Microarray device with optimized indicator polynucleotides

Abstract

Optimization techniques for selecting indicator polynucleotides for an experiment and for determining expression levels resulting from the experiment. The optimization technique corrects for variations in polynucleotide melting temperatures during analysis of the experimental results. The optimization technique selects set of indicator polynucleotides for the experiment. The optimization technique then performs the experiment with the indicator polynucleotides and a sample and identifies the relative amounts of the indicated polynucleotides. The optimization technique then adjusts the relative amounts of the indicated polynucleotides based on melting temperatures associated with the indicator polynucleotides.

1 - 22 . (canceled)  
     
     
         23 . A nucleotide array, comprising: an exon-exon junction indicator polynucleotide, comprised of a first portion that indicates a 5′ exon of an exon-exon junction and a second portion that indicates a 3′ exon of an exon-exon junction, the first portion and the second portion each having a length, wherein the length of the first portion is equal to the length of the second portion.  
     
     
         24 . The array of  claim 23 , comprised of a plurality of said exon-exon junction indicator polynucleotides.  
     
     
         25 . The array of  claim 24 , wherein the plurality comprises indicator polynucleotides for all exon-exon junctions of a splice variant of a gene.  
     
     
         26 . The array of  claim 24 , wherein the plurality comprises indicator polynucleotides for exon-exon junctions of multiple splice variants of a gene.  
     
     
         27 . The array of  claim 24 , wherein the plurality comprises indicator polynucleotides for all exon-exon junctions of multiple splice variants of a gene.  
     
     
         28 . The array of  claim 24 , wherein the plurality comprises at least about 17 indicator polynucleotides.  
     
     
         29 . The array of  claim 24 , wherein each indicator polynucleotide has a length, and wherein the length of each indicator polynucleotide is the same.  
     
     
         30 . The array of  claim 23 , wherein the array further comprises a plurality of exon indicator polynucleotides.  
     
     
         31 . A nucleotide array, comprising: an exon-exon junction indicator polynucleotide comprised of a first portion that indicates a 5′ exon of an exon-exon junction and a second portion that indicates a 3′ exon of an exon-exon junction, the first portion and the second portion each having a length, wherein the length of the first portion is not equal to the length of the second portion.  
     
     
         32 . The array of  claim 31 , comprised of a plurality of said exon-exon junction indicator polynucleotides.  
     
     
         33 . The array of  claim 32 , wherein the plurality comprises indicator polynucleotides for all exon-exon junctions of a splice variant of a gene.  
     
     
         34 . The array of  claim 32 , wherein the plurality comprises indicator polynucleotides for exon-exon junctions of multiple splice variants of a gene.  
     
     
         35 . The array of  claim 32 , wherein the plurality comprises indicator polynucleotides for all exon-exon junctions of multiple splice variants of a gene.  
     
     
         36 . The array of  claim 32 , wherein the plurality comprises at least about 17 indicator polynucleotides.  
     
     
         37 . The array of  claim 32 , wherein each indicator polynucleotide has a length, and wherein the length of each indicator polynucleotide is the same.  
     
     
         38 . The array of  claim 32 , wherein each indicator polynucleotide has a length, and wherein the length of each indicator polynucleotide is not the same.  
     
     
         39 . A nucleotide array, comprising: an exon-exon junction indicator polynucleotide comprised of a first portion that indicates a 5′ exon of an exon-exon junction and a second portion that indicates a 3′ exon of an exon-exon junction, wherein the first portion has a melting temperature and the second portion has a melting temperature, and wherein the melting temperature of the first portion approximately equals the melting temperature of the second portion.  
     
     
         40 . The array of  claim 39 , wherein the first portion has a length and the second portion has a length, and wherein the length of the first portion is equal to the length of the second portion.  
     
     
         41 . The array of  claim 39 , wherein the first portion has a length and the second portion has a length, and wherein the length of the first portion is not equal to the length of the second portion.  
     
     
         42 . The array of  claim 39 , comprised of a plurality of said exon-exon indicator polynucleotides.  
     
     
         43 . The array of  claim 40 , wherein the plurality comprises indicator polynucleotides for all exon-exon junctions of a splice variant of a gene.  
     
     
         44 . The array of  claim 40 , wherein the plurality comprises indicator polynucleotides for exon-exon junctions of multiple splice variants of a gene.  
     
     
         45 . The array of  claim 40 , wherein the plurality comprises indicator polynucleotides for all exon-exon junctions of multiple splice variants of a gene.  
     
     
         46 . The array of  claim 40 , wherein the plurality comprises at least about 17 indicator polynucleotides.  
     
     
         47 . The array of  claim 40 , wherein each indicator polynucleotide has a length, and wherein the length of each indicator polynucleotide is the same.  
     
     
         48 . The array of  claim 40 , wherein each indicator polynucleotide has a length, and wherein the length of each indicator polynucleotide is not the same.  
     
     
         49 . The array of  claim 43 , wherein for each indicator polynucleotide for the exon-exon junctions of the splice variant, the melting temperature of the first portion and the melting temperature of the second portion differ by about 0.95 degrees Celsius or less.  
     
     
         50 . A nucleotide array, comprising: a plurality of exon indicator polynucleotides for exons of a splice variant of a gene comprised of a plurality of exons.  
     
     
         51 . The array of  claim 50 , further comprising a plurality of exon indicator polynucleotides for exons of multiple splice variants of the gene.  
     
     
         52 . The array of  claim 50 , further comprising a plurality of exon indicator polynucleotides for all exons of multiple splice variants of the gene.  
     
     
         53 . The array of  claim 50 , wherein each indicator polynucleotide has a length, and wherein the length of each indicator polynucleotide is the same.  
     
     
         54 . The array of  claim 50 , wherein the gene is comprised of a plurality of at least about 18 exons.  
     
     
         55 . The array of  claim 50 , wherein each indicator polynucleotide has a length, and wherein the length of each indicator polynucleotide is not the same.  
     
     
         56 . The array of  claim 55 , wherein each indicator polynucleotide has a melting temperature, and wherein the melting temperatures of each indicator polynucleotides is approximately the same.  
     
     
         57 . The array of  claim 55 , wherein each indicator polynucleotide has a melting temperature, and wherein the melting temperatures of the indicator polynucleotides differ by about 2.52 degrees Celsius or less.