Expression monitoring to high density oligonucleotide arrays
First Claim
1. A method of simultaneously monitoring the expression of a multiplicity of genes, said method comprising:
- (a) providing a pool of target nucleic acids comprising RNA transcripts of one or more of said genes, or nucleic acids derived from said RNA transcripts;
(b) hybridizing said pool of nucleic acids to an array of oligonucleotide probes immobilized on a surface, said array comprising more than 100 different oligonucleotides wherein each different oligonucleotide is localized in a predetermined region of said surface, the density of said different oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and said oligonucleotide probes are complementary to said RNA transcripts or said nuceic acids derived from said RNA transcripts; and
(c) quantifying the hybridization of said nucleic acids to said array.
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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
94 Claims
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1. A method of simultaneously monitoring the expression of a multiplicity of genes, said method comprising:
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(a) providing a pool of target nucleic acids comprising RNA transcripts of one or more of said genes, or nucleic acids derived from said RNA transcripts;
(b) hybridizing said pool of nucleic acids to an array of oligonucleotide probes immobilized on a surface, said array comprising more than 100 different oligonucleotides wherein each different oligonucleotide is localized in a predetermined region of said surface, the density of said different oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and said oligonucleotide probes are complementary to said RNA transcripts or said nuceic acids derived from said RNA transcripts; and
(c) quantifying the hybridization of said nucleic acids to said array. - View Dependent Claims (88, 89)
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2. -54. (canceled)
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55. A method for evaluating whether a sample of at least one labeled target biomolecule is suitable for use in a biopolymeric array assay, said method comprising:
- (a) providing a substrate having an array thereon;
(b) contacting said array with a volume that does not exceed about 5 μ
l of said sample;
(c) detecting any resultant surface bound target biomolecules to obtain signal data; and
(d) processing said signal data to evaluate whether said sample of at least one detectably labeled target biomolecule is suitable for use in a biopolymeric array assay. - View Dependent Claims (56, 57, 58, 59, 60, 61, 62, 63, 64, 75, 76, 77, 78, 79)
- (a) providing a substrate having an array thereon;
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65. A method for evaluating the quality a sample of at least one detectably-labeled target biomolecule as suitable for use in a biopolymeric array assay, said method comprising:
- (a) providing a substrate having an array thereon;
(b) contacting said array with said sample;
(c) incubating said array and said sample for a period of time that does not exceed about 4 hours;
(d) detecting any resultant surface bound detectably-labeled target biomolecules to obtain signal data; and
(e) processing said signal data to evaluate whether said sample of at least one detectably labeled target biomolecule is suitable for use in a biopolymeric array assay. - View Dependent Claims (66, 67, 68, 69, 70, 71, 72, 73, 74)
- (a) providing a substrate having an array thereon;
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80. A device for evaluating the quality of a sample of at least one labeled target biomolecule as suitable for use in a biopolymeric array assay, said device comprising:
- a substrate having at least one evaluation array thereon, wherein said at least one evaluation array is configured to evaluate said sample using a volume of said sample that does not exceed about 5 μ
l. - View Dependent Claims (81, 82, 83, 84, 85, 86, 87)
- a substrate having at least one evaluation array thereon, wherein said at least one evaluation array is configured to evaluate said sample using a volume of said sample that does not exceed about 5 μ
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90. A method for evaluating whether a sample of at least one labeled target biomolecule is suitable for use in a biopolymeric array assay, said method comprising:
- (a) providing a substrate having an array thereon;
(b) contacting said array with a volume that does not exceed about 10 μ
l of said sample;
(c) detecting any resultant surface bound target biomolecules to obtain signal data; and
(d) processing said signal data to evaluate whether said sample of at least one detectably labeled target biomolecule is suitable for use in a biopolymeric array assay. - View Dependent Claims (91)
- (a) providing a substrate having an array thereon;
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92. A method for evaluating the quality a sample of at least one detectably-labeled target biomolecule as suitable for use in a biopolymeric array assay, said method comprising:
- (a) providing a substrate having an array thereon;
(b) contacting said array with said sample;
(c) incubating said array and said sample for a period of time is 90 minutes;
(d) detecting any resultant surface bound detectably-labeled target biomolecules to obtain signal data; and
(e) processing said signal data to evaluate whether said sample of at least one detectably labeled target biomolecule is suitable for use in a biopolymeric array assay. - View Dependent Claims (93)
- (a) providing a substrate having an array thereon;
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94. A device for evaluating the quality of a sample of at least one labeled target biomolecule as suitable for use in a biopolymeric array assay, said device comprising:
- a substrate having at least one evaluation array thereon, wherein said at least one evaluation array is configured to evaluate said sample using a volume of said sample that does not exceed about 10 μ
l.
- a substrate having at least one evaluation array thereon, wherein said at least one evaluation array is configured to evaluate said sample using a volume of said sample that does not exceed about 10 μ
Specification