Strategies for gene expression analysis
First Claim
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1. A method for screening a compound library to identify a compound with a physiological effect on a biological sample, the method comprising:
- (a) contacting a plurality of biological samples with a plurality of members of a compound library;
(b) obtaining an expressed RNA sample from each of the plurality of biological samples;
(c) producing a plurality of nucleic acid samples from the plurality of expressed RNA samples, said nucleic acid samples selected from;
(i) total cellular RNA or a subset thereof isolated from said biological samples;
(ii) mRNA isolated from said biological samples;
(iii) cDNA produced from (i) or (ii); and
(iv) nucleic acids amplified from (i), (ii) or (iii); and
wherein each nucleic acid sample comprises a plurality of different nucleic acid species;
(d) arraying said plurality of nucleic acid samples to produce a nucleic acid array, wherein each sample is deposited at a single unique location on the array;
(e) hybridizing a plurality of defined sequence probes to said nucleic acid array, which probes each comprise a different polynucleotide sequence, and which probes are each capable of generating a different detectable signal;
(f) quantitating a signal corresponding to hybridization of each of the plurality of defined sequence probes to the nucleic acid array, thereby generating a quantitated hybridization signal; and
,(g) detecting at least one quantitated hybridization signal that differs from a control hybridization signal, thereby identifying a compound that exerts a physiological effect on a biological sample; and
,(h) entering the quantitated hybridization signal into a database.
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Abstract
The invention provides methods for screening compound or chemical libraries by analyzing expressed RNA samples from biological samples treated with members of a compound library in a high throughput format.
21 Citations
50 Claims
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1. A method for screening a compound library to identify a compound with a physiological effect on a biological sample, the method comprising:
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(a) contacting a plurality of biological samples with a plurality of members of a compound library; (b) obtaining an expressed RNA sample from each of the plurality of biological samples; (c) producing a plurality of nucleic acid samples from the plurality of expressed RNA samples, said nucleic acid samples selected from; (i) total cellular RNA or a subset thereof isolated from said biological samples; (ii) mRNA isolated from said biological samples; (iii) cDNA produced from (i) or (ii); and (iv) nucleic acids amplified from (i), (ii) or (iii); and wherein each nucleic acid sample comprises a plurality of different nucleic acid species; (d) arraying said plurality of nucleic acid samples to produce a nucleic acid array, wherein each sample is deposited at a single unique location on the array; (e) hybridizing a plurality of defined sequence probes to said nucleic acid array, which probes each comprise a different polynucleotide sequence, and which probes are each capable of generating a different detectable signal; (f) quantitating a signal corresponding to hybridization of each of the plurality of defined sequence probes to the nucleic acid array, thereby generating a quantitated hybridization signal; and
,(g) detecting at least one quantitated hybridization signal that differs from a control hybridization signal, thereby identifying a compound that exerts a physiological effect on a biological sample; and
,(h) entering the quantitated hybridization signal into a database. - 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, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49)
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24. A method for simultaneously quantitating a plurality of expression products from a plurality of biological samples, the method comprising:
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(a) providing a plurality of biological samples; (b) obtaining expressed RNA samples from said biological samples; (c) amplifying a plurality of different members in said expressed RNA samples by selective amplification, thereby producing selectively amplified nucleic acid samples, said selectively amplified nucleic acid samples each comprising a plurality of amplified nucleic acid species; (d) arraying a plurality of said selectively amplified nucleic acid samples to produce at least one nucleic acid array, wherein each sample is deposited at a single unique location on the array; and (e) hybridizing a plurality of defined sequence probes to said nucleic acid array, which defined sequence probes each comprise a different polynucleotide sequence, and which probes are each capable of generating a different detectable signal, to the nucleic acid array; and
,(f) detecting a signal corresponding to hybridization to each of the plurality of defined sequence probes.
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50. A method of screening a compound library for an effect on an expression level in a biological sample, the method comprising:
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a.) contacting a plurality of biological samples with a plurality of members of the compound library; b.) obtaining an expressed RNA sample from each of the plurality of biological samples; c.) producing a nucleic acid sample from each of the expressed RNA samples, wherein each nucleic acid sample comprises a plurality of different nucleic acid species; d.) depositing the nucleic acid samples onto a solid phase array, wherein each sample is deposited at a single unique location on the array; e.) hybridizing a plurality of solution based defined sequence probes to the array, wherein each of the defined sequence probes comprises a different detectable label; and
,f.) detecting a signal from each of the defined sequence probes and comparing the signal to a control signal, thereby identifying a compound that has an effect on an expression level in the biological sample.
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Specification