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Table 1 Nomenclature

From: An analysis of the use of genomic DNA as a universal reference in two channel DNA microarrays

Symbol Description
S cDNA sample anti-sense strand
R Genomic DNA anti-sense strand
R' Genomic DNA sense strand
B Bound (immobilized) anti-sense strand
B' Bound (immobilized) sense strand
Subscript 0 Initial concentration
SR' Double strand formed in solution by hybridization of anti-sense cDNA strand and sense genomic DNA strand
RR' Double strand formed in solution by hybridization of anti-sense and sense genomic DNA strands
SB' Double strand formed on surface by hybridization of anti-sense cDNA strand and sense bound strands
RB' Double strand formed on surface by hybridization of anti-sense genomic DNA strand and sense bound strands
R'B Double strand formed on surface by hybridization of sense genomic DNA strand and anti-sense bound strands
h Height of spot phase
r Radius of spot phase
kb Rate constant of backward reaction of hybridization
kf Rate constant of forward reaction of hybridization between mobile species
kf-bound Rate constant of forward reaction of hybridization between mobile and bound species
kt Rate constant for transport between the two phases
γ Ratio obtained from a hybridization assay using genomic DNA as a reference { = [SB']/([RB']+[R'B])}
α Assay efficiency = (γ12)/(S10/S20), where 1 and 2 denote samples 1 and 2
εS Amount of S reacted with R'
εR Amount of R reacted with R'