Single Cell Sequencing And Methylation

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Single Cell Sequencing And Methylation

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Author : Buwei Yu
language : en
Publisher: Springer Nature
Release Date : 2020-09-19

Single Cell Sequencing And Methylation written by Buwei Yu and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-09-19 with Science categories.

With the rapid development of biotechnologies, single-cell sequencing has become an important tool for understanding the molecular mechanisms of diseases, defining cellular heterogeneities and characteristics, and identifying intercellular communications and single-cell-based biomarkers. Providing a clear overview of the clinical applications, the book presents state-of-the-art information on immune cell function, cancer progression, infection, and inflammation gained from single-cell DNA or RNA sequencing. Furthermore, it explores the role of target gene methylation in the pathogenesis of diseases, with a focus on respiratory cancer, infection and chronic diseases. As such it is a valuable resource for clinical researchers and physicians, allowing them to refresh their knowledge and improve early diagnosis and therapy for patients.

Bioinformatics Analysis Of Single Cell Sequencing And Multi Omics In The Aging And Age Associated Diseases

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Author : Shouneng Peng
language : en
Publisher: Frontiers Media SA
Release Date : 2024-03-13

Bioinformatics Analysis Of Single Cell Sequencing And Multi Omics In The Aging And Age Associated Diseases written by Shouneng Peng 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 2024-03-13 with Science categories.

Integrative Analysis Of Single Cell And Or Bulk Multi Omics Sequencing Data

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Author : Geng Chen
language : en
Publisher: Frontiers Media SA
Release Date : 2023-03-13

Integrative Analysis Of Single Cell And Or Bulk Multi Omics Sequencing Data written by Geng Chen 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 2023-03-13 with Science categories.

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.

Single Molecule And Single Cell Sequencing

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Author : Yutaka Suzuki
language : en
Publisher: Springer
Release Date : 2019-04-09

Single Molecule And Single Cell Sequencing written by Yutaka Suzuki and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-04-09 with Medical categories.

This book presents an overview of the recent technologies in single molecule and single cell sequencing. These sequencing technologies are revolutionizing the way of the genomic studies and the understanding of complex biological systems. The PacBio sequencer has enabled extremely long-read sequencing and the MinION sequencer has made the sequencing possible in developing countries. New developments and technologies are constantly emerging, which will further expand sequencing applications. In parallel, single cell sequencing technologies are rapidly becoming a popular platform. This volume presents not only an updated overview of these technologies, but also of the related developments in bioinformatics. Without powerful bioinformatics software, where rapid progress is taking place, these new technologies will not realize their full potential. All the contributors to this volume have been involved in the development of these technologies and software and have also made significant progress on their applications. This book is intended to be of interest to a wide audience ranging from genome researchers to basic molecular biologists and clinicians.

Single Cell Intelligence And Tissue Engineering

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Author : Zhaoyuan Fang
language : en
Publisher: Frontiers Media SA
Release Date : 2022-10-17

Single Cell Intelligence And Tissue Engineering written by Zhaoyuan Fang 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 2022-10-17 with Science categories.

Single Cell Omics Of Neuronal Cells

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Author : Jonathan V. Sweedler
language : en
Publisher: Springer Nature
Release Date : 2022-08-10

Single Cell Omics Of Neuronal Cells written by Jonathan V. Sweedler and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-08-10 with Medical categories.

This volume discusses the latest techniques used in the diverse fields of single cell ‘omics and covers topics such as quantifying the single cell transcriptome; isolation of cells in nanoliter volumes for single cell proteomics measurements by nano-LC-MS/MS; and single cell protein characterization by immunoblotting. A wide range of methodologies are highlighted, ranging from high-yield chemical amplification to mass spectrometry and nanotechnology for the analysis of the chemical constituents of cells. In the Neuromethods series style, chapters include both in-depth overviews, as well as detailed protocols that provide the key advice from specialists you need to get successful results in your laboratory. Cutting-edge and comprehensive, Single Cell ‘Omics of Neuronal Cells is a valuable resource for experienced and novice researchers interested in learning more about this field and its future developments.

Ultra High Throughput Single Cell Co Sequencing Of Dna Methylation And Rna Using 3 Level Combinatorial Indexing

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Author : Huy Lam
language : en
Publisher:
Release Date : 2022

Ultra High Throughput Single Cell Co Sequencing Of Dna Methylation And Rna Using 3 Level Combinatorial Indexing written by Huy Lam and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022 with categories.

DNA methylation at cytosines has long been associated with early development, maturation, and aging of human tissues. Traditionally, DNA methylation is associated with gene silencing. However, recent single cell multi-omic DNA methylation and RNA sequencing methods have shown that the role of DNA methylation on the expression of nearby genes could silence or activate them depending on the gene and cell type. The recent developments these assays have detected cell type specific DNA methylation and RNA coupling in stem cell rich and human brain tissues. This specificity underscores the need for future growth in DNA methylation and RNA co-sequencing technologies and analysis tools. Presently, about 100,000 single cell profiles are required to adequately map tissues. DNA methylation and RNA co-sequencing methods require the physical isolation of single cells in individual wells. There is no method that can assay 100,000 cells without utilizing extensive liquid handling systems. We address this challenge by developing a novel ultra-high throughput DNA methylation and RNA co-sequencing platform, sci-Gel, that utilizes three levels of combinatorial indexing to increase the throughput of existing technologies to 50,000-100,000 cells per experiment with just three 96 well plates. In this dissertation, we first push the boundaries of present combinatorial indexing techniques where the DNA and RNA of single cells are simultaneously extracted and immobilized within polyacrylamide gel beads that are used for indexing. This resulted in the development of a 2-level combinatorial indexing platform that could be used to co-sequence DNA copy-number variations, relevant in cancers, and RNA at the scale of thousands of cells. We then describe the adaptations made from existing bisulfite conversion chemistries to our gel beads to incorporate the DNA methylation feature. We then describe the development of a 3-level combinatorial indexing platform to increase the cell throughput of our technology to 50,000-100,000 cells per experiment. Finally, we discuss future efforts to utilize sci-Gel to create the first single cell DNA methylation and RNA co-sequencing map of peripheral blood mononuclear cells.

Single Cell Biomedicine

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Author : Jianqin Gu
language : en
Publisher: Springer
Release Date : 2018-06-25

Single Cell Biomedicine written by Jianqin Gu and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-06-25 with Science categories.

The book focuses on various detection targets applied in single cell studies, including tumor tissue cells, circulating tumor cells (CTCs), disseminated tumor cells (DTCs), circulating tumor DNA (ctDNA), cell-free DNA (cfDNA) and cancer stem cells (CSCs). It also discusses and compares detection methods using these detection targets in different fields to reveal single cell biomedical functions. The volume focuses not only on the methods already been established and validated, and also the methods newly developed. The book also highlights the importance and potential of single cell biomedicine in the development and validation of precision medicine strategies. It is useful for researchers and students in the field of cell biology, molecular medicine and precision medicine etc.

Single Cell Omics

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Author : Debmalya Barh
language : en
Publisher: Academic Press
Release Date : 2019-06-06

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 2019-06-06 with Medical categories.

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 research and applications, diverse technologies applied in the topic, such as pangenomics, metabolomics, and multi-omics of single cells, data analysis, and several applications of single-cell omics within the biomedical field, for example in cancer, metabolic and neuro diseases, immunology, pharmacogenomics, personalized medicine and reproductive health. This book is a valuable source for bioinformaticians, molecular diagnostic researchers, clinicians and members of the biomedical field who are interested in understanding more about single-cell omics and its potential for research and diagnosis. - Covers not only the technological aspects, but also the diverse applications of single cell omics 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, bringing different points-of-view and case studies to give a comprehensive overview on the topic