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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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Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
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What is Gene Expression?01:36

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A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and...
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Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform
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A Brassica exon array for whole-transcript gene expression profiling.

Christopher G Love1, Neil S Graham, Seosamh O Lochlainn

  • 1Rothamsted Research, Harpenden, UK.

Plos One
|September 24, 2010
PubMed
Summary
This summary is machine-generated.

A new whole-transcript (WT) exon array for Brassica transcriptomics was developed. This robust Affymetrix GeneChip® platform enhances the study of complex crop genomes like Brassica.

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Area of Science:

  • Plant genomics and transcriptomics
  • Development of high-throughput molecular tools
  • Crop science and breeding

Background:

  • Affymetrix GeneChip® arrays are widely used for studying transcriptional changes.
  • Existing plant GeneChip® arrays primarily target 3' exons, limiting resolution for complex genomes.
  • Complex crop genomes like Brassica require whole-transcript (WT) array resolution due to duplications and polyploidy.

Purpose of the Study:

  • To develop a comprehensive public whole-transcript (WT) exon array for Brassica transcriptomics.
  • To address the limitations of existing arrays for studying complex Brassica genomes.
  • To provide a robust platform for high-resolution transcriptomic analysis in Brassica.

Main Methods:

  • Assembled 142,997 gene models from Brassica A and C genomes.
  • Designed the Affymetrix GeneChip® Brassica Exon 1.0 ST Array with 2.4 million probes targeting 135,201 gene models.
  • Validated the array by comparing transcriptomes of leaf and root tissues and cross-validating with a 60-mer array platform.

Main Results:

  • Developed a 135 k Brassica Exon Array with 15 probes per gene distributed across exons.
  • The array demonstrated robust performance in differentiating transcriptomes between tissues.
  • Gene models were discriminated using an E-value cut-off of 1E(-5) and ≤98% sequence identity.

Conclusions:

  • The 135 k Brassica Exon Array is a validated and robust platform for Brassica transcriptomics.
  • This array facilitates high-resolution studies of complex Brassica genomes.
  • All array design data are publicly available via the BrassEnsembl genome viewer.