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Universal Reference RNA as a standard for microarray experiments.

Natalia Novoradovskaya1, Michael L Whitfield, Lee S Basehore

  • 1Stratagene, 11011 N, Torrey Pines Road, La Jolla, CA 92037, USA. nnovo@stratagene.com

BMC Genomics
|April 29, 2004
PubMed
Summary
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Universal Reference RNA (URR) provides a reliable standard for two-color microarray gene expression experiments. Pooled RNA from multiple cell lines ensures reproducible results and diverse gene representation, reducing experimental variation.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Two-color microarray gene expression analysis is crucial for biological research.
  • Controlling variables like RNA preparation and hybridization is challenging.
  • Universal Reference RNA (URR) minimizes experimental variation by normalizing signal output.

Purpose of the Study:

  • To assess the reproducibility and gene representation of Universal Reference RNA (URR).
  • To establish URR as a standard for reducing variability in microarray experiments.

Main Methods:

  • Prepared human, mouse, and rat URR (UHRR, UMRR, URRR) from pooled RNA of diverse cell lines.
  • Utilized various microarrays to determine microarray coverage with URR.
  • Assessed reproducibility by comparing independently prepared batches of URR.

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Main Results:

  • Microarray coverage with URR consistently exceeded 80%.
  • Pooled RNA from multiple cell lines demonstrated diverse gene representation.
  • Independently prepared URR batches showed high correlation (Pearson's r=0.97), indicating reproducibility.

Conclusions:

  • Pooled RNA from individual cell lines can be reproducibly prepared in large quantities with diverse gene representation.
  • URR serves as a valuable standard for reducing variation in microarray experiments.
  • URR enables more reliable comparisons of gene expression data across experiments and laboratories.