Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Extraction: Advanced Methods00:56

Extraction: Advanced Methods

1.3K
Metal ions can be separated from one another by complexation with organic ligands–the chelating agent– to form uncharged chelates. Here, the chelating agent must contain hydrophobic groups and behave as a weak acid, losing a proton to bind with the metal. Since most organic ligands used in this process are insoluble or undergo oxidation in the aqueous phase, the chelating agent is initially added to the organic phase and extracted into the aqueous phase. The metal-ligand complex is...
1.3K
Sample Preparation for Analysis: Overview01:21

Sample Preparation for Analysis: Overview

3.4K
Sample preparation is an essential step in the analytical process. It involves preparing a sample so that it can be analyzed accurately. The goal is to extract the analyte, the substance you want to measure, from the sample while removing any components that may interfere with the analysis. Sample preparation techniques vary depending on the physical state of the sample.
Bulk or large solid samples are typically reduced in size using grinding, crushing, or milling techniques to increase the...
3.4K
Sample Preparation for Analysis: Advanced Techniques01:08

Sample Preparation for Analysis: Advanced Techniques

1.9K
Accurate analysis of complex samples often requires advanced preparation techniques to achieve reliable and reproducible results. Samples containing inorganic or organic materials can be challenging to dissolve or decompose effectively. Standard sample preparation methods include acid digestion, fusion, dry ashing, and wet digestion.
Acid digestion with strong acids is commonly used to dissolve inorganic materials that are insoluble (do not dissolve) in water. This method can be useful for...
1.9K
Overview of Minitab01:11

Overview of Minitab

1.1K
Minitab is a statistical software package designed for data analysis. With its origins in the 1970s and development at Pennsylvania State University, Minitab has grown significantly in its capabilities and applications. It plays a crucial role in quality management projects, especially in Six Sigma initiatives, by offering tools for process improvement and statistical analysis. Minitab's significance lies in its user-friendly interface, making complex statistical analysis accessible to...
1.1K
Methods to Assess Microbial Communities01:19

Methods to Assess Microbial Communities

66
Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
66
Automated Microbial Diagnostics01:24

Automated Microbial Diagnostics

79
Automated diagnostic analyzers have transformed clinical microbiology by providing rapid and reliable methods for pathogen identification and antibiotic susceptibility testing. Among these systems, the Vitek 2 is widely used because it automates the traditionally labor-intensive processes of microbial identification (ID) and antibiotic susceptibility testing (AST), delivering standardized and timely results that are essential for effective patient care.Microbial Identification with ID CardsThe...
79

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Regulation of pericentromeric DNA loop size via Scc2-cohesin interaction.

iScience·2025
Same author

A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes.

Current biology : CB·2025
Same author

Cornelia de Lange syndrome, related disorders, and the Cohesin complex: Abstracts from the 8th biennial scientific and educational symposium 2018.

American journal of medical genetics. Part A·2024
Same author

Biallelic variants in GTF3C5, a regulator of RNA polymerase III-mediated transcription, cause a multisystem developmental disorder.

Human genetics·2024
Same author

Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils.

Molecular cell·2024
Same author

Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors.

Nature communications·2023
Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: May 5, 2026

An Analytical Tool-box for Comprehensive Biochemical, Structural and Transcriptome Evaluation of Oral Biofilms Mediated by Mutans Streptococci
11:09

An Analytical Tool-box for Comprehensive Biochemical, Structural and Transcriptome Evaluation of Oral Biofilms Mediated by Mutans Streptococci

Published on: January 25, 2011

17.7K

Micro-C Analysis Workflow Using Pairtools and Juicer.

Toyonori Sakata1,2,3

  • 1Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, University of Tokyo, Bunkyo City, Tokyo, Japan. toyonori.sakata@ki.se.

Methods in Molecular Biology (Clifton, N.J.)
|September 16, 2024
PubMed
Summary
This summary is machine-generated.

This chapter details the Micro-C method for analyzing three-dimensional (3D) chromosome structures at nucleosome resolution. It covers data analysis from mapping to loop detection for understanding chromosomal functions.

Keywords:
3D genome structureChromatin loopCompartmentMicro-CTAD

More Related Videos

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
00:09

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

Published on: August 21, 2019

7.3K
Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

2.2K

Related Experiment Videos

Last Updated: May 5, 2026

An Analytical Tool-box for Comprehensive Biochemical, Structural and Transcriptome Evaluation of Oral Biofilms Mediated by Mutans Streptococci
11:09

An Analytical Tool-box for Comprehensive Biochemical, Structural and Transcriptome Evaluation of Oral Biofilms Mediated by Mutans Streptococci

Published on: January 25, 2011

17.7K
A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
00:09

A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools

Published on: August 21, 2019

7.3K
Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

2.2K

Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Three-dimensional (3D) chromosome structures are integral to chromosomal functions.
  • Chromosome conformation capture (3C) techniques coupled with next-generation sequencing (NGS) have advanced the study of 3D genome organization.
  • Understanding these structures is key to elucidating their functional roles.

Purpose of the Study:

  • To provide a foundational method for Micro-C analysis.
  • To detail the steps involved in analyzing Micro-C data.
  • To facilitate the investigation of 3D chromosome organization and function.

Main Methods:

  • Micro-C technique for high-resolution 3D chromosome structure determination.
  • Next-generation sequencing (NGS) for comprehensive data acquisition.
  • Bioinformatic pipelines for data processing, including mapping and downstream analyses.

Main Results:

  • A reproducible protocol for Micro-C data analysis is presented.
  • The method allows for the detection of structural features like loops at nucleosome resolution.
  • Demonstrates a workflow from raw sequencing reads to biologically relevant insights.

Conclusions:

  • Micro-C offers a powerful approach to study 3D genome architecture at an unprecedented resolution.
  • The provided methods enable researchers to perform detailed analyses of chromosome conformation.
  • This facilitates a deeper understanding of the relationship between genome structure and function.