SRP198624 Track Settings
 
Whole genome bisulfite sequencing of esophagus squamous cell carcinoma

Maximum display mode:       Reset to defaults   
Select views (Help):
hmr       amr       pmd       sym counts ▾       sym coverage ▾      
Select subtracks by views and experiment:
 All views hmr  amr  pmd  sym counts  sym coverage 
experiment
SRX5846246 
SRX5846247 
SRX5846248 
SRX5846249 
SRX5846250 
SRX5846251 
SRX5846252 
SRX5846253 
SRX5846254 
SRX5846255 
SRX5846256 
SRX5846257 
SRX5846258 
SRX5846259 
SRX5846260 
SRX5846261 
SRX5846262 
SRX5846263 
SRX5846264 
SRX5846265 
SRX5846266 
SRX5846267 
SRX5846268 
SRX5846269 
SRX5846270 
SRX5846271 
SRX5846272 
SRX5846273 
SRX5846274 
SRX5846275 
SRX5846276 
SRX5846277 
SRX5846278 
SRX5846279 
SRX5846280 
SRX5846281 
SRX5846282 
SRX5846283 
SRX5846284 
SRX5846285 
SRX5846286 
SRX5846287 
SRX5846288 
SRX5846289 
SRX5846290 
SRX5846291 
SRX5846292 
SRX5846293 
SRX5846294 
SRX5846295 
SRX5846296 
SRX5846297 
SRX5846298 
SRX5846299 
SRX5846300 
SRX5846301 
SRX5846302 
SRX5846303 
SRX5846304 
SRX5846305 
SRX5846306 
SRX5846307 
SRX5846308 
SRX5846309 
SRX5846310 
SRX5846311 
SRX5846312 
SRX5846313 
SRX5846314 
SRX5846315 
SRX5846316 
SRX5846317 
SRX5846318 
SRX5846319 
SRX5846320 
SRX5846321 
SRX5846322 
SRX5846323 
SRX5846324 
SRX5846325 
SRX5846326 
SRX5846327 
SRX5846328 
SRX5846329 
experiment
 All views hmr  amr  pmd  sym counts  sym coverage 
List subtracks: only selected/visible    all    ()
  experiment↓1 views↓2   Track Name↓3  
hide
 SRX5846246  hmr  SRX5846246 hmr   Data format 
hide
 Configure 		 SRX5846246  sym counts  SRX5846246 sym   Data format 
hide
 SRX5846247  hmr  SRX5846247 hmr   Data format 
hide
 Configure 		 SRX5846247  sym counts  SRX5846247 sym   Data format 
hide
 SRX5846248  hmr  SRX5846248 hmr   Data format 
hide
 Configure 		 SRX5846248  sym counts  SRX5846248 sym   Data format 
hide
 SRX5846249  hmr  SRX5846249 hmr   Data format 
hide
 Configure 		 SRX5846249  sym counts  SRX5846249 sym   Data format 
hide
 SRX5846250  hmr  SRX5846250 hmr   Data format 
hide
 Configure 		 SRX5846250  sym counts  SRX5846250 sym   Data format 
hide
 SRX5846251  hmr  SRX5846251 hmr   Data format 
hide
 Configure 		 SRX5846251  sym counts  SRX5846251 sym   Data format 
hide
 SRX5846252  hmr  SRX5846252 hmr   Data format 
hide
 Configure 		 SRX5846252  sym counts  SRX5846252 sym   Data format 
hide
 SRX5846253  hmr  SRX5846253 hmr   Data format 
hide
 Configure 		 SRX5846253  sym counts  SRX5846253 sym   Data format 
hide
 SRX5846254  hmr  SRX5846254 hmr   Data format 
hide
 Configure 		 SRX5846254  sym counts  SRX5846254 sym   Data format 
hide
 SRX5846255  hmr  SRX5846255 hmr   Data format 
hide
 Configure 		 SRX5846255  sym counts  SRX5846255 sym   Data format 
hide
 SRX5846256  hmr  SRX5846256 hmr   Data format 
hide
 Configure 		 SRX5846256  sym counts  SRX5846256 sym   Data format 
hide
 SRX5846257  hmr  SRX5846257 hmr   Data format 
hide
 Configure 		 SRX5846257  sym counts  SRX5846257 sym   Data format 
hide
 SRX5846258  hmr  SRX5846258 hmr   Data format 
hide
 Configure 		 SRX5846258  sym counts  SRX5846258 sym   Data format 
hide
 SRX5846259  hmr  SRX5846259 hmr   Data format 
hide
 Configure 		 SRX5846259  sym counts  SRX5846259 sym   Data format 
hide
 SRX5846260  hmr  SRX5846260 hmr   Data format 
hide
 Configure 		 SRX5846260  sym counts  SRX5846260 sym   Data format 
hide
 SRX5846261  hmr  SRX5846261 hmr   Data format 
hide
 Configure 		 SRX5846261  sym counts  SRX5846261 sym   Data format 
hide
 SRX5846262  hmr  SRX5846262 hmr   Data format 
hide
 Configure 		 SRX5846262  sym counts  SRX5846262 sym   Data format 
hide
 SRX5846263  hmr  SRX5846263 hmr   Data format 
hide
 Configure 		 SRX5846263  sym counts  SRX5846263 sym   Data format 
hide
 SRX5846264  hmr  SRX5846264 hmr   Data format 
hide
 Configure 		 SRX5846264  sym counts  SRX5846264 sym   Data format 
hide
 SRX5846265  hmr  SRX5846265 hmr   Data format 
hide
 Configure 		 SRX5846265  sym counts  SRX5846265 sym   Data format 
hide
 SRX5846266  hmr  SRX5846266 hmr   Data format 
hide
 Configure 		 SRX5846266  sym counts  SRX5846266 sym   Data format 
hide
 SRX5846267  hmr  SRX5846267 hmr   Data format 
hide
 Configure 		 SRX5846267  sym counts  SRX5846267 sym   Data format 
hide
 SRX5846268  hmr  SRX5846268 hmr   Data format 
hide
 Configure 		 SRX5846268  sym counts  SRX5846268 sym   Data format 
hide
 SRX5846269  hmr  SRX5846269 hmr   Data format 
hide
 Configure 		 SRX5846269  sym counts  SRX5846269 sym   Data format 
hide
 SRX5846270  hmr  SRX5846270 hmr   Data format 
hide
 Configure 		 SRX5846270  sym counts  SRX5846270 sym   Data format 
hide
 SRX5846271  hmr  SRX5846271 hmr   Data format 
hide
 Configure 		 SRX5846271  sym counts  SRX5846271 sym   Data format 
hide
 SRX5846272  hmr  SRX5846272 hmr   Data format 
hide
 Configure 		 SRX5846272  sym counts  SRX5846272 sym   Data format 
hide
 SRX5846273  hmr  SRX5846273 hmr   Data format 
hide
 Configure 		 SRX5846273  sym counts  SRX5846273 sym   Data format 
hide
 SRX5846274  hmr  SRX5846274 hmr   Data format 
hide
 Configure 		 SRX5846274  sym counts  SRX5846274 sym   Data format 
hide
 SRX5846275  hmr  SRX5846275 hmr   Data format 
hide
 Configure 		 SRX5846275  sym counts  SRX5846275 sym   Data format 
hide
 SRX5846276  hmr  SRX5846276 hmr   Data format 
hide
 Configure 		 SRX5846276  sym counts  SRX5846276 sym   Data format 
hide
 SRX5846277  hmr  SRX5846277 hmr   Data format 
hide
 Configure 		 SRX5846277  sym counts  SRX5846277 sym   Data format 
hide
 SRX5846278  hmr  SRX5846278 hmr   Data format 
hide
 Configure 		 SRX5846278  sym counts  SRX5846278 sym   Data format 
hide
 SRX5846279  hmr  SRX5846279 hmr   Data format 
hide
 Configure 		 SRX5846279  sym counts  SRX5846279 sym   Data format 
hide
 SRX5846280  hmr  SRX5846280 hmr   Data format 
hide
 Configure 		 SRX5846280  sym counts  SRX5846280 sym   Data format 
hide
 SRX5846281  hmr  SRX5846281 hmr   Data format 
hide
 Configure 		 SRX5846281  sym counts  SRX5846281 sym   Data format 
hide
 SRX5846282  hmr  SRX5846282 hmr   Data format 
hide
 Configure 		 SRX5846282  sym counts  SRX5846282 sym   Data format 
hide
 SRX5846283  hmr  SRX5846283 hmr   Data format 
hide
 Configure 		 SRX5846283  sym counts  SRX5846283 sym   Data format 
hide
 SRX5846284  hmr  SRX5846284 hmr   Data format 
hide
 Configure 		 SRX5846284  sym counts  SRX5846284 sym   Data format 
hide
 SRX5846285  hmr  SRX5846285 hmr   Data format 
hide
 Configure 		 SRX5846285  sym counts  SRX5846285 sym   Data format 
hide
 SRX5846286  hmr  SRX5846286 hmr   Data format 
hide
 Configure 		 SRX5846286  sym counts  SRX5846286 sym   Data format 
hide
 SRX5846287  hmr  SRX5846287 hmr   Data format 
hide
 Configure 		 SRX5846287  sym counts  SRX5846287 sym   Data format 
hide
 SRX5846288  hmr  SRX5846288 hmr   Data format 
hide
 Configure 		 SRX5846288  sym counts  SRX5846288 sym   Data format 
hide
 SRX5846289  hmr  SRX5846289 hmr   Data format 
hide
 Configure 		 SRX5846289  sym counts  SRX5846289 sym   Data format 
hide
 SRX5846290  hmr  SRX5846290 hmr   Data format 
hide
 Configure 		 SRX5846290  sym counts  SRX5846290 sym   Data format 
hide
 SRX5846291  hmr  SRX5846291 hmr   Data format 
hide
 Configure 		 SRX5846291  sym counts  SRX5846291 sym   Data format 
hide
 SRX5846292  hmr  SRX5846292 hmr   Data format 
hide
 Configure 		 SRX5846292  sym counts  SRX5846292 sym   Data format 
hide
 SRX5846293  hmr  SRX5846293 hmr   Data format 
hide
 Configure 		 SRX5846293  sym counts  SRX5846293 sym   Data format 
hide
 SRX5846294  hmr  SRX5846294 hmr   Data format 
hide
 Configure 		 SRX5846294  sym counts  SRX5846294 sym   Data format 
hide
 SRX5846295  hmr  SRX5846295 hmr   Data format 
hide
 Configure 		 SRX5846295  sym counts  SRX5846295 sym   Data format 
hide
 SRX5846296  hmr  SRX5846296 hmr   Data format 
hide
 Configure 		 SRX5846296  sym counts  SRX5846296 sym   Data format 
hide
 SRX5846297  hmr  SRX5846297 hmr   Data format 
hide
 Configure 		 SRX5846297  sym counts  SRX5846297 sym   Data format 
hide
 SRX5846298  hmr  SRX5846298 hmr   Data format 
hide
 Configure 		 SRX5846298  sym counts  SRX5846298 sym   Data format 
hide
 SRX5846299  hmr  SRX5846299 hmr   Data format 
hide
 Configure 		 SRX5846299  sym counts  SRX5846299 sym   Data format 
hide
 SRX5846300  hmr  SRX5846300 hmr   Data format 
hide
 Configure 		 SRX5846300  sym counts  SRX5846300 sym   Data format 
hide
 SRX5846301  hmr  SRX5846301 hmr   Data format 
hide
 Configure 		 SRX5846301  sym counts  SRX5846301 sym   Data format 
hide
 SRX5846302  hmr  SRX5846302 hmr   Data format 
hide
 Configure 		 SRX5846302  sym counts  SRX5846302 sym   Data format 
hide
 SRX5846303  hmr  SRX5846303 hmr   Data format 
hide
 Configure 		 SRX5846303  sym counts  SRX5846303 sym   Data format 
hide
 SRX5846304  hmr  SRX5846304 hmr   Data format 
hide
 Configure 		 SRX5846304  sym counts  SRX5846304 sym   Data format 
hide
 SRX5846305  hmr  SRX5846305 hmr   Data format 
hide
 Configure 		 SRX5846305  sym counts  SRX5846305 sym   Data format 
hide
 SRX5846306  hmr  SRX5846306 hmr   Data format 
hide
 Configure 		 SRX5846306  sym counts  SRX5846306 sym   Data format 
hide
 SRX5846307  hmr  SRX5846307 hmr   Data format 
hide
 Configure 		 SRX5846307  sym counts  SRX5846307 sym   Data format 
hide
 SRX5846308  hmr  SRX5846308 hmr   Data format 
hide
 Configure 		 SRX5846308  sym counts  SRX5846308 sym   Data format 
hide
 SRX5846309  hmr  SRX5846309 hmr   Data format 
hide
 Configure 		 SRX5846309  sym counts  SRX5846309 sym   Data format 
hide
 SRX5846310  hmr  SRX5846310 hmr   Data format 
hide
 Configure 		 SRX5846310  sym counts  SRX5846310 sym   Data format 
hide
 SRX5846311  hmr  SRX5846311 hmr   Data format 
hide
 Configure 		 SRX5846311  sym counts  SRX5846311 sym   Data format 
hide
 SRX5846312  hmr  SRX5846312 hmr   Data format 
hide
 Configure 		 SRX5846312  sym counts  SRX5846312 sym   Data format 
hide
 SRX5846313  hmr  SRX5846313 hmr   Data format 
hide
 Configure 		 SRX5846313  sym counts  SRX5846313 sym   Data format 
hide
 SRX5846314  hmr  SRX5846314 hmr   Data format 
hide
 Configure 		 SRX5846314  sym counts  SRX5846314 sym   Data format 
hide
 SRX5846315  hmr  SRX5846315 hmr   Data format 
hide
 Configure 		 SRX5846315  sym counts  SRX5846315 sym   Data format 
hide
 SRX5846316  hmr  SRX5846316 hmr   Data format 
hide
 Configure 		 SRX5846316  sym counts  SRX5846316 sym   Data format 
hide
 SRX5846317  hmr  SRX5846317 hmr   Data format 
hide
 Configure 		 SRX5846317  sym counts  SRX5846317 sym   Data format 
hide
 SRX5846318  hmr  SRX5846318 hmr   Data format 
hide
 Configure 		 SRX5846318  sym counts  SRX5846318 sym   Data format 
hide
 SRX5846319  hmr  SRX5846319 hmr   Data format 
hide
 Configure 		 SRX5846319  sym counts  SRX5846319 sym   Data format 
hide
 SRX5846320  hmr  SRX5846320 hmr   Data format 
hide
 Configure 		 SRX5846320  sym counts  SRX5846320 sym   Data format 
hide
 SRX5846321  hmr  SRX5846321 hmr   Data format 
hide
 Configure 		 SRX5846321  sym counts  SRX5846321 sym   Data format 
hide
 SRX5846322  hmr  SRX5846322 hmr   Data format 
hide
 Configure 		 SRX5846322  sym counts  SRX5846322 sym   Data format 
hide
 SRX5846323  hmr  SRX5846323 hmr   Data format 
hide
 Configure 		 SRX5846323  sym counts  SRX5846323 sym   Data format 
hide
 SRX5846324  hmr  SRX5846324 hmr   Data format 
hide
 Configure 		 SRX5846324  sym counts  SRX5846324 sym   Data format 
hide
 SRX5846325  hmr  SRX5846325 hmr   Data format 
hide
 Configure 		 SRX5846325  sym counts  SRX5846325 sym   Data format 
hide
 SRX5846326  hmr  SRX5846326 hmr   Data format 
hide
 Configure 		 SRX5846326  sym counts  SRX5846326 sym   Data format 
hide
 SRX5846327  hmr  SRX5846327 hmr   Data format 
hide
 Configure 		 SRX5846327  sym counts  SRX5846327 sym   Data format 
hide
 SRX5846328  hmr  SRX5846328 hmr   Data format 
hide
 Configure 		 SRX5846328  sym counts  SRX5846328 sym   Data format 
hide
 SRX5846329  hmr  SRX5846329 hmr   Data format 
hide
 Configure 		 SRX5846329  sym counts  SRX5846329 sym   Data format 
    
Assembly: Human Dec. 2013 (GRCh38/hg38)

SRP198624

Whole genome bisulfite sequencing of esophagus squamous cell carcinoma

Publication

Experiment Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Selection Label Title
SRX5846246 0.696 10.7 37872 1301.1 607 838.7 2146 10325.8 0.993 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846247 0.602 15.5 59829 9906.6 2523 898.6 1642 763359.6 0.983 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846248 0.700 14.7 36838 1211.6 1731 897.3 2131 10472.0 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846249 0.464 13.2 65764 11312.1 1411 1049.9 3730 279966.9 0.990 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846250 0.641 11.1 35076 1301.1 849 843.1 1321 10338.9 0.990 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846251 0.670 9.8 32852 1408.3 362 897.6 1731 19197.1 0.986 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846252 0.623 9.6 33454 1315.5 2178 898.9 795 1409837.7 0.989 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846253 0.659 14.3 43749 2343.4 2027 1035.6 1205 1054746.9 0.979 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846254 0.649 8.1 40898 1546.2 1067 844.0 1671 12048.3 0.987 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846255 0.609 9.1 56181 7158.9 2672 11304.5 2658 288447.6 0.988 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846256 0.681 16.2 36174 1246.6 2043 964.7 1584 21848.8 0.983 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846257 0.582 9.0 50160 8334.3 740 987.9 2120 416501.9 0.989 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846258 0.728 12.9 38491 1180.7 2208 879.2 2366 9953.0 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846259 0.694 15.0 37722 1232.2 1894 892.2 2164 13613.2 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846260 0.690 16.0 38045 1205.6 2498 955.0 1912 10474.2 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846261 0.602 19.6 69591 4827.9 1274 1013.8 2749 151918.7 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846262 0.707 12.4 37915 1234.7 2642 925.5 2277 12083.0 0.990 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846263 0.723 11.7 37446 1314.3 1312 869.1 2091 9616.2 0.990 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846264 0.532 13.7 58868 10073.3 3860 993.2 2339 471515.3 0.993 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846265 0.590 14.0 59896 8974.6 12310 1748.8 1850 710798.0 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846266 0.584 13.1 40413 1751.0 8955 4017.8 2348 353046.8 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846267 0.739 10.2 37163 1316.7 840 923.4 2334 9831.0 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846268 0.697 14.4 36279 1274.1 987 839.5 1879 10728.1 0.990 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846269 0.664 14.5 45945 1098.8 23211 1120.8 1883 15286.0 0.992 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846270 0.713 13.5 37491 1226.9 2750 898.5 2678 11654.5 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846271 0.547 13.2 40891 15068.0 4728 6792.4 1467 826967.3 0.980 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846272 0.580 12.9 35383 1256.0 4570 880.3 870 1286567.7 0.993 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846273 0.557 13.6 65809 9307.9 1758 955.9 2972 385706.3 0.993 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846274 0.730 12.8 38147 1212.2 487 1012.7 1832 11721.1 0.974 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846275 0.528 16.5 36241 11214.9 14721 1072.8 748 1542864.7 0.984 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846276 0.726 11.7 38336 1304.3 1240 873.6 2083 12574.2 0.990 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846277 0.733 13.4 57598 963.5 694 917.3 3101 8934.7 0.993 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846278 0.691 12.2 36040 1261.5 743 855.7 2016 11379.6 0.993 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846279 0.660 15.5 36898 1191.1 4306 1169.7 1851 12578.3 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846280 0.487 18.7 43203 17783.6 3195 862.4 3489 433917.3 0.989 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846281 0.741 15.8 39855 1232.9 1395 846.5 2467 10675.6 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846282 0.521 12.7 75030 8519.0 705 925.2 3102 305095.5 0.990 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846283 0.632 9.5 48405 5370.4 579 938.9 1854 276201.7 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846284 0.580 12.3 59749 5034.7 3942 921.6 2319 437805.6 0.990 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846285 0.714 14.9 36798 1249.7 3416 964.6 2487 10453.0 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846286 0.591 14.6 46089 2698.3 73651 1698.4 1204 1111897.1 0.992 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846287 0.716 13.2 35699 1208.0 3428 964.2 2448 10088.6 0.990 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846288 0.636 12.7 59085 5917.4 832 952.3 2041 504887.8 0.982 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846289 0.718 14.4 37461 1244.8 1455 844.9 2004 10803.0 0.990 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846290 0.682 13.9 39306 1210.9 6712 970.0 1505 13248.8 0.992 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846291 0.740 11.0 38207 1336.0 812 870.2 2469 9457.5 0.990 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846292 0.628 15.3 70323 4088.8 6573 962.8 1879 566832.3 0.992 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846293 0.685 11.1 36715 1186.0 4093 917.1 2132 14119.0 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846294 0.601 18.1 68773 9029.6 2555 957.1 2722 439831.9 0.988 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846295 0.560 15.8 63369 9553.5 9207 964.3 2191 552039.6 0.992 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846296 0.677 8.9 55554 2628.9 1050 919.2 2108 355894.7 0.986 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846297 0.678 10.5 29297 1289.4 275 981.6 473 17110.9 0.966 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846298 0.701 9.3 59194 5231.5 282 1019.4 1518 277993.4 0.989 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846299 0.618 9.1 30623 1643.5 301 913.5 368 2691749.1 0.984 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846300 0.580 13.7 54559 13068.5 445 912.0 2735 384745.0 0.983 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846301 0.753 9.6 32621 1393.3 161 985.4 1263 17538.6 0.986 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846302 0.603 9.0 57340 7381.3 984 903.6 2522 385550.0 0.986 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846303 0.689 7.0 28690 1606.1 498 852.0 772 14953.5 0.981 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846304 0.603 12.8 50266 2257.4 17845 1024.7 2311 460451.1 0.994 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846305 0.672 15.4 41004 1257.6 1128 920.8 1736 12267.6 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846306 0.631 8.8 43666 3188.6 835 923.6 1094 944955.0 0.988 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846307 0.692 15.5 36812 1209.2 597 879.5 1672 13181.0 0.978 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846308 0.710 10.0 37595 1460.2 553 937.6 1916 11788.5 0.989 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846309 0.606 11.0 65118 4152.0 3646 1031.9 2625 317057.7 0.993 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846310 0.752 11.6 36131 1232.6 3658 985.9 2252 13724.4 0.992 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846311 0.507 14.7 55453 12553.2 16188 3995.6 2695 432602.1 0.992 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846312 0.759 13.6 39726 1179.0 467 988.0 1817 15050.6 0.969 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846313 0.691 14.4 38860 1151.3 5216 913.3 1757 12409.9 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846314 0.652 17.5 35839 1285.3 5253 983.6 2331 299968.6 0.988 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846315 0.640 10.3 35119 1242.0 1017 884.9 1389 11073.8 0.993 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846316 0.619 8.8 52927 5617.5 1197 993.9 1659 664413.1 0.993 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846317 0.587 14.9 54820 5375.2 17687 1028.1 855 1456391.1 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846318 0.647 15.7 35864 1274.3 3837 868.7 2921 34490.7 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846319 0.725 12.8 35361 1234.3 2051 898.4 2409 9212.5 0.990 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846320 0.598 9.9 30562 1478.6 617 910.8 1939 417223.8 0.993 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846321 0.646 16.1 36828 1204.6 7306 2269.8 2535 334303.3 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846322 0.627 13.0 44019 2820.4 1704 876.1 1666 655759.6 0.981 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846323 0.594 17.0 40050 1164.8 42990 2098.5 1243 789108.4 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846324 0.699 15.5 39012 1168.9 3346 896.9 2736 10627.8 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846325 0.607 11.1 57832 4199.7 1586 995.3 2877 145813.0 0.991 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846326 0.670 17.0 40539 1128.8 14425 1008.6 5077 123682.9 0.993 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846327 0.634 11.6 46058 2322.4 1272 46237.3 3282 67817.3 0.988 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846328 0.734 13.1 38451 1118.2 356 879.4 1348 14985.7 0.976 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma
SRX5846329 0.664 11.7 34430 1270.8 1396 869.1 2004 10181.6 0.993 RANDOM Whole genome bisulfite sequencing of esophagus squamous cell carcinoma

Methods

All analysis was done using a bisulfite sequnecing data analysis pipeline DNMTools developed in the Smith lab at USC.

Mapping reads from bisulfite sequencing: Bisulfite treated reads are mapped to the genomes with the abismal program. Input reads are filtered by their quality, and adapter sequences in the 3' end of reads are trimmed. This is done with cutadapt. Uniquely mapped reads with mismatches/indels below given threshold are retained. For pair-end reads, if the two mates overlap, the overlapping part of the mate with lower quality is discarded. After mapping, we use the format command in dnmtools to merge mates for paired-end reads. We use the dnmtools uniq command to randomly select one from multiple reads mapped exactly to the same location. Without random oligos as UMIs, this is our best indication of PCR duplicates.

Estimating methylation levels: After reads are mapped and filtered, the dnmtools counts command is used to obtain read coverage and estimate methylation levels at individual cytosine sites. We count the number of methylated reads (those containing a C) and the number of unmethylated reads (those containing a T) at each nucleotide in a mapped read that corresponds to a cytosine in the reference genome. The methylation level of that cytosine is estimated as the ratio of methylated to total reads covering that cytosine. For cytosines in the symmetric CpG sequence context, reads from the both strands are collapsed to give a single estimate. Very rarely do the levels differ between strands (typically only if there has been a substitution, as in a somatic mutation), and this approach gives a better estimate.

Bisulfite conversion rate: The bisulfite conversion rate for an experiment is estimated with the dnmtools bsrate command, which computes the fraction of successfully converted nucleotides in reads (those read out as Ts) among all nucleotides in the reads mapped that map over cytosines in the reference genome. This is done either using a spike-in (e.g., lambda), the mitochondrial DNA, or the nuclear genome. In the latter case, only non-CpG sites are used. While this latter approach can be impacted by non-CpG cytosine methylation, in practice it never amounts to much.

Identifying hypomethylated regions (HMRs): In most mammalian cells, the majority of the genome has high methylation, and regions of low methylation are typically the interesting features. (This seems to be true for essentially all healthy differentiated cell types, but not cells of very early embryogenesis, various germ cells and precursors, and placental lineage cells.) These are valleys of low methylation are called hypomethylated regions (HMR) for historical reasons. To identify the HMRs, we use the dnmtools hmr command, which uses a statistical model that accounts for both the methylation level fluctations and the varying amounts of data available at each CpG site.

Identifying hypermethylated regions (HyperMRs) and mosaic methylation: Hyper-methylated regions (which we call HyperMRs) are of interest in plant methylomes, invertebrate methylomes and other methylomes showing "mosaic methylation" pattern. We identify HyperMRs with the dnmtools hypermr command for those samples showing "mosaic methylation" pattern.

Partially methylated domains: Partially methylated domains are large genomic regions showing partial methylation observed in immortalized cell lines and cancerous cells. The pmd program is used to identify PMDs.

Allele-specific methylation: Allele-Specific methylated regions refers to regions where the parental allele is differentially methylated compared to the maternal allele. The program allelic is used to compute allele-specific methylation score can be computed for each CpG site by testing the linkage between methylation status of adjacent reads, and the program amrfinder is used to identify regions with allele-specific methylation.

For more detailed description of the methods of each step, please refer to the DNMTools documentation.