Regulation of many nuclear functions in eukaryotic cells, such as transcription and splicing, relies on the association of specific genomic loci and/or transcripts with nuclear microenvironments having high molecular crowding, such as nuclear bodies. These membrane-less organelles are typically self-assembled through mechanisms of phase separation, and because of their liquid-like nature, analyzing their composition remains challenging. Here we present a detailed protocol of the RNA–DNA High-salt Recovered Sequence (RD-HRS) method, an extended version of the High-salt Recovered Sequence-sequencing (HRS-seq). Using high-salt treatments to make nuclear bodies insoluble, this extended version allows the profiling of both their RNA and genomic DNA contents, simultaneously, from the same biological sample.