A method is disclosed for the modification of an end of RNA molecules and the use of such modified RNA molecules in cDNA synthesis for the purpose of cloning, detection, sequencing, and amplification of parts of the RNAs, the entire RNAs, or any cDNAs derived from such modified RNAs. The invention relates further to the amplification and the identification of nucleic acid molecules for the purpose of single molecule detection and/or high-throughput sequencing. In addition, a method is provided for the preparation of pooled samples that contains molecules each of which is marked by an “Identifier Sequence” for its origin. The invention facilitates studies on biological systems and analysis of genes expressed therein.