Analysis of gene expression, methods and reagents therefor

A method for detecting the presence of a selected nucleotide sequence in a nucleic acid sample, comprising

• (i) isolating discrete nucleotide sequences representative of a nucleic acid sample, by
• (a) cleaving, at a first cleavage site, the nucleic acids of the sample to produce cleaved nucleic acids,
• (b) ligating a linker nucleic acid sequence to the cleaved nucleic acids to produce chimeric linker nucleic acids of the general formula L--N, wherein L is the linker nucleotide sequence and N is a sample nucleotide sequence from the nucleic acid sample,
• (c) cleaving, at a second cleavage site, the chimeric linker nucleic acids within the sample nucleotide sequence to produce linker-TAG fragments of the general formula L--N', wherein L is the linker nucleotide sequence and N' is a portion of the nucleic acid sequence N,
• (ii) ligating the linker-TAG fragments to form variegated head to tail concatenated arrays, and
• (iii) determining the number of occurrences of a selected nucleotide sequence in the concatenated arrays.