AMPLIFIED PROBES FOR DNA ARRAYS

Sidney Kimmel Cancer Center, San Diego CA

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Linked publications & trials

Abstract

We have developed a simple and generally accessible method to allow inexpensive arrays of EST clones on membranes to be used for differential gene expression studies. This method, based non- stoichiometric sampling of mRNAs, allows extremely rare mRNAs to be detected on inexpensive arrays while also lowering the background hybridization. As our first aims, we propose technology development to further explore non-stoichiometric sampling and reduction of probe complexity. These efforts will be directed towards increasing the number of genes detected by each probe and biasing sampling towards particular gene sets. The method uses two orders of magnitude less RNA than other current non-amplification methods. We aim to reduced the RNA requirement even further so that we may be able to apply the method to very small tissue samples. As a final aim we propose a simple demonstration project for this technology. We will treat a cell line with twenty drugs and hormones to define over three billion potential co-regulatory patterns (up, down, unchanged), of which only a small subset will actually be occupied by genes. Genes that parse into regulated regulatory groups, as defined by the database of arbitrary treatments, are likely to share physiologically relevant regulatory components.