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 sites_covgMean sites_covgMedian sites_covgPerc25 sites_covgPerc75 sites_numCovg5 sites_numCovg10 sites_numCovg30 sites_numCovg60 tiling_num tiling_covgMean tiling_covgMedian tiling_covgPerc25 tiling_covgPerc75 tiling_numCovg5 tiling_numCovg10 tiling_numCovg30 tiling_numCovg60 tiling_numSitesMean tiling_numSitesMedian tiling_numSites2 tiling_numSites5 tiling_numSites10 tiling_numSites20 genes_num genes_covgMean genes_covgMedian genes_covgPerc25 genes_covgPerc75 genes_numCovg5 genes_numCovg10 genes_numCovg30 genes_numCovg60 genes_numSitesMean genes_numSitesMedian genes_numSites2 genes_numSites5 genes_numSites10 genes_numSites20 promoters_num promoters_covgMean promoters_covgMedian promoters_covgPerc25 promoters_covgPerc75 promoters_numCovg5 promoters_numCovg10 promoters_numCovg30 promoters_numCovg60 promoters_numSitesMean promoters_numSitesMedian promoters_numSites2 promoters_numSites5 promoters_numSites10 promoters_numSites20 cpgislands_num cpgislands_covgMean cpgislands_covgMedian cpgislands_covgPerc25 cpgislands_covgPerc75 cpgislands_numCovg5 cpgislands_numCovg10 cpgislands_numCovg30 cpgislands_numCovg60 cpgislands_numSitesMean cpgislands_numSitesMedian cpgislands_numSites2 cpgislands_numSites5 cpgislands_numSites10 cpgislands_numSites20
HSC_1 HSC_1 bigBed bed 1235911 66.2867666037441 55 29 88 1235911 1157152 921325 567628 156316 525.329032216792 157 79 385 156316 153783 142894 127558 7.15895059940928 3 139434 58427 28415 14115 21524 2561.17213343245 1619.5 457 3546 21524 21435 21040 20487 35.6253038077235 22 20961 18234 15525 11868 18853 2011.27958415106 1509 369 3097 18853 18749 18235 17667 23.8678587664798 17 18238 15209 12541 9133 14410 2662.32755031228 2071.5 979 3695.5 14410 14396 14311 14161 32.5673116228369 24 14313 13673 12000 8697
HSC_2 HSC_2 bigBed bed 1276370 77.9783307348183 65 35 104 1276370 1209841 1011803 701130 160929 619.475482976965 203 103 474 160929 158685 149011 136570 7.3933341055192 3 142830 60606 29465 14497 21739 3009.95772574635 1923 546.5 4140.5 21739 21656 21300 20847 36.8080835358718 23 21135 18430 15770 12099 19170 2285.54136671883 1718 429 3530 19170 19062 18593 18047 24.3655099257463 18 18458 15383 12718 9323 14504 3036.01068670712 2377.5 1136 4199.5 14504 14496 14425 14288 33.160716718899 25 14413 13766 12140 8865
CLP_1 CLP_1 bigBed bed 1324526 42.346316342601 37 21 56 1324526 1232452 807677 291351 166694 337.362562539743 99 42 259 166694 162781 143053 107541 7.67221868303701 3 144306 63049 31579 15289 22030 1727.98338629142 1013 287 2373 22030 21884 21247 20338 37.9351426771087 24 21265 18536 15925 12345 19547 1271.49071468768 852 203 1932 19547 19358 18578 17511 24.4487043491438 18 18649 15521 12857 9372 14625 1763.85818803419 1293 583 2450 14625 14607 14475 14271 33.3242267338874 25 14531 13891 12273 8921
CLP_2 CLP_2 bigBed bed 1371313 34.2409690566632 29 17 46 1371313 1265890 683373 161971 171763 273.828670901184 99 52 237 171763 169080 151908 117573 7.94325592170035 3 154048 66577 32533 15487 22183 1380.74376775008 852 264 1868 22183 22078 21465 20505 39.0417229273562 25 21540 18763 16119 12548 19713 927.476233957287 657 181 1408 19713 19599 18775 17607 24.6126685861494 18 18934 15717 12924 9438 14640 1255.45020491803 954 447 1737 14640 14619 14453 14188 33.2865513012672 25 14538 13909 12288 8929
CMP_1 CMP_1 bigBed bed 1357079 41.3543375146178 36 20 56 1357079 1257918 811289 288518 170074 330.603778355304 106 47 273 170074 166109 148533 113291 7.8608096368796 3 150327 65283 32241 15442 22122 1678.82718560709 1005 296.25 2289 22122 21997 21373 20520 38.7285534251508 24 21432 18688 16045 12479 19647 1169.91846083372 801 206 1772.5 19647 19447 18697 17647 24.6311057230894 18 18836 15624 12888 9426 14645 1608.95247524752 1200 550 2224 14645 14620 14487 14252 33.4371849025753 25 14554 13911 12284 8932
CMP_2 CMP_2 bigBed bed 1384069 37.9897013804948 33 20 50 1384069 1314111 791153 210905 172309 305.409084841767 112 58 266 172309 170363 156382 127444 8.01714252620606 3 155198 67180 32889 15625 22202 1540.22034050986 949 295 2077.75 22202 22129 21625 20791 39.3976505536052 25 21580 18809 16161 12591 19759 1027.82843261299 732 202 1562 19759 19661 18966 17982 24.7933020154569 18 19016 15727 12975 9476 14656 1393.95912936681 1060 499 1929 14656 14629 14509 14278 33.5228914020984 25 14560 13927 12324 8962
CD4_1 CD4_1 bigBed bed 1357854 50.9557485561776 45 27 68 1357854 1295008 961049 454953 169818 407.982628461058 127 60 325 169818 166768 153559 128506 7.86527480164476 3 149307 65070 32243 15512 22129 2080.12296082064 1252 362 2839 22129 22031 21508 20862 38.8019173642992 24 21423 18677 16067 12504 19671 1491.93884398353 1023 257 2278 19671 19525 18926 18048 24.7692074556751 18 18830 15645 12943 9472 14656 2060.78766375546 1542 716 2850.5 14656 14639 14548 14368 33.6446382340918 25 14562 13931 12332 8969
CD4_2 CD4_2 bigBed bed 1382289 39.2290591909507 34 21 51 1382289 1312709 803435 235326 171745 316.004046697138 113 61 264 171745 169761 156093 130219 8.00683384490647 3 154953 66977 32772 15608 22174 1589.196265897 970 296 2140 22174 22092 21582 20784 39.3445404626879 25 21556 18808 16146 12582 19727 1093.70654433011 766 203 1667.5 19727 19621 18966 17972 24.8447239480729 18 18985 15727 12965 9481 14648 1489.20466957946 1116 518 2054 14648 14629 14506 14282 33.6015805968116 25 14556 13928 12320 8983
B_cell_1 B_cell_1 bigBed bed 1360890 47.9284144934565 41 24 65 1360890 1290543 894902 403853 170057 384.061526429374 107 54 282 170057 166922 151068 120131 7.88287484797591 3 149225 65232 32326 15536 22127 2002.43833325801 1188 325.5 2760 22127 22029 21502 20677 38.9115581960572 24 21426 18697 16093 12515 19683 1492.55596199766 1011 233 2282 19683 19552 18888 17875 24.8339142294287 18 18832 15661 12958 9493 14656 2079.35159661572 1546.5 703 2893 14656 14638 14547 14368 33.7105872734705 26 14564 13933 12338 8998
B_cell_2 B_cell_2 bigBed bed 1377347 35.2052155339214 31 18 46 1377347 1283938 716745 170245 171857 282.515411068505 102 54 241 171857 169221 153495 121901 7.97821277581514 3 154560 66816 32648 15532 22168 1418.30819198845 871 267 1904 22168 22066 21484 20576 39.1948420199838 25 21534 18774 16144 12574 19737 962.244819374778 681 184 1467 19737 19610 18853 17719 24.7513259584786 18 18971 15730 12956 9452 14650 1307.39740614334 985 466 1810 14650 14622 14488 14231 33.4678430303856 25 14552 13924 12304 8948
Eryth_1 Eryth_1 bigBed bed 1169323 20.8486021398707 17 11 25 1169323 946328 188932 15202 168403 146.227276236172 55 27 127 168403 162343 121236 79326 6.77326113395494 3 146809 58771 27497 13049 22052 745.779475784509 444 143 969.25 22052 21856 20673 19155 33.1795391124314 21 21251 18282 15472 11507 19561 485.548029241859 326 98 689 19561 19312 17866 16158 20.4185987775926 15 18611 15133 12215 8284 14597 649.540042474481 457 218 842 14597 14563 14249 13774 27.4284643684426 21 14448 13598 11537 7781
Eryth_2 Eryth_2 bigBed bed 873811 13.33719648757 10 7 14 873811 453270 23638 7004 147403 84.5867044768424 31 15 72 147403 133406 76302 43677 5.06151039555221 2 113546 45084 20937 9804 21291 398.857827250951 229 79 485 21291 20933 18988 16929 25.2814384733099 16 20206 17139 14041 9690 18564 269.914835164835 172 58 349.25 18564 18104 15954 13825 15.9349901500227 12 17346 14026 10896 6553 14204 355.124260771614 227 111 424 14204 14149 13625 12510 21.3126447744924 16 13988 12825 10312 6239
Mono_1 Mono_1 bigBed bed 1147526 19.7252576412212 16 10 23 1147526 902468 148257 12142 167325 137.020851636038 52 27 119 167325 160739 119736 75818 6.64697978803498 3 145578 57834 26945 12814 22005 681.180413542377 396 130 868 22005 21774 20533 18990 32.4537762174813 20 21210 18203 15375 11364 19497 442.628301790019 297 90 617 19497 19203 17713 15939 19.9783805627115 15 18570 15076 12121 8110 14557 594.220855945593 409 197 756 14557 14509 14204 13681 26.8391470227551 20 14405 13574 11445 7630
Mono_2 Mono_2 bigBed bed 1049614 16.0959333621693 12 8 18 1049614 708271 57199 8034 161934 107.400459446441 40 21 92 161934 153089 98400 59438 6.07984015752592 3 137110 53338 24636 11811 21763 526.648118366034 299 100.5 649 21763 21481 19872 18041 29.6665316410118 18 20894 17822 14916 10769 19170 346.398069900887 224 72 462 19170 18785 16907 15006 18.3057028842754 13 18139 14674 11675 7555 14425 462.577954939341 303 147 561 14425 14379 13985 13212 24.5177135849571 19 14267 13286 11013 7117

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 mm9 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 (mm9). 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