Toolkit

Because of its repetitive nature, ribosomal DNA is challenging to map and study. Standard genome assemblies and pipelines omit it. Assays like qPCR and sequencing are difficult to apply quantitatively to ribosomal RNA. This page contains tools and resources we have generated to enable studies of ribosomal DNA and RNA.

Resources

rDNA mapping genomes and pipeline

Genomes, annotations, and tracks: github.com/vikramparalkar/rDNA-Mapping-Genomes

Pipeline and methods: our Bioinformatic Methods paper (George et al, Journal of Biological Chemistry 2023)

Custom genome builds that add a reference rDNA sequence as a dedicated chromosome (chrR) to human hg19 (GRCh37), hg38 (GRCh38), hs1 (T2T-CHM13), and mouse mm10 (GRCm38), mm39 (GRCm39) genomes, with annotation BED files for rDNA promoters, transcribed regions, and intergenic spacers, plus sample tracks. The original genomes themselves have been masked of all rDNA-like sequences. The mapping pipeline is described in the accompanying methods paper.

Genome-browser tracks over the rDNA chromosome chrR of the hg38-rDNA genome, showing CTCF, TBP, POLR1A and UBTF ChIP-seq signal against their inputs, with the rDNA annotation beneath.

FISH-Flow protocol

Cell line FISH-Flow protocol: our STAR Protocols paper (Antony et al, STAR Protocols 2023)

Primary bone marrow FISH-Flow protocol: our preprint (Sams et al, bioRxiv 2026)

A flow cytometry assay for quantifying nascent and mature ribosomal RNA in single cells, including rare and heterogeneous populations. The step-by-step protocol is published, and a modification for primary bone marrow is described in our 2026 preprint.

Expected FISH-Flow results: flow cytometry histograms of 47S, 18S and 28S rRNA signal against unstained controls, and rRNA against DAPI showing the G1, S and G2-M phases of the cell cycle.

Using these tools

If you use these tools, please cite the relevant paper. Questions and requests are welcome at vikram.paralkar@pennmedicine.upenn.edu.