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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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Related Experiment Video

Updated: Jun 10, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression.

Hang He1, Huiyong Zhang, Xiangfeng Wang

  • 1Bioinformatics Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Genomics
|August 7, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a novel oligonucleotide tiling microarray for distinguishing gene expression from different rice alleles. The method effectively identifies and quantifies allele-specific transcripts, aiding in the study of gene expression.

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Last Updated: Jun 10, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
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Published on: November 3, 2010

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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
11:52

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Area of Science:

  • Genomics
  • Molecular Biology
  • Plant Science

Background:

  • Distinguishing allele-specific transcripts is crucial for understanding gene expression.
  • Existing methods may lack the specificity or scalability for large-scale SNP analysis.

Purpose of the Study:

  • To develop and validate an oligonucleotide tiling microarray for interrogating single nucleotide polymorphisms (SNPs) between rice subspecies.
  • To quantify allele-specific gene expression in rice hybrids.

Main Methods:

  • Designed a tiling microarray targeting 518 SNPs between indica and japonica rice subspecies.
  • Utilized a titration series and regression model to identify diagnostic probe sets.
  • Validated findings using RNA-sequencing and allele-specific real-time PCR.

Main Results:

  • Developed a microarray capable of interrogating 518 SNPs.
  • Identified diagnostic probe pairs for 55% of the targeted SNPs.
  • Detected imbalanced allele-specific expression in approximately one third of SNPs in rice hybrids.

Conclusions:

  • Oligonucleotide tiling microarrays are effective for quantifying allele-specific gene expression.
  • This method offers advantages for large-scale SNP interrogation and gene expression analysis in plants.