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Introduction to Single Cell Omics

Introduction to Single Cell Omics
A Book

by Xinghua Pan,Shixiu Wu,Sherman M. Weissman

  • Publisher : Frontiers Media SA
  • Release : 2019-09-19
  • Pages : 129
  • ISBN : 2889459209
  • Language : En, Es, Fr & De
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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-Cell Omics

Single-Cell Omics
Volume 1: Technological Advances and Applications

by Debmalya Barh,Vasco Azevedo

  • Publisher : Academic Press
  • Release : 2019-06-06
  • Pages : 490
  • ISBN : 0128149205
  • Language : En, Es, Fr & De
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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

Single-Cell Omics

Single-Cell Omics
Volume 2: Applications in Biomedicine and Agriculture

by Debmalya Barh,Vasco Azevedo

  • Publisher : Academic Press
  • Release : 2019-07-31
  • Pages : 384
  • ISBN : 012817532X
  • Language : En, Es, Fr & De
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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

Single-Cell Omics

Single-Cell Omics
Emerging Technologies and Markets

by BCC Research

  • Publisher : Unknown Publisher
  • Release : 2017-12
  • Pages : 129
  • ISBN : 9781622966158
  • Language : En, Es, Fr & De
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Single Cell Analysis

Single Cell Analysis
The New Frontier in 'Omics'

by Anonim

  • Publisher : Unknown Publisher
  • Release : 2010
  • Pages : 129
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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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 is expected to accelerate owing to emerging technologies that range from micro/nanofluidics to microfabricated interfaces for mass spectrometry to third- and fourth-generation automated DNA sequencers. As described in this review, single cell analysis is the new frontier in Omics, and single cell Omics has the potential to transform systems biology through new discoveries derived from cellular heterogeneity.

Novel Single-cell Omics Assays of Corticogenesis

Novel Single-cell Omics Assays of Corticogenesis
A Dissertation

by Ryan M.. Mulquee

  • Publisher : Unknown Publisher
  • Release : 2020
  • Pages : 264
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Single Cell Analysis

Single Cell Analysis
A Book

by Tuhin Subhra Santra,Fan-Gang Tseng

  • Publisher : MDPI
  • Release : 2021-06-02
  • Pages : 254
  • ISBN : 3036506284
  • Language : En, Es, Fr & De
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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 general information on cells, but it cannot evolve the cellular heterogeneity and molecular dynamics in a certain cell population. Compared to this bulk or the average measurement of a large number of cells together, single-cell analysis can provide detailed information on each cell, which could assist in developing an understanding of the specific biological context of cells, such as tumor progression or issues around stem cells. Single-cell omics can provide valuable information about functional mutation and a copy number of variations of cells. Information from single-cell investigations can help to produce a better understanding of intracellular interactions and environmental responses of cellular organelles, which can be beneficial for therapeutics development and diagnostics purposes. This Special Issue is inviting articles related to single-cell analysis and its advantages, limitations, and future prospects regarding health benefits.

Single-Cell Omics

Single-Cell Omics
Volume 2: Technological Advances and Applications

by Debmalya Barh,Vasco Azevedo

  • Publisher : Academic Press
  • Release : 2019-07-30
  • Pages : 384
  • ISBN : 0128175338
  • Language : En, Es, Fr & De
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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

Handbook of Single Cell Technologies

Handbook of Single Cell Technologies
A Book

by Tuhin Subhra Santra,Fan-Gang Tseng

  • Publisher : Springer
  • Release : 2021-02-10
  • Pages : 1200
  • ISBN : 9789811089527
  • Language : En, Es, Fr & De
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This book provides an overview of single cell manipulation, injection, lysis, and dynamics analysis with the aid of various miniaturized devices. The role of single cell analysis in system biology, proteomics, genomics, metabolomics and fluxomics, the applications of single cell analysis for bio-catalysis, metabolic and bioprocess engineering, and the future challenges for single cell analysis given its advantages and limitations are also elaborated. The respective chapters introduce readers to various approaches for single cell analysis. Further, they address the fabrication of different types of bio-micro/nano devices in the context of cutting-edge analysis and screening for e.g. cancers, HIV etc., which is beneficial for society at large. This book is intended for academic researchers, undergraduate and graduate students in the fields of Biomedical Engineering, Bio-nanoengineering, and Bio-micro/nano Fabrication. It can be used for courses on Bio-MEMS/Bio-NEMS, Biomicrofluidics, Biomicrofabrications, Micro/Nanofluidics, Biophysics, Single Cell Analysis, Bionanotechnology, Drug Delivery Systems and Biomedical Microdevices. Bringing together contributions from respected experts, it will also benefit researchers and practitioners in the biotechnology industry, where diseases analysis, diagnosis and drug screening continue to grow in importance. In addition to hard copies, the book is also published online and is often updated by the authors.

The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling

The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling
A Book

by Johan H. J. Leveau,Ferdi L. Hellweger,Jan-Ulrich Kreft,Clara Prats,Weiwen Zhang

  • Publisher : Frontiers Media SA
  • Release : 2019-02-19
  • Pages : 129
  • ISBN : 2889457494
  • Language : En, Es, Fr & De
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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 (µIBE). µIBE has elucidated genetic and phenotypic heterogeneity that has important consequences for a number of human interests, including antibiotic or biocide resistance, the productivity and stability of industrial fermentations, the efficacy of food preservatives, and the potential of pathogens to cause disease. Individual-based models can help us to understand how these sets of traits of individual microbes influence the above. This eBook compiles all publications from a recent Research Topic in Frontiers in Microbiology. It features recent research where individual observational and/or modelling techniques are applied to gain unique insights into the ecology of microorganisms. The Research Topic “The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling” arose from the 2016 @ASM conference of the same name hosted by the American Society for Microbiology at its headquarters in Washington, D.C. We are grateful to ASM for funding and hosting this conference.

Single Cell Methods

Single Cell Methods
Sequencing and Proteomics

by Valentina Proserpio

  • Publisher : Unknown Publisher
  • Release : 2019
  • Pages : 452
  • ISBN : 9781493992423
  • Language : En, Es, Fr & De
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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 Sequencing and Systems Immunology

Single Cell Sequencing and Systems Immunology
A Book

by Xiangdong Wang

  • Publisher : Springer
  • Release : 2015-03-27
  • Pages : 177
  • ISBN : 9401797536
  • Language : En, Es, Fr & De
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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.

Statistical Methods for the Integrative Analysis of Single-cell Multi-omics Data

Statistical Methods for the Integrative Analysis of Single-cell Multi-omics Data
A Book

by Ricardo Argelaguet

  • Publisher : Unknown Publisher
  • Release : 2020
  • Pages : 129
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Analyses of Genome Structures in Testate Amoeba (Arcellinida, Amoebozoa) Uning Single-cell 'omics and Flurescence Microscopy

Analyses of Genome Structures in Testate Amoeba (Arcellinida, Amoebozoa) Uning Single-cell 'omics and Flurescence Microscopy
A Book

by Ketty Munyenyembe

  • Publisher : Unknown Publisher
  • Release : 2020
  • Pages : 34
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Essentials of Single-Cell Analysis

Essentials of Single-Cell Analysis
Concepts, Applications and Future Prospects

by Fan-Gang Tseng,Tuhin Subhra Santra

  • Publisher : Springer
  • Release : 2016-01-21
  • Pages : 414
  • ISBN : 3662491184
  • Language : En, Es, Fr & De
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This book provides an overview of single-cell isolation, separation, injection, lysis and dynamics analysis as well as a study of their heterogeneity using different miniaturized devices. As an important part of single-cell analysis, different techniques including electroporation, microinjection, optical trapping, optoporation, rapid electrokinetic patterning and optoelectronic tweezers are described in detail. It presents different fluidic systems (e.g. continuous micro/nano-fluidic devices, microfluidic cytometry) and their integration with sensor technology, optical and hydrodynamic stretchers etc., and demonstrates the applications of single-cell analysis in systems biology, proteomics, genomics, epigenomics, cancer transcriptomics, metabolomics, biomedicine and drug delivery systems. It also discusses the future challenges for single-cell analysis, including the advantages and limitations. This book is enjoyable reading material while at the same time providing essential information to scientists in academia and professionals in industry working on different aspects of single-cell analysis. Dr. Fan-Gang Tseng is a Distinguished Professor of Engineering and System Science at the National Tsing Hua University, Taiwan. Dr. Tuhin Subhra Santra is a Research Associate at the California Nano Systems Institute, University of California at Los Angeles, USA.

Single-cell Multi-omics Analysis Reveals the Progression and the Specific T Cell Receptor of Ankylosing Spondylitis in Adalimumab Treatment

Single-cell Multi-omics Analysis Reveals the Progression and the Specific T Cell Receptor of Ankylosing Spondylitis in Adalimumab Treatment
A Book

by Anonim

  • Publisher : Unknown Publisher
  • Release : 2020
  • Pages : 129
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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Single Cell Methods

Single Cell Methods
Sequencing and Proteomics

by Valentina Proserpio

  • Publisher : Unknown Publisher
  • Release : 2019
  • Pages : 452
  • ISBN : 9781493992416
  • Language : En, Es, Fr & De
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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.

Microfluidic Tools for Connecting Single-Cell Optical and Gene Expression Phenotype

Microfluidic Tools for Connecting Single-Cell Optical and Gene Expression Phenotype
A Book

by Jesse Qiuxu Zhang

  • Publisher : Unknown Publisher
  • Release : 2020
  • Pages : 129
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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The single cell is the fundamental unit of biology. Understanding how the identity of individual cells in multicellular organisms contribute to their function remains a key question in Biology. Traditionally, most observations of cells were made through imaging-based techniques. Today, advances in Next Generation Sequencing have led to the widespread adoption of sequencing-based techniques for investigating the genotype and phenotype at single-cell resolution. Microfluidics, including droplet-based microfluidics, have been instrumental in the most successful commercial single-cell genomics platforms.Integrating sequencing and imaging techniques will provide additional information than either of the techniques alone. Both single-cell imaging and genomics techniques measure orthogonal targets, and when combined reveal additional insights into cellular function. However, when performing sequential single-cell assays, there currently exists a tradeoff between throughput and information content. This dissertation will describe progress made towards reducing that gap. I will describe novel microfluidic platforms and techniques and applications involving integrating single-cell sequencing and optical measurements at high throughput. The microfluidics tools that will be discussed in this Dissertation aim to be a platform for performing single-cell multi-parameter and multi-omics techniques that will help further our understanding of cellular identity and how genotype informs phenotype at the single-cell level.

The Applications of Single-cell Genomic Analysis in Development and Disease

The Applications of Single-cell Genomic Analysis in Development and Disease
A Book

by QIN AN

  • Publisher : Unknown Publisher
  • Release : 2020
  • Pages : 221
  • ISBN : 9876543210XXX
  • Language : En, Es, Fr & De
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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 demonstrated to be very powerful in dissecting cell types within a heterogeneous tissue, as well as revealing cell type specific responses to stimuli. It has also been used to reconstruct cell trajectory during complex biological progress, such as cell differentiation. More importantly, it can be used to reveal gene co-expression networks among cell types, and ultimately the molecular mechanism of gene regulation. In the first two projects of my thesis, I described how we use single-cell RNA sequencing to understand the molecular mechanism controlling trophoblasts proliferation and differentiation during human peri-implantation embryo development, as well as the mechanism of retinal progenitor cells commitment during early human retinogenesis. In the first project, we profiled human embryonic stem cell derived retinal organoids using single-cell RNA sequencing, to understand the molecular mechanism of early retinogenesis. The development of the mammalian retina is a complicated process involving generating distinct types of neurons from retinal progenitor cells (RPCs) in a spatiotemporal-specific manner. The progression of RPCs during retinogenesis includes RPC proliferation, cell fate commitment, and specific neuronal differentiation. In this study, by performing single-cell RNA-sequencing (scRNA-seq) on cells isolated from human embryonic stem cell (hESC)-derived 3D retinal organoids, we successfully deconstructed the temporal progression of RPCs during early human retinogenesis. We identified two distinct subtypes of RPCs with unique molecular profiles, namely multipotent RPCs and neurogenic RPCs. We found genes related to the Notch and Wnt signaling pathway, as well as chromatin remodeling, were dynamically regulated during RPC commitment. Interestingly, our analysis identified CCND1, a G1-phase cell cycle regulator, was co-expressed with ASCL1 in a cell-cycle independent manner. Temporally-controlled overexpression of CCND1 in retinal organoids demonstrated a role for CCND1 in promoting early retinal neurogenesis. Together, our results revealed critical pathways and novel genes in the early retinogenesis of humans. In the second project, we profiled transcriptome from individual trophoblast cells collected from human peri-implantation embryos, to reveal how these cells proliferate and differentiate to establish placenta. Multipotent trophoblasts undergo dynamic morphological movement and cellular differentiation after conceptus implantation to generate placenta. However, the mechanism controlling trophoblast development and differentiation during peri-implantation development in human remains elusive. In this study, we modeled human conceptus peri-implantation development from blastocyst to early post-implantation stages by using an in vitro coculture system and profiled the transcriptome of 476 individual trophoblast cells from these conceptuses. We revealed the genetic networks regulating peri-implantation trophoblast development. While determining when trophoblast differentiation happens, our bioinformatic analysis identified T-box transcription factor 3 (TBX3) as a key regulator for the differentiation of cytotrophoblast into syncytiotrophoblast. The function of TBX3 in trophoblast differentiation is then validated by a loss-of-function experiment. In conclusion, our results provided a valuable resource to study the regulation of trophoblasts development and differentiation during human peri-implantation development. In parallel with the development of single-cell RNA sequencing, many efforts have been put in profiling other molecular modalities from single cells, such as genome, epigenome, and proteome. By elaborately combining these protocols, we can profile more than one types of "omes" from individual cells simultaneously. These techniques, commonly termed as "single-cell multimodal profiling", can generate data that has certain advantages compared to single-cell "mono-omics" approaches. Specifically, since each molecular modality provides orthogonal information about cell identities and status, the joint clustering of single-cell multi-omics data can better resolve cell types within a heterogeneous cell population. Also, because more than one molecular modalities were profiled simultaneously from every single cell, we could have better inferences about the relationship between these omics. In the third project, we demonstrated how to use scMT-seq (simultaneous profiling of transcriptome and DNA methylome from a single cell), to investigate the gene regulatory role of DNA methylation in sensory neurons during peripheral nerve injury response and regeneration. DNA methylation is implicated in neuronal injury response and regeneration, but its role in regulating stable transcription changes in different types of dorsal root ganglion (DRG) neurons is unclear. In this study, we simultaneously profiled both the DNA methylome and mRNA transcriptome from single DRG neurons at different ages under either control or peripheral nerve injury condition. We found that age-related expression changes in Notch signaling genes and methylation changes at Notch receptor binding sites are associated with the age-dependent decline in peripheral nerve regeneration potential. Moreover, selective hypomethylation of AP-1 complex binding sites on regeneration-associated gene (RAG) promoters coincides with RAG transcriptional upregulation after injury. Consistent with the findings that different subtypes of DRG neurons exhibit distinct methylome changes upon injury responses, in a hybrid CAST/Ei; C57BL/6 genetic background, we further observed allele-specific gene regulation and methylation changes for many RAGs after injury. We suggest that the genetic background determines distinct allele-specific DNA methylomes, which contribute to age-dependent regulation and neuronal subtype-specific injury-responses in different mouse strains.

Lab-on-Chips for Cellomics

Lab-on-Chips for Cellomics
Micro and Nanotechnologies for Life Science

by Albert Berg,Helene Andersson

  • Publisher : Springer Science & Business Media
  • Release : 2007-09-07
  • Pages : 364
  • ISBN : 1402029756
  • Language : En, Es, Fr & De
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This volume is volume entirely dedicated to microfabricated cell-based systems. It will provide readers with a quick introduction to the field as well as with a variety of specific examples of such Lab-on-Chip systems for cellomics applications. It will give investigators inspiration for innovative research topics, whereas end users will be surprised about the wide variety of new and exciting applications.