Expression monitoring by hybridization to high density oligonucleotide arrays
First Claim
1. A method for monitoring hybridization of an eukaryotic nucleic acid sample to a nucleic acid array, said method comprising the steps of:
- (a) providing a nucleic acid array comprising a plurality of nucleic acid test probes that specifically bind to eukaryotic nucleic acid targets and at least one control probe that specifically binds to a bacterial gene;
(b) providing a spiked sample comprising an eukaryotic nucleic acid sample with a nucleic acid control, said control comprising a nucleic acid that specifically binds to the control probe;
(c) contacting said spiked sample with said array; and
(d) determining whether hybridization occurred between the control probe and the nucleic acid control.
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Abstract
This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample. In one embodiment, the method involves providing a pool of target nucleic acids comprising RNA transcripts of one or more target genes, or nucleic acids derived from the RNA transcripts, hybridizing said pool of nucleic acids to an array of oligonucleotide probes immobilized on surface, where the array comprising more than 100 different oligonucleotides and each different oligonucleotide is localized in a predetermined region of the surface, the density of the different oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and the olignucleotide probes are complementary to the RNA transcripts or nucleic acids derived from the RNA transcripts; and quantifying the hybridized nucleic acids in the array.
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Citations
25 Claims
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1. A method for monitoring hybridization of an eukaryotic nucleic acid sample to a nucleic acid array, said method comprising the steps of:
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(a) providing a nucleic acid array comprising a plurality of nucleic acid test probes that specifically bind to eukaryotic nucleic acid targets and at least one control probe that specifically binds to a bacterial gene;
(b) providing a spiked sample comprising an eukaryotic nucleic acid sample with a nucleic acid control, said control comprising a nucleic acid that specifically binds to the control probe;
(c) contacting said spiked sample with said array; and
(d) determining whether hybridization occurred between the control probe and the nucleic acid control. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24)
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25. A method for performing control hybridization reactions for hybridization of an eukaryotic nucleic acid sample to a nucleic acid array, the method comprising the steps of:
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(a) providing a nucleic acid array comprising a plurality of probes, wherein two or more of said probes comprise control probes that specifically bind to different bacterial genes not normally found in said eukaryotic nucleic acid sample;
(b) providing a spike sample comprising said eukaryotic nucleic acid sample with nucleic acid controls, each of the controls comprising a nucleic acid that specifically binds to one of the control probes;
(c) contacting said spiked sample to the array; and
(d) determining whether hybridization occurred to said control probes.
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Specification