Expression monitoring to high density oligonucleotide arrays

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 cm 2 , 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.

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.    
     
     
         2 - 54 . (canceled)  
     
     
         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 μl 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.  
     
     
         56 . The method according to  claim 55 , wherein said sample volume ranges from about 1 μl to about 5 μl.  
     
     
         57 . The method according to  claim 55 , wherein said conditions comprise incubating said array with said sample for a period of time that does not exceed about 4 hours.  
     
     
         58 . The method according to  claim 57 , wherein said period of time ranges from about 1 hour to about 3 hours.  
     
     
         59 . The method according to  claim 55 , wherein said at least one target biomolecule is a nucleic acid.  
     
     
         60 . The method according to  claim 55 , wherein said substrate comprises a plurality of arrays and said method further comprises contacting each of said plurality of arrays with a sample comprising at least one labeled target biomolecule to simultaneously evaluate each sample of said plurality of samples.  
     
     
         61 . The method according to  claim 60 , wherein at least two of said plurality of arrays are different.  
     
     
         62 . The method according to  claim 60 , wherein each of said plurality of samples is the same.  
     
     
         63 . The method according to  claim 60 , wherein at least two samples of said plurality of samples are different.  
     
     
         64 . The method according to  claim 55 , wherein said at least one labeled target biomolecule is a fluorescently labeled target biomolecule.  
     
     
         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.  
     
     
         66 . The method according to  claim 65 , wherein said period of time ranges from about 1 hour to about 3 hours.  
     
     
         67 . The method according to  claim 65 , wherein a quantity of said sample that does not exceed about 5 μl is contacted to said array.  
     
     
         68 . The method according to  claim 67 , wherein said quantity ranges in size from about 1 μl to about 5 μl.  
     
     
         69 . The method according to  claim 65 , wherein said at least one labeled target biomolecule is a nucleic acid.  
     
     
         70 . The method according to  claim 65 , wherein said substrate comprises a plurality of arrays and said method further comprises contacting each of said plurality of arrays with a plurality of samples, respectively, each sample comprising at least one detectably-labeled target biomolecule, to simultaneously evaluate each sample of said plurality of samples.  
     
     
         71 . The method according to  claim 70 , wherein at least two of said plurality of arrays are different.  
     
     
         72 . The method according to  claim 70 , wherein each of said plurality of samples is the same.  
     
     
         73 . The method according to  claim 70 , wherein at least two samples of said plurality of samples are different.  
     
     
         74 . The method according to  claim 65 , wherein said at least one labeled target biomolecule is a fluorescently labeled target biomolecule.  
     
     
         75 . A method of performing a biopolymeric array assay, said method comprising: (a) evaluating whether a sample of at least one detectably labeled target biomolecule is suitable for use in an array assay according to the method of  claim 55;  and (b) performing an array assay with said evaluated sample.  
     
     
         76 . The method according to  claim 75 , further comprising reading the result of said array assay.  
     
     
         77 . A method comprising forwarding data representing a result of a reading obtained by the method of  claim 75 .  
     
     
         78 . The method according to  claim 77 , wherein said data is transmitted to a remote location.  
     
     
         79 . A method comprising receiving data representing a result of a reading obtained by the method of  claim 75 .  
     
     
         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 μl.  
     
     
         81 . The device according to  claim 80 , wherein said evaluation array comprises from about 4 to about 1000 features of probe molecules.  
     
     
         82 . The device according to  claim 81 , wherein about 1,000 to about 100,000 probe molecules are present in each feature.  
     
     
         83 . The device according to  claim 81 , wherein at least some of said features comprise probes of repetitive sequences.  
     
     
         84 . The device according to  claim 80 , wherein at lease one evaluation array comprises tiled probes.  
     
     
         85 . The device according to  claim 80 , wherein said substrate comprises a plurality of evaluation arrays.  
     
     
         86 . The device according to  claim 85 , wherein at least two of said plurality of evaluation arrays are different.  
     
     
         87 . The device according to  claim 80 , wherein said at least one evaluation array includes probes to relatively well-conserved genes between at least two species.  
     
     
         88 . A kit for evaluating the quality of a sample of at least one labeled target biomolecule as suitable for use in a biopolymeric array assay, said kit comprising: (a) at least one array; and (b) instructions for using said at least one evaluation array to evaluate the whether a sample is suitable for use in a biopolymeric array assay according to the method of  claim 1 .  
     
     
         89 . The kit according to  claim 88 , further including components for labeling said sample with a detectable label.  
     
     
         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 μl 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.  
     
     
         91 . A method according to  claim 90 , wherein said conditions comprise incubating said array with said sample for 90 minutes.  
     
     
         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.  
     
     
         93 . A method according to  claim 92 , wherein a quantity of said sample that does not exceed about 10 μl is contacted to said array.  
     
     
         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 μl.