Introduction to Single Cell Omics

Written By Xinghua Pan
Introduction to Single Cell Omics
  • Publsiher : Frontiers Media SA
  • Release : 19 September 2019
  • ISBN : 2889459209
  • Pages : 212 pages
  • Rating : 4/5 from 21 reviews
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Read or download book entitled Introduction to Single Cell Omics written by Xinghua Pan which was release on 19 September 2019, this book published by Frontiers Media SA. Available in PDF, EPUB and Kindle Format. Book excerpt: Single-cell omics is a progressing frontier that stems from the sequencing of the human genome and the development of omics technologies, particularly genomics, transcriptomics, epigenomics and proteomics, but the sensitivity is now improved to single-cell level. The new generation of methodologies, especially the next generation sequencing (NGS) technology, plays a leading role in genomics related fields; however, the conventional techniques of omics require number of cells to be large, usually on the order of millions of cells, which is hardly accessible in some cases. More importantly, harnessing the power of omics technologies and applying those at the single-cell level are crucial since every cell is specific and unique, and almost every cell population in every systems, derived in either vivo or in vitro, is heterogeneous. Deciphering the heterogeneity of the cell population hence becomes critical for recognizing the mechanism and significance of the system. However, without an extensive examination of individual cells, a massive analysis of cell population would only give an average output of the cells, but neglect the differences among cells. Single-cell omics seeks to study a number of individual cells in parallel for their different dimensions of molecular profile on genome-wide scale, providing unprecedented resolution for the interpretation of both the structure and function of an organ, tissue or other system, as well as the interaction (and communication) and dynamics of single cells or subpopulations of cells and their lineages. Importantly single-cell omics enables the identification of a minor subpopulation of cells that may play a critical role in biological process over a dominant subpolulation such as a cancer and a developing organ. It provides an ultra-sensitive tool for us to clarify specific molecular mechanisms and pathways and reveal the nature of cell heterogeneity. Besides, it also empowers the clinical investigation of patients when facing a very low quantity of cell available for analysis, such as noninvasive cancer screening with circulating tumor cells (CTC), noninvasive prenatal diagnostics (NIPD) and preimplantation genetic test (PGT) for in vitro fertilization. Single-cell omics greatly promotes the understanding of life at a more fundamental level, bring vast applications in medicine. Accordingly, single-cell omics is also called as single-cell analysis or single-cell biology. Within only a couple of years, single-cell omics, especially transcriptomic sequencing (scRNA-seq), whole genome and exome sequencing (scWGS, scWES), has become robust and broadly accessible. Besides the existing technologies, recently, multiplexing barcode design and combinatorial indexing technology, in combination with microfluidic platform exampled by Drop-seq, or even being independent of microfluidic platform but using a regular PCR-plate, enable us a greater capacity of single cell analysis, switching from one single cell to thousands of single cells in a single test. The unique molecular identifiers (UMIs) allow the amplification bias among the original molecules to be corrected faithfully, resulting in a reliable quantitative measurement of omics in single cells. Of late, a variety of single-cell epigenomics analyses are becoming sophisticated, particularly single cell chromatin accessibility (scATAC-seq) and CpG methylation profiling (scBS-seq, scRRBS-seq). High resolution single molecular Fluorescence in situ hybridization (smFISH) and its revolutionary versions (ex. seqFISH, MERFISH, and so on), in addition to the spatial transcriptome sequencing, make the native relationship of the individual cells of a tissue to be in 3D or 4D format visually and quantitatively clarified. On the other hand, CRISPR/cas9 editing-based In vivo lineage tracing methods enable dynamic profile of a whole developmental process to be accurately displayed. Multi-omics analysis facilitates the study of multi-dimensional regulation and relationship of different elements of the central dogma in a single cell, as well as permitting a clear dissection of the complicated omics heterogeneity of a system. Last but not the least, the technology, biological noise, sequence dropout, and batch effect bring a huge challenge to the bioinformatics of single cell omics. While significant progress in the data analysis has been made since then, revolutionary theory and algorithm logics for single cell omics are expected. Indeed, single-cell analysis exert considerable impacts on the fields of biological studies, particularly cancers, neuron and neural system, stem cells, embryo development and immune system; other than that, it also tremendously motivates pharmaceutic RD, clinical diagnosis and monitoring, as well as precision medicine. This book hereby summarizes the recent developments and general considerations of single-cell analysis, with a detailed presentation on selected technologies and applications. Starting with the experimental design on single-cell omics, the book then emphasizes the consideration on heterogeneity of cancer and other systems. It also gives an introduction of the basic methods and key facts for bioinformatics analysis. Secondary, this book provides a summary of two types of popular technologies, the fundamental tools on single-cell isolation, and the developments of single cell multi-omics, followed by descriptions of FISH technologies, though other popular technologies are not covered here due to the fact that they are intensively described here and there recently. Finally, the book illustrates an elastomer-based integrated fluidic circuit that allows a connection between single cell functional studies combining stimulation, response, imaging and measurement, and corresponding single cell sequencing. This is a model system for single cell functional genomics. In addition, it reports a pipeline for single-cell proteomics with an analysis of the early development of Xenopus embryo, a single-cell qRT-PCR application that defined the subpopulations related to cell cycling, and a new method for synergistic assembly of single cell genome with sequencing of amplification product by phi29 DNA polymerase. Due to the tremendous progresses of single-cell omics in recent years, the topics covered here are incomplete, but each individual topic is excellently addressed, significantly interesting and beneficial to scientists working in or affiliated with this field.

Introduction to Single Cell Omics

Introduction to Single Cell Omics
  • Author : Xinghua Pan,Shixiu Wu,Sherman M. Weissman
  • Publisher : Frontiers Media SA
  • Release Date : 2019-09-19
  • Total pages : 212
  • ISBN : 2889459209
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Summary : Single-cell omics is a progressing frontier that stems from the sequencing of the human genome and the development of omics technologies, particularly genomics, transcriptomics, epigenomics and proteomics, but the sensitivity is now improved to single-cell level. The new generation of methodologies, especially the next generation sequencing (NGS) technology, plays a ...

Single Cell Omics

Single Cell Omics
  • Author : Debmalya Barh,Vasco Azevedo
  • Publisher : Academic Press
  • Release Date : 2019-07-30
  • Total pages : 384
  • ISBN : 2889459209
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Summary : Single-cell Omics, Volume 2: Advances in Applications provides the latest single-cell omics applications in the field of biomedicine. The advent of omics technologies have enabled us to identify the differences between cell types and subpopulations at the level of the genome, proteome, transcriptome, epigenome, and in several other fields of omics. ...

Single Cell Analysis

Single Cell Analysis
  • Author : Anonim
  • Publisher : Unknown
  • Release Date : 2010
  • Total pages : 212
  • ISBN : 2889459209
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Summary : Cellular heterogeneity arising from stochastic expression of genes, proteins, and metabolites is a fundamental principle of cell biology, but single cell analysis has been beyond the capabilities of 'Omics' technologies. This is rapidly changing with the recent examples of single cell genomics, transcriptomics, proteomics, and metabolomics. The rate of change ...

Single Cell Analysis

Single Cell Analysis
  • Author : Tuhin Subhra Santra,Fan-Gang Tseng
  • Publisher : MDPI
  • Release Date : 2021-06-02
  • Total pages : 254
  • ISBN : 2889459209
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Summary : Cells are the most fundamental building block of all living organisms. The investigation of any type of disease mechanism and its progression still remains challenging due to cellular heterogeneity characteristics and physiological state of cells in a given population. The bulk measurement of millions of cells together can provide some ...

Single Cell Omics

Single Cell Omics
  • Author : Debmalya Barh,Vasco Azevedo
  • Publisher : Academic Press
  • Release Date : 2019-06-06
  • Total pages : 490
  • ISBN : 2889459209
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Summary : Single-Cell Omics: Volume 1: Technological Advances and Applications provides the latest technological developments and applications of single-cell technologies in the field of biomedicine. In the current era of precision medicine, the single-cell omics technology is highly promising due to its potential in diagnosis, prognosis and therapeutics. Sections in the book cover ...

Single Cell Omics

Single Cell Omics
  • Author : BCC Research
  • Publisher : Unknown
  • Release Date : 2017-12
  • Total pages : 212
  • ISBN : 2889459209
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Summary : Download or read online Single Cell Omics written by BCC Research, published by which was released on 2017-12. Get Single Cell Omics Books now! Available in PDF, ePub and Kindle....

Single Cell Sequencing and Systems Immunology

Single Cell Sequencing and Systems Immunology
  • Author : Xiangdong Wang
  • Publisher : Springer
  • Release Date : 2015-03-27
  • Total pages : 177
  • ISBN : 2889459209
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Summary : The volume focuses on the genomics, proteomics, metabolomics, and bioinformatics of a single cell, especially lymphocytes and on understanding the molecular mechanisms of systems immunology. Based on the author’s personal experience, it provides revealing insights into the potential applications, significance, workflow, comparison, future perspectives and challenges of single-cell sequencing ...

Single Cell Methods

Single Cell Methods
  • Author : Valentina Proserpio
  • Publisher : Unknown
  • Release Date : 2019
  • Total pages : 452
  • ISBN : 2889459209
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Summary : This volume provides a comprehensive overview for investigating biology at the level of individual cells. Chapters are organized into eight parts detailing a single-cell lab, single cell DNA-seq, RNA-seq, single cell proteomic and epigenetic, single cell multi-omics, single cell screening, and single cell live imaging. Written in the highly successful ...

Novel Single cell Omics Assays of Corticogenesis

Novel Single cell Omics Assays of Corticogenesis
  • Author : Ryan M.. Mulquee
  • Publisher : Unknown
  • Release Date : 2020
  • Total pages : 264
  • ISBN : 2889459209
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Summary : Download or read online Novel Single cell Omics Assays of Corticogenesis written by Ryan M.. Mulquee, published by which was released on 2020. Get Novel Single cell Omics Assays of Corticogenesis Books now! Available in PDF, ePub and Kindle....

The Individual Microbe Single Cell Analysis and Agent Based Modelling

The Individual Microbe  Single Cell Analysis and Agent Based Modelling
  • Author : Johan H. J. Leveau,Ferdi L. Hellweger,Jan-Ulrich Kreft,Clara Prats,Weiwen Zhang
  • Publisher : Frontiers Media SA
  • Release Date : 2019-02-19
  • Total pages : 212
  • ISBN : 2889459209
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Summary : Recent technological advances in single-cell microbiology, using flow cytometry, microfluidics, x-ray fluorescence microprobes, and single-cell -omics, allow for the observation of individuals within populations. Simultaneously, individual-based models (or more generally agent-based models) allow for individual microbes to be simulated. Bridging these techniques forms the foundation of individual-based ecology of microbes (µ...

Systems Biology and Omics Approaches to Understand Complex Diseases Biology

Systems Biology and Omics Approaches to Understand Complex Diseases Biology
  • Author : Amit Kumar Yadav,Sanjay Kumar Banerjee,Kumardeep Chaudhary,Bhabatosh Das
  • Publisher : Frontiers Media SA
  • Release Date : 2022-05-03
  • Total pages : 212
  • ISBN : 2889459209
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Summary : Download or read online Systems Biology and Omics Approaches to Understand Complex Diseases Biology written by Amit Kumar Yadav,Sanjay Kumar Banerjee,Kumardeep Chaudhary,Bhabatosh Das, published by Frontiers Media SA which was released on 2022-05-03. Get Systems Biology and Omics Approaches to Understand Complex Diseases Biology Books now! ...

The Applications of Single cell Genomic Analysis in Development and Disease

The Applications of Single cell Genomic Analysis in Development and Disease
  • Author : QIN AN
  • Publisher : Unknown
  • Release Date : 2020
  • Total pages : 221
  • ISBN : 2889459209
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Summary : Single-cell genomics is the study of molecular modalities, or "-omes" from individual cells. Many protocols have been developed to profile genome, epigenome, transcriptome, and proteome from single cells. Among all these protocols, single-cell transcriptome profiling using single-cell RNA sequencing is the most popular and mature one. This technique has been ...

Single cell Molecular Characterization for Improving Cancer Immunotherapy

Single cell Molecular Characterization for Improving Cancer Immunotherapy
  • Author : Qihui Shi,Wei Wei,Ziming Li
  • Publisher : Frontiers Media SA
  • Release Date : 2022-02-22
  • Total pages : 212
  • ISBN : 2889459209
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Summary : Topic Editor Qihui Shi is the scientific co-founder of JunHealth, a company aiming to developing single-cell sequencing technologies for clinical applications, and received research funding from BeiGene....

Single cell Omics

Single cell Omics
  • Author : Debmalya Barh,Vasco Azevedo
  • Publisher : Academic Press
  • Release Date : 2019-08-15
  • Total pages : 600
  • ISBN : 2889459209
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Summary : Single-cell Omics: Technological Advances and Applications provides the latest technological developments and the applications of single-cell technologies in the field of biomedicine. The advent of omics technologies have enable us to identify the differences between cell types and subpopulations at the level of the genome, proteome, transcriptome, epigenome, and in ...

Handbook of Single Cell Technologies

Handbook of Single Cell Technologies
  • Author : Tuhin Subhra Santra,Fan-Gang Tseng
  • Publisher : Springer
  • Release Date : 2021-10-29
  • Total pages : 1096
  • ISBN : 2889459209
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Summary : This book provides a brief overview of single-cell analysis using recent advanced technologies. The different sections cover different aspect of single cell analysis and applications with their advantages, limitations, and future challenges. The book has covered how different physical energies such as optical, electrical, and mechanical energy have been applied ...