Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer

We describe a flexible system for gene expression profiling using arrays of tens of thousands of oligonucleotides synthesized in situ by an ink-jet pr inting method employing standard phosphoramidite chemistry. We have charact erized the dependence of hybridization specificity and sensitivity on param eters including oligonucleotide length, hybridization stringency, sequence identity, sample abundance, and sample preparation method. We find that 60- mer oligonucleotides reliably detect transcript ratios at one copy per cell in complex biological samples, and that ink-jet arrays are compatible with several different sample amplification and labeling techniques. Furthermor e, results using only a single carefully selected oligonucleotide per gene correlate closely with those obtained using complementary DNA (cDNA) arrays . Most of the genes for which measurements differ are members of gene famil ies that can only be distinguished by oligonucleotides. Because different o ligonucleotide sequences can be specified for each array, we anticipate tha t ink-jet oligonucleotide array technology will be useful in a wide variety of DNA microarray applications.