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Denisova Track Settings
 
Denisova Sequence Reads   (All Denisova Assembly and Analysis tracks)

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Data schema/format description and download
Assembly: Human Mar. 2006 (NCBI36/hg18)
Data last updated at UCSC: 2010-11-16
Denisova cave
Denisova cave entrance in the Altai Mountains of Siberia, Russia where the bones were found from which DNA was sequenced (Copyright (C) 2010, Johannes Krause)

Description

This track shows Denisova sequence reads mapped to the human genome, but to the old hg18 assembly from 2006. We provide updated annotation tracks with the called variants on more recent assemblies: Denisova variants on hg19, and Neanderthal and Denisova variants on hg38. There is no actual "Neanderthal" or "Denisova" genome assembly, the short fragments obtained from ancient samples can be aligned to the human genome and analyses are based on short variants.

The Denisova sequence was generated from a phalanx bone excavated from Denisova Cave in the Altai Mountains in southern Siberia.

Methods

Denisova sequence libraries were prepared by treating DNA extracted from a single phalanx bone with two enzymes: uracil-DNA-glycosylase, which removes uracil residues from DNA to leave abasic sites, and endonuclease VIII, which cuts DNA at the 59 and 39 sides of abasic sites. Subsequent incubation with T4 polynucleotide kinase and T4 DNA polymerase was used to generate phosphorylated blunt ends that are amenable to adaptor ligation. Because the great majority of uracil residues occur close to the ends of ancient DNA molecules, this procedure leads to only a moderate reduction in average length of the molecules in the library, but a several-fold reduction in uracil-derived nucleotide misincorporation. Reads were aligned to human sequence Mar. 2006 (NCBI36/hg18) using the Burrows-Wheeler Aligner.

Download the Denisova track data sets from the Genome Browser downloads server.

References

Briggs A.W., Stenzel U., Meyer M., Krause J., Kircher M., Pääbo S. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 2009 Dec 22:38(6) e87.

Reich D., Green R.E., Kircher M., Krause J., Patterson N., Durand E.Y., Viola B., Briggs A.W., Stenzel U., Johnson P.L.F. et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 2010 Dec 23;468:1053-1060.

Credits

This track was produced at UCSC using data generated by the Max Planck Institute for Evolutionary Anthropology.