Abstract: Methods are described to derive design sequences for the production of nucleic acid microarrays. The present methods use high throughput 3? sequencing of transcripts in a tissue sample or diseased state to design probes for nucleic acid microarrays. Also described are nucleic acid microarrays that possess probes directed to the extreme 3? end of transcripts in a tissue. These microarrays preferably represent alternate polyadenylation sequences that are specific to the tissue from which the transcripts are derived. Also described are methods of using the microarrays directed to the extreme 3? end of the transcript for evaluating gene expression in a tissue where there are reduced false positive and false negative results.