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Our findings confirm that calculus yields more total DNA when compared to dentin, with a low, albeit consistent, proportion of endogenous human DNA.
While a large proportion of endogenous proteins can be extracted with non-ionic detergents as in untransfected control cells, >90% of N-moesin and >60% of N-ezrin and N-radixin remain insoluble.
Thus, SMN deficiency unevenly alters the physiological proportion of endogenous snRNPs in SMA.
Analysing the proportion of endogenous sequence products in the library should give insight into the sensitivity of the Hbb-b1 gene to restriction digestion.
Thus, impairment of a ubiquitous function of SMN changes the snRNP profile of SMA tissues by unevenly altering the normal proportion of endogenous snRNPs.
Since only a small proportion of endogenous CD44 pre-mRNA molecules include CD44 exon v5 upon phorbol-ester stimulation in our lymphoma cell model [23], changes in protein binding to this minority of molecules would be difficult to detect.
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Susceptibility to contamination and molecular degradation appears to be tissue specific, with petrous bone and tooth cementum generally exhibiting the highest proportions of endogenous human DNA among archaeological skeletal and soft tissues22,23,24,25.
Last, but not least, ancient samples typically feature relatively low proportions of endogenous DNA [ 13, 16] such that sequencing multiple samples to higher coverage depths (for example >20× depth) to enable confident genomic assembly and variant calling, is often either cost-prohibitive or simply not possible due to limited sample or DNA availability.
Although typically higher than in dental calculus, the proportion of human endogenous DNA in dentin varies substantially, ranging more than 3 orders of magnitude in this study, from 0.034% to 70.1% of all reads (Fig. 4a).
4Cv libraries from 18.5E brain cells contained a higher proportion of the endogenous sequence than those from 18.5E liver cells (53% compared to 42%).
The high proportion of authentic, endogenous aurochs DNA preserved in this sample bodes well for future efforts to determine the complete genome sequence of a wild ancestor of domestic cattle.
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