Methods for gene expression profiling

A method for determining differences in gene expression profiles between control and tester nucleic acid samples comprising;

• a) providing a control nucleic acid sample and a tester nucleic acid sample;
• b) fragmenting said control and tester nucleic acid samples;
• c) ligating a first adapter molecule to said control nucleic acid sample and ligating a second adapter molecule to said tester nucleic acid sample;
• d) subjecting said control and tester nucleic acid sample to conditions wherein hybridization between said control and tester nucleic acids samples occurs;
• e) further subjecting said hybridized nucleic acid samples to a first polymerase chain reaction using a plurality of primers which are complementary to said first and second adapter molecules respectively, in the presence of a first and second detectable label;
• g) isolating products obtained from the polymerase chain reactions of step e);
• h) denaturing said polymerase chain reaction products;
• i) hybridizing said labeled, denatured products to a microarray chip comprising a multitude of target gene sequences;
• j) determining the amount and identity of said nucleic acids in the control and tester samples as a function of position on said microarray chip, and presence of said detectable label;
• and
• k) comparing the amplified products obtained from said control and tester nucleic acid samples to determine differences in gene expression profiles between said control and tester nucleic acid samples.