Schema for Neandertal Methyl - Neandertal Reconstructed DNA Methylation Map
  Database: hg19    Primary Table: neandertalMethylation    Row Count: 26,681,234   Data last updated: 2014-08-28
Format description: Browser extensible data
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
chrom chr1varchar(255) Reference sequence chromosome or scaffold
chromStart 10469int(10) unsigned Start position in chromosome
chromEnd 10470int(10) unsigned End position in chromosome
name 48.9178varchar(255) Name of item
score 489int(10) unsigned Optional score, nominal range 0-1000
strand +char(1) + or -
thickStart 10469int(10) unsigned Start of where display should be thick (start codon)
thickEnd 10470int(10) unsigned End of where display should be thick (stop codon)
itemRgb 16776960int(10) unsigned Used as itemRgb as of 2004-11-22

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEnditemRgb
585chr1104691047048.9178489+1046910470255,255,0
585chr1104711047248.9178489+1047110472255,255,0
585chr1104841048548.9178489+1048410485255,255,0
585chr1104891049048.9178489+1048910490255,255,0
585chr1104931049448.9178489+1049310494255,255,0
585chr1105251052665.36463653+1052510526255,155,0
585chr1105421054390.90573909+1054210543255,55,0
585chr110563105641001000+1056310564255,0,0
585chr110571105721001000+1057110572255,0,0
585chr110577105781001000+1057710578255,0,0

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Neandertal Methyl (neandertalMethylation) Track Description
 

Description

This track shows the reconstructed DNA methylation map of the Neandertal genome, derived from bone tissues.

Display conventions and configuration

Green to red scaling is used as a rough indicator of methylation. Values range from 0% (green, unmethylated) to 100% (red, methylated). Data are displayed for CpG positions across the genome.

Methods

Gokhman et al. reconstructed the DNA methylation maps of two archaic humans, the Neandertal and the Denisovan, based on the natural deamination of cytosines in ancient DNA. With time, cytosines (C's) in post-mortem DNA lose their amine group (deamination). However, deamination of methylated vs. unmethylated C's results in different products - Methylated C's are deaminated with time to T's, whereas unmethylated C's are deaminated to U's. The U's are later removed during ancient DNA library preparation and as a result, a distinct pattern is observed: methylated regions in the genome display high C-->T conversion rate, whereas unmethylated regions display a low C-->T conversion rate. These patterns were used to reconstruct the full DNA methylation maps of the archaic humans.

Credits

This track was produced at UCSC using data generated by Gokhman et al., 2014.

References

Gokhman D, Lavi E, Prüfer K, Fraga MF, Riancho JA, Kelso J, Pääbo S, Meshorer E, Carmel L. Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science. 2014 May 2;344(6183):523-7. PMID: 24786081