Use of bioanalyzer electropherograms for quality control and target evaluation in microarray expression profiling studies of ocular tissues

Christina (Chris) Harrington, Winther Michael Winther, M. Garred Michelle

    Research output: Contribution to journalArticle

    4 Citations (Scopus)

    Abstract

    Expression profiling with DNA microarrays has been used to examine the transcriptome of a wide spectrum of vertebrate cells and tissues. The sensitivity and accuracy of the data generated is dependent on the quality and composition of the input RNA. In this report, we examine the quality and array performance of over 200 total RNA samples extracted from ocular tissues and cells that have been processed in a microarray core laboratory over a 7-year period. Total RNA integrity and cRNA target size distribution were assessed using the 2100 Bioanalyzer. We present Affymetrix GeneChip array performance metrics for different ocular samples processed according to a standard microarray assay workflow including several quality control checkpoints. Our review of ocular sample performance in the microarray assay demonstrates the value of considering tissue-specific characteristics in evaluating array data. Specifically, we show that Bioanalyzer electropherograms reveal highly abundant mRNAs in lacrimal gland targets that are correlated with variation in array assay performance. Our results provide useful benchmarks for other gene expression studies of ocular systems.

    Original languageEnglish (US)
    Pages (from-to)243-249
    Number of pages7
    JournalJournal of Ocular Biology, Diseases, and Informatics
    Volume2
    Issue number4
    DOIs
    StatePublished - Dec 2009

    Fingerprint

    Quality Control
    RNA
    Benchmarking
    Lacrimal Apparatus
    Complementary RNA
    Workflow
    Oligonucleotide Array Sequence Analysis
    Transcriptome
    Vertebrates
    Gene Expression
    Messenger RNA

    Keywords

    • Capillary electrophoresis
    • DNA microarrays
    • Gene expression
    • Lacrimal gland
    • MRNA
    • RNA quality

    ASJC Scopus subject areas

    • Ophthalmology
    • Genetics

    Cite this

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    abstract = "Expression profiling with DNA microarrays has been used to examine the transcriptome of a wide spectrum of vertebrate cells and tissues. The sensitivity and accuracy of the data generated is dependent on the quality and composition of the input RNA. In this report, we examine the quality and array performance of over 200 total RNA samples extracted from ocular tissues and cells that have been processed in a microarray core laboratory over a 7-year period. Total RNA integrity and cRNA target size distribution were assessed using the 2100 Bioanalyzer. We present Affymetrix GeneChip array performance metrics for different ocular samples processed according to a standard microarray assay workflow including several quality control checkpoints. Our review of ocular sample performance in the microarray assay demonstrates the value of considering tissue-specific characteristics in evaluating array data. Specifically, we show that Bioanalyzer electropherograms reveal highly abundant mRNAs in lacrimal gland targets that are correlated with variation in array assay performance. Our results provide useful benchmarks for other gene expression studies of ocular systems.",
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    author = "Harrington, {Christina (Chris)} and {Michael Winther}, Winther and Michelle, {M. Garred}",
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    AU - Michael Winther, Winther

    AU - Michelle, M. Garred

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    KW - MRNA

    KW - RNA quality

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