Tracks and Tables

Methylation Data

Methylation Data was exported to the following formats:

Sample summary

This section contains summary metrics for each sample as well as links to exported files. The summary table below contains the following metrics. It is also available as csv file.

Bed files for each sample contain the locations of methylation sites and regions the methylation level (in the score column). The following table links to the files. The files can be quite large in size, so you might want to consider using the "save as" option instead of opening the links directly.

sampleName sites_bigBedFile sites_bedFile sites_num tiling_num tiling_numSitesMean tiling_numSitesMedian tiling_numSites2 tiling_numSites5 tiling_numSites10 tiling_numSites20 genes_num genes_numSitesMean genes_numSitesMedian genes_numSites2 genes_numSites5 genes_numSites10 genes_numSites20 promoters_num promoters_numSitesMean promoters_numSitesMedian promoters_numSites2 promoters_numSites5 promoters_numSites10 promoters_numSites20 cpgislands_num cpgislands_numSitesMean cpgislands_numSitesMedian cpgislands_numSites2 cpgislands_numSites5 cpgislands_numSites10 cpgislands_numSites20
hES_HUES13_p47 hES_HUES13_p47 bigBed bed 465661 132485 3.51557534815262 1 62064 31554 13914 1227 29829 13.0772737939589 8 25620 19952 12831 5476 30005 6.76347275454091 6 25388 18366 8411 357 25853 5.59494062584613 4 24786 11829 3641 274
hiPS_20b_p43 hiPS_20b_p43 bigBed bed 465648 132484 3.51547722383666 1 62064 31553 13913 1227 29829 13.0769050253109 8 25620 19952 12831 5476 30005 6.76313947675387 6 25387 18365 8410 357 25852 5.59482458515453 4 24786 11829 3640 274
hES_HUES1_p29 hES_HUES1_p29 bigBed bed 465660 132485 3.51556780012832 1 62064 31553 13914 1227 29829 13.0772737939589 8 25620 19952 12831 5476 30005 6.76343942676221 6 25388 18365 8411 357 25853 5.59494062584613 4 24786 11829 3641 274
hiPS_11c_p23 hiPS_11c_p23 bigBed bed 465662 132485 3.51558289617693 1 62064 31554 13914 1227 29829 13.0773073183814 8 25620 19952 12831 5476 30005 6.76350608231961 6 25388 18366 8411 357 25853 5.59497930607666 4 24786 11829 3641 274
hES_HUES1_p28 hES_HUES1_p28 bigBed bed 465662 132485 3.51558289617693 1 62064 31554 13914 1227 29829 13.0773073183814 8 25620 19952 12831 5476 30005 6.76350608231961 6 25388 18366 8411 357 25853 5.59497930607666 4 24786 11829 3641 274
hiPS_20b_p49_TeSR hiPS_20b_p49_TeSR bigBed bed 465660 132485 3.51556780012832 1 62064 31554 13914 1227 29829 13.0772737939589 8 25620 19952 12831 5476 30005 6.76343942676221 6 25388 18366 8410 357 25853 5.5949019456156 4 24786 11829 3641 274
hiPS_20b_p49_KOSR hiPS_20b_p49_KOSR bigBed bed 465661 132485 3.51557534815262 1 62064 31554 13914 1227 29829 13.0773073183814 8 25620 19952 12831 5476 30005 6.76350608231961 6 25388 18366 8411 357 25853 5.59497930607666 4 24786 11829 3641 274
hiPS_17b_p35_TeSR hiPS_17b_p35_TeSR bigBed bed 465662 132485 3.51558289617693 1 62064 31554 13914 1227 29829 13.0773073183814 8 25620 19952 12831 5476 30005 6.76350608231961 6 25388 18366 8411 357 25853 5.59497930607666 4 24786 11829 3641 274
hiPS_27b_p31 hiPS_27b_p31 bigBed bed 465662 132485 3.51558289617693 1 62064 31554 13914 1227 29829 13.0773073183814 8 25620 19952 12831 5476 30005 6.76350608231961 6 25388 18366 8411 357 25853 5.59497930607666 4 24786 11829 3641 274
hES_HUES64_p19 hES_HUES64_p19 bigBed bed 465662 132485 3.51558289617693 1 62064 31554 13914 1227 29829 13.0773073183814 8 25620 19952 12831 5476 30005 6.76350608231961 6 25388 18366 8411 357 25853 5.59497930607666 4 24786 11829 3641 274
hiPS_17b_p35_KOSR hiPS_17b_p35_KOSR bigBed bed 465661 132485 3.51557534815262 1 62064 31554 13914 1227 29829 13.0772737939589 8 25620 19952 12831 5476 30005 6.76350608231961 6 25388 18366 8411 357 25853 5.59497930607666 4 24786 11829 3641 274
hES_H9_p58 hES_H9_p58 bigBed bed 465661 132485 3.51557534815262 1 62064 31554 13914 1227 29829 13.0772737939589 8 25620 19952 12831 5476 30005 6.76350608231961 6 25388 18366 8411 357 25853 5.59494062584613 4 24786 11828 3641 274

Tracks Hubs

Track Hub data was generated for export to various genome browsers. Note that you need a server that is capable of serving the tracks to the genome browser via URL. Below, instructions are provided to view the tracks in the UCSC genome browser. Of course the files can also be viewed in other browsers such as the Ensembl genome browser.

  1. Make sure you are viewing this report via the internet and not locally (simply look at the URL in the address line of your browser). If this is not the case, copy the files belonging to this report to a directory which is accessible via the internet and enter the corresponding URL in your browser. If you don't want to copy the entire report, it suffices to copy the track hub directories (see table(s) below).
  2. Make sure the hg19 subdirectories in the track hub directory (for its location be referred to the table(s) below) contain all the required bigBed/bigWig files
  3. Go to the UCSC hub connection website to the "My Hubs" tab and add the web-URL of the hub.txt file in the directory you just copied. Hint: You can use the copy link functionality of your browser (right mouse click) on the track hub txt column in the table(s) below. Don't forget to click on "Load Selected Hubs".
  4. Make sure you are looking at the correct genome (hg19). The loaded hubs should now appear below the browsing window where you can modify their display settings.
More information on UCSC track hubs can be found here. Below, you find table(s) containing the directory names for the bed/bedGraph and track hub directories for all exported data, site and region types.

bigBed

bigWig