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DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Related Experiment Video

Updated: Apr 3, 2026

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

HiCPlotter integrates genomic data with interaction matrices.

Kadir Caner Akdemir¹, Lynda Chin^2,3

¹Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. kcakedemir@mdanderson.org.

|September 23, 2015

Summary

This summary is machine-generated.

This study introduces HiCPlotter, an open-source tool for visualizing chromatin architecture. It aids in understanding the link between nuclear organization and gene regulation by comparing genomic data.

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Last Updated: Apr 3, 2026

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

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Published on: November 3, 2023

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Published on: May 6, 2010

Capturing Chromosome Conformation Across Length Scales

Capturing Chromosome Conformation Across Length Scales

Published on: January 20, 2023

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Metazoan genomes fold into complex chromosomal structures influencing gene expression and DNA replication.
Chromatin architecture is regulated by factors like pluripotency factors, long non-coding RNAs, and architectural proteins.

Purpose of the Study:

To develop a user-friendly tool for visualizing and comparing complex chromatin interaction data.
To facilitate the integration of Hi-C data with other genomic assays for a comprehensive understanding of nuclear organization.

Main Methods:

Development of an open-source software tool named HiCPlotter.
Implementation of features for juxtaposing Hi-C matrices with diverse genomic assay outputs.
Enabling comparison of interaction matrices across different experimental conditions.

Main Results:

HiCPlotter provides an accessible platform for visualizing multi-faceted chromatin structures.
The tool simplifies the comparison of Hi-C data, aiding in the analysis of nuclear architecture.
Facilitates research into the connections between chromatin organization and transcriptional regulation.

Conclusions:

HiCPlotter is a valuable open-source resource for researchers studying chromatin architecture and its regulatory roles.
The tool enhances the ability to analyze and interpret complex genomic interaction data.
Aids in unraveling the intricate relationship between nuclear organization and cellular functions.