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Cellular RNAs are believed to be comprehensively and reproducibly extracted by the conventional RNA purification methods. However, some RNA species – semi-extractable (SE) RNAs – seems to be purified less effectively by some reasons. Protein-coding transcripts along with long non-coding RNAs are able to demonstrate semi-extractability when are purified with improved extraction method. The improved method may become a powerful tool for understanding the roles of architectural RNAs and nuclear bodies composition under specific conditions. We showed that predominantly lncRNAs demonstrate semi-extractability, as well as nascent transcripts.