Single Cell Genomics
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Introduction To Single Cell Omics
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Author : Xinghua Pan
language : en
Publisher: Frontiers Media SA
Release Date : 2019-09-19
Introduction To Single Cell Omics written by Xinghua Pan and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-09-19 with categories.
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.
Unravelling Single Cell Genomics
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Author : Nathalie Bontoux
language : en
Publisher: Royal Society of Chemistry
Release Date : 2010-10-18
Unravelling Single Cell Genomics written by Nathalie Bontoux and has been published by Royal Society of Chemistry this book supported file pdf, txt, epub, kindle and other format this book has been release on 2010-10-18 with Technology & Engineering categories.
This unique introduction to the growing field of microfluidics applied to genomics provides an overview of the latest technologies and emphasizes its potential in answering important biological questions. Written by a physicist and a biologist, it offers a more comprehensive view than the previous literature. The book starts with key ideas in molecular biology, developmental biology and microtechnology before going on to cover the specifics of single cell analysis and microfluidic devices for single cell molecular analysis. Review chapters discuss the state-of-the art and will prove invaluable to all those planning to develop microdevices for molecular analysis of single cells. Methods allowing complete analysis of gene expression in the single cell are stressed - as opposed the more commonly used techniques that allow analysis of only a few genes at a time. As pioneers in the field, the authors understand how critical it is for a physicist to understand the biological issues and questions related to single cell analysis, as well for biologists to understand what microfluidics is all about. Aimed predominantly at graduate students, this book will also be of significant interest to scientists working in or affiliated with this field.
Single Cell Genomics
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Author : Parwinder Kaur
language : en
Publisher: Springer
Release Date : 2025-06-13
Single Cell Genomics written by Parwinder Kaur and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2025-06-13 with Science categories.
Cells, the basic units of biological structure and function, vary broadly in type and state. Individual cells are the building blocks of tissues, organs, and organisms. Each tissue contains cells of many types, and cells of each type can switch among biological states. Single-cell genomics, transcriptomics and epigenomics open a whole new era with the possibility to interrogate every cell of an organism in order to decipher the important biological processes that occur within. This has emerged as a ground-breaking technology that has greatly enhanced our understanding of the complexity of gene expression dynamics at a microscopic resolution. It is anticipated that in the next 5-10 years, the wider research community will be routinely employing this powerful technology as a laboratory staple. Single-cell genomics, transcriptomics and epigenomics hold the potential to revolutionize the way we characterize complex cell assemblies and study their spatial organization, dynamics, clonal distribution, pathways, function, and crosstalks. These fascinating advances have opened up a new field of cell population genomics. Single-cell genomics, transcriptomics and epigenomics research is providing new insights into inter-cellular population genomic diversity, heterogeneity, specialization, taxonomy, spatial and temporal gene regulation, and cellular and organismal development and evolution. It is facilitating plant breeding, understanding of human disease conditions and personalized medicine. This book discusses the perspectives, progress, and promises of single-cell genomics, transcriptomics and epigenomics research and applications in addressing the above and other key biological aspects in all organisms. It establishes the current state-of-the-field and serves as the foundation for future developments in single-cell genomics, transcriptomics, and epigenomics.
Single Cell Methods
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Author : Valentina Proserpio
language : en
Publisher:
Release Date : 2019
Single Cell Methods written by Valentina Proserpio and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019 with Cytology categories.
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 Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Single Cell Methods: Sequencing and Proteomics aims to make each experiment easily reproducible in every lab.
Single Cell Genomics
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Author :
language : en
Publisher:
Release Date : 2017
Single Cell Genomics written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017 with categories.
Single Cell Omics
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Author : Debmalya Barh
language : en
Publisher: Academic Press
Release Date : 2019-07-31
Single Cell Omics written by Debmalya Barh and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-07-31 with categories.
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. The book is divided into two sections: the first is dedicated to biomedical applications, such as cell diagnostics, non-invasive prenatal testing (NIPT), circulating tumor cells, breast cancer, gliomas, nervous systems and autoimmune disorders, and more. The second focuses on cell omics in plants, discussing micro algal and single cell omics, and more. This book is a valuable source for bioinformaticians, molecular diagnostic researchers, clinicians and several members of biomedical field interested in understanding more about single-cell omics and its potential for research and diagnosis. Covers the diverse single cell omics applications in the biomedical field Summarizes the latest progress in single cell omics and discusses potential future developments for research and diagnosis Written by experts across the world, it brings different points-of-view and study cases to fully give a comprehensive overview of the topic
Bioinformatics Analysis Of Single Cell Sequencing Data And Applications In Precision Medicine
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Author : Jialiang Yang
language : en
Publisher: Frontiers Media SA
Release Date : 2020-02-27
Bioinformatics Analysis Of Single Cell Sequencing Data And Applications In Precision Medicine written by Jialiang Yang and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-02-27 with categories.
Single Cell Sequencing And Systems Immunology
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Author : Xiangdong Wang
language : en
Publisher: Springer
Release Date : 2015-03-27
Single Cell Sequencing And Systems Immunology written by Xiangdong Wang and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2015-03-27 with Medical categories.
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 for identifying and developing disease-specific biomarkers in order to understand the biological function, activation and dysfunction of single cells and lymphocytes and to explore their functional roles and responses to therapies. It also provides detailed information on individual subgroups of lymphocytes, including cell characters, function, surface markers, receptor function, intracellular signals and pathways, production of inflammatory mediators, nuclear receptors and factors, omics, sequencing, disease-specific biomarkers, bioinformatics, networks and dynamic networks, their role in disease and future prospects. Dr. Xiangdong Wang is a Professor of Medicine, Director of Shanghai Institute of Clinical Bioinformatics, Director of Fudan University Center for Clinical Bioinformatics, Director of the Biomedical Research Center of Zhongshan Hospital, Deputy Director of Shanghai Respiratory Research Institute, Shanghai, China.
Integrative Analysis Of Genome Wide Association Studies And Single Cell Sequencing Studies
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Author : Sheng Yang
language : en
Publisher: Frontiers Media SA
Release Date : 2021-09-09
Integrative Analysis Of Genome Wide Association Studies And Single Cell Sequencing Studies written by Sheng Yang and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-09-09 with Science categories.
Single Cell Research
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Author : Aleksei Anatoliyovych Stepanenko
language : en
Publisher: Delve Publishing
Release Date : 2017-11
Single Cell Research written by Aleksei Anatoliyovych Stepanenko and has been published by Delve Publishing this book supported file pdf, txt, epub, kindle and other format this book has been release on 2017-11 with Cytology categories.
Analysis of single cells has become a key technique in biological and biomedical research. Single-cell genomics, transcriptomics, epigenomics, and proteomics now allow many enduring questions in biological and biomedical sciences to be answered. The new single-cell approaches offer the potential to revolutionize our understanding of diseases and associated biological processes, with the capacity to reveal the intercellular heterogeneity within a specific tissue at an unprecedented resolution. The single cell technology has proven to be a valuable tool to explore DNA, RNA, or proteins in one single cell at a time. Using single-cell level features, we can infer cell lineages, identify subpopulations and highlight cell-specific biological characteristics. Moreover, single-cell analyses have already demonstrated their utilities in the clinical applications, ranging from characterizing cancer cells subpopulations, highlighting specific resistance mechanisms to being used as diagnostic tools. For example, by employing single-cell sequencing to circulating tumor cells, metastasis and progression diagnoses may aid in therapeutic design. Single-cell sequencing analyses have been applied in the field of virology, providing new ways to explore viral diversity and cell response to viral infection. Single-cell RNA sequencing have been used to dissect plant tissue organization, developmental dynamics, and physiological responses. Single-cell analysis have made increasingly significant contributions to our understanding of the role that somatic genome variations play in neuronal diversity and behaviors In this book, the technologies recently developed for single cell isolation, genome acquisition, transcriptome, and proteome analyses, their applications and the future potentials are thoroughly discussed.