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Array Analysis: The Basics

  • Hybridizing the labeled cDNA to identical membrane or glass slide arrays
  • Removing the unhybridized cDNA
  • Detecting and quantitating the hybridized cDNA, and
  • Comparing the quantitative data from the various samples
  • Some array manufacturers offer custom analysis services and may perform the probe labeling and hybridization reactions as a service.


    Nylon Membrane Arrays
    Nylon membrane arrays are typically hybridized with 33P-dNTP labeled probes and analyzed by a phosphorimager along with the appropriate software. A different array must be used for each sample analyzed. A typical experiment involves isolating RNA from two tissue or cell samples. The RNAs are reverse transcribed using labeled nucleotides and target specific, oligo dT, or random-sequence primers to create two labeled cDNA populations. The two cDNAs are hybridized to two identical arrays. After washing, the hybridized signal on each array is detected and analyzed. The signal emitting from each gene-specific spot is compared between the populations. Genes expressed at different levels in two samples generate different amounts of labeled cDNA and this results in spots on the array with different amounts of signal.


    Glass Slide Arrays
    Glass slide arrays analysis involves the same steps, but rather than labeling with isotopes during reverse
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