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Related Concept Videos

DNA Microarrays02:34

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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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

A genome-wide 20 K citrus microarray for gene expression analysis.

M Angeles Martinez-Godoy1, Nuria Mauri, Jose Juarez

  • 1Instituto de Biología Molecular y Celular de Plantas (IBMCP), Laboratorio de Genomica (Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas), Avenida de los Naranjos s/n, E46022 Valencia, Spain. mmargodo@ibmcp.upv.es

BMC Genomics
|July 5, 2008
PubMed
Summary
This summary is machine-generated.

A new citrus microarray with 21,081 unigenes and a companion database enables large-scale gene expression analysis. This tool improves functional genomics and aids in understanding citrus biology for crop improvement.

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Area of Science:

  • * Plant genomics
  • * Functional genomics
  • * Crop improvement

Background:

  • * Understanding genetic elements is crucial for improving citrus, an economically important crop.
  • * Global gene expression analysis requires high-genome-coverage microarray platforms.
  • * Genome-wide expressed sequence tag (EST) collections in citrus enable new functional genomics tools.

Purpose of the Study:

  • * To design and construct a publicly available, genome-wide cDNA microarray for citrus.
  • * To create a functional, web-browsable database for microarray unigene information.
  • * To assess the microarray's genome coverage and usability for gene expression studies.

Main Methods:

  • * Designed and constructed a genome-wide cDNA microarray with 21,081 putative unigenes.
  • * Developed a web-browsable database with comprehensive unigene annotation (sequences, BLAST hits, GO classification, etc.).
  • * Performed Gene Ontology comparison with Arabidopsis proteins for genome coverage estimation and microarray hybridizations for usability testing.

Main Results:

  • * A publicly available genome-wide cDNA microarray with 21,081 citrus unigenes was successfully created.
  • * A companion database provides extensive structural and functional annotation for all represented unigenes.
  • * Microarray hybridizations confirmed its usability and good representation of the citrus genome.

Conclusions:

  • * The new microarray enables gene expression analysis at a global scale, replacing the previous 7K version.
  • * Rational design minimizes cross-hybridization, ensuring utility across different citrus species.
  • * The integrated website and microarray serve as a valuable genomic tool for global citrus studies, demonstrated by cataloging gene expression in globular embryos.