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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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The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

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ArrayNinja: An Open Source Platform for Unified Planning and Analysis of Microarray Experiments.

B M Dickson¹, E M Cornett¹, Z Ramjan¹

¹Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, United States.

Methods in Enzymology

|July 18, 2016

Summary

This summary is machine-generated.

ArrayNinja software streamlines custom microarray experiment design and analysis for proteomic studies. This open-source tool enhances data interaction and centralization for chromatin biochemistry research.

Keywords:

Array construction Array quantification Array visualization Histone biochemistry Virtual tools

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Last Updated: Mar 17, 2026

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

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Published on: October 5, 2016

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

Published on: March 15, 2011

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Published on: October 11, 2012

Area of Science:

Biochemistry
Proteomics
Molecular Biology

Background:

Microarray-based proteomic platforms are essential for studying protein function, especially in chromatin biochemistry.
Current microarray technology offers design flexibility but lacks integrated software for custom print layout optimization and analysis.
Efficient experimental design and data analysis require streamlined informatics solutions.

Purpose of the Study:

To develop a portable, open-source, and interactive application for unified planning and visualization of custom microarray experiments.
To provide end users with maximum flexibility in designing and analyzing microarray experiments.
To enhance data interaction and centralization for microarray-based proteomic studies.

Main Methods:

Development of ArrayNinja, a novel software application.
Implementation of features for planning, storing, and merging microarray experimental data.
Integration of visualization tools for experiment analysis.

Main Results:

ArrayNinja offers a unified platform for planning and visualizing microarray experiments.
The application allows users to store experiments in a private database.
It enables merging of planned experiments with imaged results for enhanced data interaction.
Achieves a level of data interaction and centralization not available with current tools.

Conclusions:

ArrayNinja provides a flexible and integrated solution for custom microarray experiment design and analysis.
The software facilitates efficient multidimensional optimization of assay parameters.
ArrayNinja improves data management and accessibility in proteomic research, particularly for chromatin biochemistry.