Gene expression profiling

Disclosed are methods and compositions for manipulating and detecting nucleic acids. The method generally involves association of a rolling circle replication primer with a cDNA strand. Preferred forms of the methods involve replicating one or more amplification target circles to produce one or more tandem sequence DNAs. Such replication is referred to as rolling circle replication. Preferably, each tandem sequence DNA is coupled to a rolling circle replication primer and the rolling circle replication primer is associated with a cDNA strand. In some embodiments the rolling circle replication primer comprises a capture tag and the association occurs via the capture tag. In some embodiments the cDNA strand is hybridized to a capture probe. Preferably, the cDNA strand comprises an RT primer, wherein the cDNA strand is produced by reverse transcribing a nucleic acid sample with the RT primer.