CONTENTS -- FOREWORD -- PREFACE -- ACKNOWLEDGEMENTS -- CONFLICT OF INTEREST -- Background Introduction -- The Ultimate Frontier of Knowledge: the Myster-ious Genomes and the Gene Expression and Regul-ation in the Upstream of Biological Information Flow -- INTRODUCTION -- MICROSCOPIC STRUCTURE AND ORGANIZATION OF INFORMATION MOLECULES -- THE STRUCTURE AND ORGANIZATION OF INFORMATION MOLECULES AT THE MOLECULAR LEVEL -- DNA is the Most Magnificent Molecule Selected By Evolution -- DNA Packaging -- Nucleosome -- GENE EXPRESSION AND REGULATION IN THE EUKARYOTIC SYSTEM -- A. ATP-Dependent and ATP-Independent Chromatin Remodeling Enzyme -- B. X Chromosome Inactivation -- C. Pathway Flow from Extracellular Signal to the Nucleus -- D. TFs, Motifs, and DNA-Protein Interaction -- E. Transcription Factories (TFs) -- F. Epigenetic Modifications -- G. Alternative Splicing -- H. MicroRNA (miRNA) -- THE BOTTOM LINE -- REFERENCES -- Evolution of DNA Sequencing Technologies -- INTRODUCTION -- CHARACTERISTICS OF DNA SEQUENCING -- ADVANCES IN SEQUENCING TECHNOLOGIES -- MANUAL SANGER SEQUENCING -- AUTOMATED SANGER SEQUENCING -- KEY CHANGES FROM MANUAL TO AUTOMATED SANGER SEQUE-NCING -- THE NEXT-GENERATION SEQUENCING -- SINGLE MOLECULE SEQUENCING -- REFERENCES -- Mechanisms of Next-Generation Sequencing (NGS) -- INTRODUCTION -- Changes Made From Automated Sanger Sequencing to Next-Gen Sequencing -- In situ PCR for Clonal Amplification of Templates -- NGS Sequencing Mechanisms -- I. Sequencing-By-Synthesis -- Solexa Sequencers Manufactured By Illumina - HiSeq 2000 as an Example (Fig. 1) -- Sequencing Library Preparation -- 454 Sequencers By Roche -- Sequencing Library Preparation -- Sequencing-By-Synthesis on Picotiter Plate -- II. Sequencing By Ligation: SOLiD Sequencers (Fig. 8) Manufactured By Life Technologies Inc. -- REFERENCES.

Genome Assembly, the Genomic Era and the Rise of the Omics Era -- INTRODUCTION -- PART I. REVIEW OF THE STRATEGIES EMPLOYED FOR GENOME ASSEMBLY -- Technological impacts on genome assembly -- Next-Generation Sequencing (NGS) -- Oligo-mediated technologies -- PART II. THE GENOMIC ERA -- The Human Genome Project -- Genomic Era -- Post Genomic Era -- KEY EVENTS LEADING TO THE DEVELOPMENT OF THE GENOMIC ERA -- GENERAL PROCEDURE FOR RESEQUENCING -- ADVANTAGES OF DIRECT MAPPING AGAINST A REFERENCE (NORMAL) GENOME -- PART III. THE RISE OF THE OMICS ERA -- The Omics Era -- REFERENCES -- Application of DNA Sequencing in Biological Investigations -- Laboratory Setup and Fundamental Works -- INTRODUCTION -- I. WETLAB -- Setting up a Wetlab -- Protocols to Use -- II. DRYLAB -- Setting Up a Drylab -- Sequence Data Processing -- Methods Used for Sequence Data Processing and Analysis -- REFERENCES -- Sequencing Libraries and Basic Procedure for Sequencing Library Construction -- INTRODUCTION -- CLASSIFICATION OF SEQUENCING LIBRARIES -- GENERAL PROCEDURE FOR SEQUENCING LIBRARY CONSTRUCTION -- Step I. Libraries Constructed Prior to Sequencing Libraries -- Step II. Ligation of Sequencing Adaptors to Target DNA Molecules -- Step III. Clonal Expansion of Adaptor-ligated DNA Molecules -- A. EMULSION PCR FOR 454 AND SOLID SEQUENCERS -- B. CLUSTER GENERATION -- REFERENCES -- Paired-End (PE), Mate Pair (MP) and Paired-End Ditag (PED) Sequencing -- INTRODUCTION -- PART I. PE SEQUENCING -- I. Library Preparation -- II. Cluster Generation by in situ PCR -- III. Sequencing -- Forward Sequencing -- Reverse Sequencing -- IV. Data Analysis -- PART II. PAIRED-END DITAG (PED) SEQUENCING -- Correction of the Confusion Caused by Inconsistent Terminologies -- Advantages of PED Sequencing -- Review of PET Technology -- PET Cloning Strategy -- Identification and Selection of PET Sequences.

PET-to-genome Mapping -- Application of PET Technology in Transcriptome Analysis -- Application of PET Technology in ChIP-TFBS and ChIP-HM Analyses -- Barcoded Paired-End Ditag and Multiplex Barcoded Paired-End Ditag -- Cloning Strategies of bPED and mbPED -- Applications of bPED and mbPED -- Advantages of bPED and mbPED Comparing to PET -- Formation of an Interior Palindrome is a Unique Feature of bPED -- REFERENCES -- Genome Sequencing and Assembly -- INTRODUCTION -- CLASSIFICATION OF GENOME ASSEMBLY -- WHAT SEQUENCING STRATEGIES TO TAKE? -- GENERAL PROCEDURE FOR DE NOVO GENOME SEQUENCING -- UCSC GENOME BROWSER -- REFERENCES -- Exome Sequencing: Genome Sequencing Focusing on Exonic Regions -- [Definition of Terminologies] -- Definition of Terminologies -- Exome -- INTRODUCTION -- SEQUENCING LIBRARY CONSTRUCTION -- SEQUENCE DATA ANALYSIS -- SINGLE NUCLEOTIDE POLYMORPHISM -- REFERENCES -- Transcriptome Analysis -- INTRODUCTION -- IMPACT OF GENOME ASSEMBLY ON TRANSCRIPTOME ANALYSIS -- CONSTRUCTION OF TRANSCRIPTOMIC SEQUENCING LIBRARIES -- PAIRED-END DITAG SEQUENCING VS. SHOTGUN FRAGMENT SEQUENCING OF TRANSCRIPTOME LIBRARIES -- SEQUENCE DATA PROCESSING -- CALCULATION OF GENE EXPRESSION LEVEL -- DISPLAY OF TRANSCRIPTOMIC SEQUENCE DATA -- CATEGORIZATION OF UPREGULATED AND DOWNREGULATED GENES BY GENE ONTOLOGY ANALYSIS -- IDENTIFICATION OF MOST SIGNIFICANTLY UPREGULATED / DOWNREGULATED PATHWAYS -- REFERENCES -- Single Cell Sequencing (SCS) and Single Cell Transcriptome (SCT) Sequencing -- INTRODUCTION -- Experimental procedure for SCT sequencing -- Generation and amplification of cDNA -- Construction and sequencing of Smart-Seq sequencing libraries -- Modifications made on single cell transcriptome (SCT) libraries -- A. Using different types of material as the input -- B. Using different primers to prime cDNA synthesis.

C. Choosing shotgun fragment sequencing or Paired-End Ditag sequencing -- Sequence processing and analysis -- REFERENCES -- ChIP-TFBS Analysis -- INTRODUCTION -- Experimental Procedure -- Sequence Data Analysis -- OBSERVATIONS AND DISCUSSION -- Transcription Factor Binding Sites Can Be Well Represented Using the Paired-end Ditag Approach -- TFBS Clusters are Well Correlated With Gene-Rich Regions -- Consensus Motif Sequence can be Extracted from Sequences Bound by a Transcription Factor Using Computer Software such as GLAM or MIME -- There can be Significant Overlap Between the Binding Sites of Transcription Factors with Closely Related Functions -- REFERENCES -- ChIP-EM Libraries -- INTRODUCTION -- THE LAW OF UNCERTAINTY AT THE EPIGENETIC MODIFICATION LEVEL -- In Biology, the Law of Uncertainty is Shown in Genetic Mutations (e.g., SNVs), as Well as at the Level of Epigenetic Modifications -- EXPERIMENTAL PROCEDURE -- Construction of ChIP-EM Sequencing Libraries -- Sequence Analysis of ChIP-EM Libraries -- REFERENCES -- MicroRNA Analysis -- INTRODUCTION -- EXPERIMENTAL PROCEDURE -- Part 1: Construction of Sequencing Libraries -- Preparation of the starting material -- Part 2: Construction of the Amplified Small RNA Library -- Part 3: miRNA and mRNA Data Processing and Analysis -- DISCLOSURE -- REFERENCES -- Application of NGS in the Study of Sequence Diversity in Immune Repertoire -- INTRODUCTION -- PART I. SEQUENCING THE IMMUNE REPERTOIRE -- A. Characterization of a Natural Antibody Repertoire -- Experimental Procedure -- B. Sequencing scFv and sdAb for Therapeutics -- Selection of high-affinity variable sequences using phage display screening -- C. Single Domain Antibody (sdAb) -- Advantages and disadvantages of scFv and sdAb -- PART II. APPLICATION OF NGS IN VACCINE DEVELOPMENT.

Applications of NGS Technologies in Vaccine Development and Pathogen Control -- REFERENCES -- Introduction to Analytical Tools -- Galaxy Pipeline for Transcriptome Library Analysis -- INTRODUCTION -- GALAXY INTERFACE -- FASTQ FORMAT -- DATASET -- EXERCISE -- USER ACCOUNT -- DOWNLOAD THE DATA -- UPLOAD THE DATA -- FASTQ GROOMER -- QUALITY CONTROL -- MAPPING READS TO THE REFERENCE GENOME -- IDENTIFYING BINDING SITES -- DOWNSTREAM ANALYSIS -- WORKFLOW -- CONSTRUCT A WORKFLOW FROM A HISTORY -- REFERENCES -- SUBJECT INDEX.