STUDY NAME
GOLD Study ID Gs0056634
Study Name Fossil microbiome from Neanderthal (MPI)
Other Names Neanderthal Genomic DNA from Vindija, Croatia
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject ID
Legacy ER Study ID 11634
Legacy GOLD ID Gm00076
Added By Nikos Kyrpides on 2007-11-27
Last Modified By Michelle Isbandi on 2013-11-22
STUDY DESCRIPTION
PI Name Paabo S
Description High-throughput direct sequencing techniques have recently opened the possibility to sequence genomes from Pleistocene organisms. Here we analyze DNA sequences determined from a Neandertal, a mammoth, and a cave bear. We show that purines are overrepresented at positions adjacent to the breaks in the ancient DNA, suggesting that depurination has contributed to its degradation. We furthermore show that substitutions resulting from miscoding cytosine residues are vastly overrepresented in the DNA sequences and drastically clustered in the ends of the molecules, whereas other substitutions are rare. We present a model where the observed substitution patterns are used to estimate the rate of deamination of cytosine residues in single- and double-stranded portions of the DNA, the length of single-stranded ends, and the frequency of nicks. The results suggest that reliable genome sequences can be obtained from Pleistocene organisms.
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Study Information Link
Study Information Link URL
Study Information Visibility Public
GOLD CLASSIFICATION
Ecosystem Environmental
Ecosystem Category Terrestrial
Ecosystem Type Soil
Ecosystem Subtype Unclassified
Specific Ecosystem Unclassified
Metagenomic Study Yes
STUDY COMPOSITION
Number of Biosamples 1
Number of Seq. Projects 1
Number of Analysis Projects 1
Number of Related Studies 0