mm10 Reference Genome with Mouse rDNA Repeat (BK000964.3) and Bowtie2 Index

This dataset provides a modified mouse reference genome (mm10) in which a full-length mouse ribosomal DNA (rDNA) repeat unit (BK000964.3; 45 kb) has been added as an additional contig.

The rDNA sequence corresponds to the complete mouse rDNA repeat unit described by Grozdanov et al. (2003) and is not included in standard mm10 genome assemblies due to its highly repetitive nature. This augmented reference enables explicit mapping and visualization of rDNA-derived reads in CUT&RUN, CUT&Tag, and ChIP-seq experiments.

The package includes:
- FASTA file of the mm10 genome with the rDNA repeat appended
- FASTA index (.fai)
- Chromosome size file (genome.chr.sizes)
- Pre-built Bowtie2 indices for direct use in read alignment

This resource is intended for epigenomic analyses involving nucleolar factors, RNA polymerase I–associated regulation, and transcription factor binding at rDNA loci.

Reference:
Grozdanov P. et al., "Complete sequence of the 45-kb mouse ribosomal DNA repeat: analysis of the intergenic spacer", Genomics 82 (6), 637-643 (2003)