Capturing Chromosome Conformation
Author | : Beatrice Bodega |
Publisher | : |
Total Pages | : |
Release | : 2021 |
Genre | : Biology |
ISBN | : 9781071606650 |
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Author | : Beatrice Bodega |
Publisher | : |
Total Pages | : |
Release | : 2021 |
Genre | : Biology |
ISBN | : 9781071606650 |
Author | : Beatrice Bodega |
Publisher | : Humana |
Total Pages | : 322 |
Release | : 2020-10-29 |
Genre | : Science |
ISBN | : 9781071606636 |
This detailed book collects methods based on the evolution of the chromosome conformation capture (3C) technique and other complementary approaches to dissect chromatin conformation with an emphasis on dissection of nuclear compartmentalization and visualization in imaging. Written for the highly successful Methods in Molecular Biology series, 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 practical, Capturing Chromosome Conformation: Methods and Protocols serves as an ideal guide for researchers working to further understand 3D genome organization.
Author | : Philippe Collas |
Publisher | : Humana Press |
Total Pages | : 0 |
Release | : 2012-03-05 |
Genre | : Science |
ISBN | : 9781617797507 |
Over the past twenty years, the development of chromatin immunoprecipitation, or ChIP, assays has immensely enhanced the biological significance of the multifaceted DNA-binding proteins. In Chromatin Immunoprecipitation Assays: Methods and Protocols, researchers deeply involved in the development and improvement of the field provide cutting-edge protocols devoted to the most recent progress in ChIP and related subjects. The thorough chapters involve topics such as the characterization of ChIP antibodies, ChIP methods for small cell numbers, fast ChIP protocols, assays adapted to various species and cell types, as well as several strategies for the analysis of genome-wide datasets, while also extending a bit beyond ChIP assays to cover immunoprecipitation-based DNA methylation analyses, determination of spatial chromatin organization of large genomic regions, and RNA immunoprecipitation. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain brief introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easy-to-use, Chromatin Immunoprecipitation Assays: Methods and Protocols is a timely guide for all those who wish to further the development of this powerful tool and continue delving into the incredible complexity of the cell’s biology.
Author | : Célia Baroux |
Publisher | : |
Total Pages | : 659 |
Release | : 2018 |
Genre | : Botany |
ISBN | : 9781493973187 |
Author | : Silvio Bicciato |
Publisher | : Humana |
Total Pages | : 0 |
Release | : 2022-09-04 |
Genre | : Science |
ISBN | : 9781071613924 |
This volume details a comprehensive set of methods and tools for Hi-C data processing, analysis, and interpretation. Chapters cover applications of Hi-C to address a variety of biological problems, with a specific focus on state-of-the-art computational procedures adopted for the data analysis. 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, Hi-C Data Analysis: Methods and Protocols aims to help computational and molecular biologists working in the field of chromatin 3D architecture and transcription regulation.
Author | : Karen Mossman |
Publisher | : |
Total Pages | : 275 |
Release | : 2017 |
Genre | : Biomedicine |
ISBN | : 9781493972371 |
This book explores methods to study the complex and evolving interplay between a virus and its host that range from model systems to the detection of chemical molecules. The collection starts with the application of humanized mice and zebrafish as model organisms to study virus-host interactions and induction of innate immune responses. Subsequent chapters outline diverse methods to detect small interfering RNAs, microRNAs, and virus-derived dsRNA from a variety of cells, tissues, and organisms, as well as to interrogating the cytosolic RNA and DNA sensing pathways, including using RNA PAMPs as molecular tools, purification of cGAMP from virus particles and infected cells, and mechanisms to visualize the subcellular localization and activation of the adaptor proteins MAVS and STING. Cutting-edge methods, including high-throughput and genome-wide CRISPR/Cas9 screens, chromosome conformation capture, and whole-exome sequencing, are described to identify novel mediators, pathways, and variants underlying host susceptibility. Given the importance of studying these pathways and players under physiologic conditions, methods describing the isolation of primary mouse sensory neurons and group 2 innate lymphoid cells are also provided. Finally, this collection comes full circle back to the whole organism level and concludes with epidemiological methods to investigate virus-host interactions and the induction of innate immunity. Written for the Methods in Molecular Biology series, 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 practical, Innate Antiviral Immunity: Methods and Protocols spans a diverse array of approaches to study and elucidate the intricacies of this vital area of study.
Author | : Narendra Wajapeyee |
Publisher | : |
Total Pages | : 278 |
Release | : 2016 |
Genre | : Biomedicine |
ISBN | : 9781493965182 |
This volume describes a variety of protocols that will allow the readers to study different aspects of transcriptional and posttranscriptional gene expression regulation in eukaryotic cells. Chapters focus on the latest use of CRISPRi and RNAi technologies for studying various aspects of transcriptional and posttranscriptional regulation and tools to navigate protocols on key bioinformatics. 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, Eukaryotic Transcription and Post-Transcription Gene Expression Regulation aims to ensure successful results in the further study of this vital field.
Author | : Minghua Deng |
Publisher | : Springer |
Total Pages | : 346 |
Release | : 2013-03-22 |
Genre | : Computers |
ISBN | : 9783642371943 |
This book constitutes the refereed proceedings of the 17th Annual International Conference on Research in Computational Molecular Biology, RECOMB 2013, held in Beijing, China, in April 2013. The 32 revised full papers were carefully reviewed and selected from 167 submissions. The papers cover a wide range of topics including molecular sequence analysis; genes and regulatory elements; molecular evolution; gene expression; biological networks; sequencing and genotyping technologies; genomics; epigenomics; metagenomics; population, statistical genetics; systems biology; computational proteomics; computational structural biology; imaging; large-scale data management.
Author | : Oldenburg Oldenburg Press |
Publisher | : |
Total Pages | : 40 |
Release | : 2016-01-29 |
Genre | : |
ISBN | : 9781523764426 |
HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs quality controls and generates intra- and inter-chromosomal contact maps. It includes a fast implementation of the iterative correction method and is based on a memory-efficient data format for Hi-C contact maps. In addition, HiC-Pro can use phased genotype data to build allele-specific contact maps. We applied HiC-Pro to different Hi-C datasets, demonstrating its ability to easily process large data in a reasonable time. Source code and documentation are available at http://github.com/nservant/HiC-Pro.
Author | : Luis M. de Pablos |
Publisher | : Humana |
Total Pages | : 336 |
Release | : 2021-07-28 |
Genre | : Medical |
ISBN | : 9781071616802 |
This detailed book provides a comprehensive series of innovative research techniques and methodologies applied to the parasite genomics research area, all applying different approaches to analyzing parasite genomes and furthering the study of genetic complexity and the mechanisms of regulation. Beginning with chapters on novel sequencing and the bioinformatics pipeline, the volume continues by exploring diagnostic approaches using genomic tools, host-parasite interactions, as well as the genomics of parasite-derived extracellular vesicles. Written for the highly successful Methods in Molecular Biology series, 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 practical, Parasite Genomics: Methods and Protocols creates a detailed picture of genomic approaches for researchers seeking a better understanding of characterizing parasite nucleic acid content.