Patent ID: 7993837

Claim:
A method of preparing an array of oligonucleotides comprising (a) immobilizing oligonucleotide tags each comprising an oligonucleotide of more than 25 bp for identifying expressed genes on a solid support, wherein the oligonucleotide tags comprise nucleotide sequences determined by the following steps: 1) synthesizing at least one cDNA pool from mRNAs of expressed genes using a primer comprising a recognition sequence of a type III restriction enzyme and an oligo-dT sequence, and treating the cDNA pool with a second restriction enzyme; 2) purifying a poly(A)-containing fragment from the cDNA pool, and dividing the purified poly(A)-containing fragment such that some of the fragment is ligated to a linker A and some of the fragment is ligated to a linker B; 3) treating the fragments with the type III restriction enzyme, and ligating the resulting linker A-containing fragment to the resulting linker B-containing fragment; 4) removing linker sequences by cleaving the ligated fragments with the second restriction enzyme to obtain ditag oligonucleotides, wherein each ditag oligonucleotide contains two individual tags; 5) ligating ditag oligonucleotides to each other to prepare polynucleotides; 6) analyzing the nucleotide sequences of the above polynucleotides to determine the nucleotide sequences of tags contained in the polynucleotides; 7) analyzing the frequency of occurrence of individual tags among the sequenced polynucleotides; and 8) selecting individual tags based on their frequency; and (b) immobilizing control oligonucleotide tags on the solid support, wherein the control oligonucleotide tags comprise nucleotide sequences of the selected tags with two-base mismatches in positions 7 and 13.