     EXPERIMENTAL PROCEDURE  131

     REFERENCES  132

CHAPTER 14  MICRORNA ANALYSIS  134

     INTRODUCTION  134

     EXPERIMENTAL PROCEDURE  135

     DISCLOSURE  137

     REFERENCES    137

CHAPTER 15  APPLICATION OF NGS IN THE STUDY OF SEQUENCE DIVERSITY IN IMMUNE REPERTOIRE  139

     INTRODUCTION  139

     PART I. SEQUENCING THE IMMUNE REPERTOIRE  140

     PART II. APPLICATION OF NGS IN VACCINE DEVELOPMENT  144

    REFERENCES  145

CHAPTER 16  INTRODUCTION TO ANALYTICAL TOOLS GALAXY PIPELINE FOR TRANSCRIPTOME LIBRARY ANALYSIS  147

     INTRODUCTION  147

     GALAXY INTERFACE  148

     FASTQ FORMAT  150

     DATASET  150

     EXERCISE  150

     USER ACCOUNT  151

     DOWNLOAD THE DATA  151

     UPLOAD THE DATA  152

     FASTQ GROOMER  153

     QUALITY CONTROL  154

     MAPPING READS TO THE REFERENCE GENOME  156

     IDENTIFYING BINDING SITES  157

     DOWNSTREAM ANALYSIS  159

     WORKFLOW  162

     CONSTRUCT A WORKFLOW FROM A HISTORY  166

     REFERENCE  168

SUBJECT INDEX  169