Mouse methylome studies SRP571561 Track Settings
 
Hypercapnia induces long-term DNA methylation changes in skeletal muscle [Skeletal Muscle]

Track collection: Mouse methylome studies

+  All tracks in this collection (604)

Maximum display mode:       Reset to defaults   
Select views (Help):
PMD       HMR       AMR       CpG methylation ▾       CpG reads ▾      
Select subtracks by views and experiment:
 All views PMD  HMR  AMR  CpG methylation  CpG reads 
experiment
SRX28054519 
SRX28054520 
SRX28054521 
SRX28054523 
SRX28054524 
SRX28054527 
SRX28054528 
SRX28054529 
SRX28054530 
SRX28054531 
SRX28054532 
SRX28054533 
SRX28054534 
SRX28054535 
SRX28054536 
SRX28054537 
SRX28054538 
SRX28054539 
SRX28054540 
SRX28054541 
SRX28054542 
SRX28054543 
SRX28054544 
SRX28054545 
SRX28054546 
SRX28054547 
SRX28054548 
SRX28054549 
SRX28054550 
SRX28054551 
SRX28054552 
SRX28054553 
SRX28054554 
SRX28054556 
SRX28054557 
SRX28054558 
SRX28054559 
SRX28054560 
SRX28054561 
SRX28054562 
SRX28054563 
SRX28054564 
SRX28054565 
SRX28054566 
SRX28054567 
SRX28054568 
experiment
 All views PMD  HMR  AMR  CpG methylation  CpG reads 
List subtracks: only selected/visible    all    ()
  experiment↓1 views↓2   Track Name↓3  
hide
 SRX28054519  HMR  Skeletal Muscle / SRX28054519 (HMR)   Schema 
hide
 Configure
 SRX28054519  CpG methylation  Skeletal Muscle / SRX28054519 (CpG methylation)   Schema 
hide
 SRX28054520  HMR  Skeletal Muscle / SRX28054520 (HMR)   Schema 
hide
 Configure
 SRX28054520  CpG methylation  Skeletal Muscle / SRX28054520 (CpG methylation)   Schema 
hide
 SRX28054521  HMR  Skeletal Muscle / SRX28054521 (HMR)   Schema 
hide
 Configure
 SRX28054521  CpG methylation  Skeletal Muscle / SRX28054521 (CpG methylation)   Schema 
hide
 SRX28054523  HMR  Skeletal Muscle / SRX28054523 (HMR)   Schema 
hide
 Configure
 SRX28054523  CpG methylation  Skeletal Muscle / SRX28054523 (CpG methylation)   Schema 
hide
 SRX28054524  HMR  Skeletal Muscle / SRX28054524 (HMR)   Schema 
hide
 Configure
 SRX28054524  CpG methylation  Skeletal Muscle / SRX28054524 (CpG methylation)   Schema 
hide
 SRX28054527  HMR  Skeletal Muscle / SRX28054527 (HMR)   Schema 
hide
 Configure
 SRX28054527  CpG methylation  Skeletal Muscle / SRX28054527 (CpG methylation)   Schema 
hide
 SRX28054528  HMR  Skeletal Muscle / SRX28054528 (HMR)   Schema 
hide
 Configure
 SRX28054528  CpG methylation  Skeletal Muscle / SRX28054528 (CpG methylation)   Schema 
hide
 SRX28054529  HMR  Skeletal Muscle / SRX28054529 (HMR)   Schema 
hide
 Configure
 SRX28054529  CpG methylation  Skeletal Muscle / SRX28054529 (CpG methylation)   Schema 
hide
 SRX28054530  HMR  Skeletal Muscle / SRX28054530 (HMR)   Schema 
hide
 Configure
 SRX28054530  CpG methylation  Skeletal Muscle / SRX28054530 (CpG methylation)   Schema 
hide
 SRX28054531  HMR  Skeletal Muscle / SRX28054531 (HMR)   Schema 
hide
 Configure
 SRX28054531  CpG methylation  Skeletal Muscle / SRX28054531 (CpG methylation)   Schema 
hide
 SRX28054532  HMR  Skeletal Muscle / SRX28054532 (HMR)   Schema 
hide
 Configure
 SRX28054532  CpG methylation  Skeletal Muscle / SRX28054532 (CpG methylation)   Schema 
hide
 SRX28054533  HMR  Skeletal Muscle / SRX28054533 (HMR)   Schema 
hide
 Configure
 SRX28054533  CpG methylation  Skeletal Muscle / SRX28054533 (CpG methylation)   Schema 
hide
 SRX28054534  HMR  Skeletal Muscle / SRX28054534 (HMR)   Schema 
hide
 Configure
 SRX28054534  CpG methylation  Skeletal Muscle / SRX28054534 (CpG methylation)   Schema 
hide
 SRX28054535  HMR  Skeletal Muscle / SRX28054535 (HMR)   Schema 
hide
 Configure
 SRX28054535  CpG methylation  Skeletal Muscle / SRX28054535 (CpG methylation)   Schema 
hide
 SRX28054536  HMR  Skeletal Muscle / SRX28054536 (HMR)   Schema 
hide
 Configure
 SRX28054536  CpG methylation  Skeletal Muscle / SRX28054536 (CpG methylation)   Schema 
hide
 SRX28054537  HMR  Skeletal Muscle / SRX28054537 (HMR)   Schema 
hide
 Configure
 SRX28054537  CpG methylation  Skeletal Muscle / SRX28054537 (CpG methylation)   Schema 
hide
 SRX28054538  HMR  Skeletal Muscle / SRX28054538 (HMR)   Schema 
hide
 Configure
 SRX28054538  CpG methylation  Skeletal Muscle / SRX28054538 (CpG methylation)   Schema 
hide
 SRX28054539  HMR  Skeletal Muscle / SRX28054539 (HMR)   Schema 
hide
 Configure
 SRX28054539  CpG methylation  Skeletal Muscle / SRX28054539 (CpG methylation)   Schema 
hide
 SRX28054540  HMR  Skeletal Muscle / SRX28054540 (HMR)   Schema 
hide
 Configure
 SRX28054540  CpG methylation  Skeletal Muscle / SRX28054540 (CpG methylation)   Schema 
hide
 SRX28054541  HMR  Skeletal Muscle / SRX28054541 (HMR)   Schema 
hide
 Configure
 SRX28054541  CpG methylation  Skeletal Muscle / SRX28054541 (CpG methylation)   Schema 
hide
 SRX28054542  HMR  Skeletal Muscle / SRX28054542 (HMR)   Schema 
hide
 Configure
 SRX28054542  CpG methylation  Skeletal Muscle / SRX28054542 (CpG methylation)   Schema 
hide
 SRX28054543  HMR  Skeletal Muscle / SRX28054543 (HMR)   Schema 
hide
 Configure
 SRX28054543  CpG methylation  Skeletal Muscle / SRX28054543 (CpG methylation)   Schema 
hide
 SRX28054544  HMR  Skeletal Muscle / SRX28054544 (HMR)   Schema 
hide
 Configure
 SRX28054544  CpG methylation  Skeletal Muscle / SRX28054544 (CpG methylation)   Schema 
hide
 SRX28054545  HMR  Skeletal Muscle / SRX28054545 (HMR)   Schema 
hide
 Configure
 SRX28054545  CpG methylation  Skeletal Muscle / SRX28054545 (CpG methylation)   Schema 
hide
 SRX28054546  HMR  Skeletal Muscle / SRX28054546 (HMR)   Schema 
hide
 Configure
 SRX28054546  CpG methylation  Skeletal Muscle / SRX28054546 (CpG methylation)   Schema 
hide
 SRX28054547  HMR  Skeletal Muscle / SRX28054547 (HMR)   Schema 
hide
 Configure
 SRX28054547  CpG methylation  Skeletal Muscle / SRX28054547 (CpG methylation)   Schema 
hide
 SRX28054548  HMR  Skeletal Muscle / SRX28054548 (HMR)   Schema 
hide
 Configure
 SRX28054548  CpG methylation  Skeletal Muscle / SRX28054548 (CpG methylation)   Schema 
hide
 SRX28054549  HMR  Skeletal Muscle / SRX28054549 (HMR)   Schema 
hide
 Configure
 SRX28054549  CpG methylation  Skeletal Muscle / SRX28054549 (CpG methylation)   Schema 
hide
 SRX28054550  HMR  Skeletal Muscle / SRX28054550 (HMR)   Schema 
hide
 Configure
 SRX28054550  CpG methylation  Skeletal Muscle / SRX28054550 (CpG methylation)   Schema 
hide
 SRX28054551  HMR  Skeletal Muscle / SRX28054551 (HMR)   Schema 
hide
 Configure
 SRX28054551  CpG methylation  Skeletal Muscle / SRX28054551 (CpG methylation)   Schema 
hide
 SRX28054552  HMR  Skeletal Muscle / SRX28054552 (HMR)   Schema 
hide
 Configure
 SRX28054552  CpG methylation  Skeletal Muscle / SRX28054552 (CpG methylation)   Schema 
hide
 SRX28054553  HMR  Skeletal Muscle / SRX28054553 (HMR)   Schema 
hide
 Configure
 SRX28054553  CpG methylation  Skeletal Muscle / SRX28054553 (CpG methylation)   Schema 
hide
 SRX28054554  HMR  Skeletal Muscle / SRX28054554 (HMR)   Schema 
hide
 Configure
 SRX28054554  CpG methylation  Skeletal Muscle / SRX28054554 (CpG methylation)   Schema 
hide
 SRX28054556  HMR  Skeletal Muscle / SRX28054556 (HMR)   Schema 
hide
 Configure
 SRX28054556  CpG methylation  Skeletal Muscle / SRX28054556 (CpG methylation)   Schema 
hide
 SRX28054557  HMR  Skeletal Muscle / SRX28054557 (HMR)   Schema 
hide
 Configure
 SRX28054557  CpG methylation  Skeletal Muscle / SRX28054557 (CpG methylation)   Schema 
hide
 SRX28054558  HMR  Skeletal Muscle / SRX28054558 (HMR)   Schema 
hide
 Configure
 SRX28054558  CpG methylation  Skeletal Muscle / SRX28054558 (CpG methylation)   Schema 
hide
 SRX28054559  HMR  Skeletal Muscle / SRX28054559 (HMR)   Schema 
hide
 Configure
 SRX28054559  CpG methylation  Skeletal Muscle / SRX28054559 (CpG methylation)   Schema 
hide
 SRX28054560  HMR  Skeletal Muscle / SRX28054560 (HMR)   Schema 
hide
 Configure
 SRX28054560  CpG methylation  Skeletal Muscle / SRX28054560 (CpG methylation)   Schema 
hide
 SRX28054561  HMR  Skeletal Muscle / SRX28054561 (HMR)   Schema 
hide
 Configure
 SRX28054561  CpG methylation  Skeletal Muscle / SRX28054561 (CpG methylation)   Schema 
hide
 SRX28054562  HMR  Skeletal Muscle / SRX28054562 (HMR)   Schema 
hide
 Configure
 SRX28054562  CpG methylation  Skeletal Muscle / SRX28054562 (CpG methylation)   Schema 
hide
 SRX28054563  HMR  Skeletal Muscle / SRX28054563 (HMR)   Schema 
hide
 Configure
 SRX28054563  CpG methylation  Skeletal Muscle / SRX28054563 (CpG methylation)   Schema 
hide
 SRX28054564  HMR  Skeletal Muscle / SRX28054564 (HMR)   Schema 
hide
 Configure
 SRX28054564  CpG methylation  Skeletal Muscle / SRX28054564 (CpG methylation)   Schema 
hide
 SRX28054565  HMR  Skeletal Muscle / SRX28054565 (HMR)   Schema 
hide
 Configure
 SRX28054565  CpG methylation  Skeletal Muscle / SRX28054565 (CpG methylation)   Schema 
hide
 SRX28054566  HMR  Skeletal Muscle / SRX28054566 (HMR)   Schema 
hide
 Configure
 SRX28054566  CpG methylation  Skeletal Muscle / SRX28054566 (CpG methylation)   Schema 
hide
 SRX28054567  HMR  Skeletal Muscle / SRX28054567 (HMR)   Schema 
hide
 Configure
 SRX28054567  CpG methylation  Skeletal Muscle / SRX28054567 (CpG methylation)   Schema 
hide
 SRX28054568  HMR  Skeletal Muscle / SRX28054568 (HMR)   Schema 
hide
 Configure
 SRX28054568  CpG methylation  Skeletal Muscle / SRX28054568 (CpG methylation)   Schema 
    

Study title: Hypercapnia induces long-term DNA methylation changes in skeletal muscle
SRA: SRP571561
GEO: not found
Pubmed: not found

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
SRX28054519 Skeletal Muscle 0.715 18.6 41619 1136.4 1678 883.6 1872 8719.9 0.968 title: GSM8856997 A101, aged male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "72 weeks aged", "age": "72 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054520 Skeletal Muscle 0.710 19.3 41729 1214.3 1553 890.1 1946 9514.2 0.937 title: GSM8856998 A102, aged male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "72 weeks aged", "age": "72 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054521 Skeletal Muscle 0.728 20.2 40824 1097.7 1792 882.8 2093 8038.3 0.984 title: GSM8856999 A103, aged male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "72 weeks aged", "age": "72 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054523 Skeletal Muscle 0.732 20.9 42098 1226.4 1341 863.8 2092 9518.5 0.932 title: GSM8857001 A105, aged male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "72 weeks aged", "age": "72 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054524 Skeletal Muscle 0.740 17.5 41944 1170.4 1288 893.7 1742 9391.2 0.959 title: GSM8857002 A201, aged female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "72 weeks aged", "age": "72 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054527 Skeletal Muscle 0.744 19.7 43856 1089.0 1744 922.1 2231 7767.6 0.975 title: GSM8857005 A204, aged female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "72 weeks aged", "age": "72 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054528 Skeletal Muscle 0.722 18.7 40966 1187.6 1334 873.2 1879 9357.6 0.947 title: GSM8857014 HC108, 6-months post-hypercapnia male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "hypercapnia, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054529 Skeletal Muscle 0.731 18.9 42038 1106.3 1557 874.4 2157 8038.5 0.979 title: GSM8857015 HC109, 6-months post-hypercapnia male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "hypercapnia, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054530 Skeletal Muscle 0.670 18.8 39029 1212.1 1055 905.5 1632 11462.6 0.963 title: GSM8857016 HC110, 6-months post-hypercapnia male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "hypercapnia, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054531 Skeletal Muscle 0.729 17.2 41859 1107.6 1103 910.2 1721 8623.6 0.977 title: GSM8857017 HC201, acute hypercapnia female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "hypercapnia, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054532 Skeletal Muscle 0.727 21.2 44271 1120.3 1450 886.9 1667 9370.2 0.961 title: GSM8857018 HC202, acute hypercapnia female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "hypercapnia, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054533 Skeletal Muscle 0.715 19.6 42970 1135.7 1455 889.8 1801 9182.2 0.958 title: GSM8857019 HC203, acute hypercapnia female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "hypercapnia, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054534 Skeletal Muscle 0.712 19.3 42601 1151.1 1523 914.4 2128 8786.5 0.954 title: GSM8857020 HC204, acute hypercapnia female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "hypercapnia, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054535 Skeletal Muscle 0.713 20.1 43204 1103.0 1789 916.5 2050 8112.8 0.974 title: GSM8857021 HC205, acute hypercapnia female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "hypercapnia, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054536 Skeletal Muscle 0.719 19.0 41815 1118.9 1474 889.9 1510 9461.5 0.969 title: GSM8857030 NC104, normoxic (acute) control male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "normoxic, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054537 Skeletal Muscle 0.711 19.9 42269 1131.3 1489 889.0 1616 9449.3 0.961 title: GSM8857031 NC105, normoxic (acute) control male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "normoxic, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054538 Skeletal Muscle 0.722 17.6 40675 1184.0 1210 892.4 1735 9301.5 0.951 title: GSM8857032 NC106, normoxic (6-months post-hypercapnia) control male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "normoxic, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054539 Skeletal Muscle 0.728 17.9 41026 1153.0 1240 864.4 1917 8411.2 0.963 title: GSM8857033 NC107, normoxic (6-months post-hypercapnia) control male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "normoxic, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054540 Skeletal Muscle 0.708 20.2 42326 1121.5 1641 883.8 1712 9075.0 0.969 title: GSM8857034 NC108, normoxic (6-months post-hypercapnia) control male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "normoxic, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054541 Skeletal Muscle 0.722 18.0 40792 1136.7 1313 869.1 1991 8427.8 0.973 title: GSM8857035 NC109, normoxic (6-months post-hypercapnia) control male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "normoxic, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054542 Skeletal Muscle 0.708 20.0 42080 1098.2 1917 873.8 1655 8876.3 0.977 title: GSM8857036 NC110, normoxic (6-months post-hypercapnia) control male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "normoxic, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054543 Skeletal Muscle 0.719 20.1 42996 1080.6 1685 915.0 1725 8782.8 0.980 title: GSM8857037 NC201, normoxic (acute) control female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "normoxic, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054544 Skeletal Muscle 0.730 19.4 42102 1108.5 1725 898.4 2011 8319.1 0.976 title: GSM8857006 A205, aged female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "72 weeks aged", "age": "72 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054545 Skeletal Muscle 0.714 17.9 40387 1133.3 1303 883.6 1968 8390.0 0.971 title: GSM8857007 HC101, acute hypercapnia male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "hypercapnia, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054546 Skeletal Muscle 0.697 21.4 42927 1169.4 1788 890.6 2067 9449.8 0.947 title: GSM8857008 HC102, acute hypercapnia male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "hypercapnia, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054547 Skeletal Muscle 0.730 21.1 42593 1148.3 1523 874.3 1933 9355.8 0.954 title: GSM8857009 HC103, acute hypercapnia male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "hypercapnia, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054548 Skeletal Muscle 0.726 19.2 41886 1106.0 1389 895.5 1741 8850.7 0.978 title: GSM8857010 HC104, acute hypercapnia male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "hypercapnia, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054549 Skeletal Muscle 0.711 19.9 41935 1164.3 1317 884.6 1908 9027.5 0.953 title: GSM8857011 HC105, acute hypercapnia male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "hypercapnia, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054550 Skeletal Muscle 0.707 19.6 41786 1131.3 1733 871.8 1608 9239.8 0.970 title: GSM8857012 HC106, 6-months post-hypercapnia male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "hypercapnia, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054551 Skeletal Muscle 0.728 20.2 41787 1150.7 1394 865.1 2071 8498.7 0.961 title: GSM8857013 HC107, 6-months post-hypercapnia male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "hypercapnia, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054552 Skeletal Muscle 0.711 22.3 44232 1155.8 1670 890.1 2026 9035.1 0.944 title: GSM8857046 NC210, normoxic (6-months post-hypercapnia) control female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "normoxic, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054553 Skeletal Muscle 0.724 22.2 43771 1128.9 1495 893.3 1768 9272.8 0.961 title: GSM8857022 HC206, 6-months post-hypercapnia female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "hypercapnia, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054554 Skeletal Muscle 0.727 21.1 43843 1133.9 1564 891.2 1912 9108.8 0.966 title: GSM8857023 HC207, 6-months post-hypercapnia female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "hypercapnia, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054556 Skeletal Muscle 0.724 20.4 44022 1130.1 1586 876.0 1901 9085.8 0.961 title: GSM8857025 HC209, 6-months post-hypercapnia female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "hypercapnia, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054557 Skeletal Muscle 0.719 19.1 42881 1108.5 1430 894.9 1866 8348.7 0.973 title: GSM8857026 HC210, 6-months post-hypercapnia female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "hypercapnia, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054558 Skeletal Muscle 0.728 20.8 42407 1132.1 1374 851.8 1918 8912.9 0.963 title: GSM8857027 NC101, normoxic (acute) control male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "normoxic, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054559 Skeletal Muscle 0.729 18.6 40860 1127.6 1263 860.0 1847 8568.9 0.975 title: GSM8857028 NC102, normoxic (acute) control male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "normoxic, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054560 Skeletal Muscle 0.730 21.4 42589 1164.1 1495 865.6 1968 9453.5 0.944 title: GSM8857029 NC103, normoxic (acute) control male, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "male", "genotype": "WT", "treatment": "normoxic, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054561 Skeletal Muscle 0.738 18.8 43049 1113.9 1321 901.4 1714 9181.5 0.966 title: GSM8857038 NC202, normoxic (acute) control female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "normoxic, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054562 Skeletal Muscle 0.726 18.0 41829 1154.9 1430 888.1 2131 8433.2 0.956 title: GSM8857039 NC203, normoxic (acute) control female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "normoxic, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054563 Skeletal Muscle 0.723 20.3 42972 1116.0 1512 898.0 1911 8925.5 0.962 title: GSM8857040 NC204, normoxic (acute) control female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "normoxic, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054564 Skeletal Muscle 0.727 21.9 43252 1082.5 1675 891.1 2127 7927.0 0.976 title: GSM8857041 NC205, normoxic (acute) control female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "normoxic, 20 weeks aged", "age": "20 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054565 Skeletal Muscle 0.734 19.1 42574 1132.5 1351 899.7 2093 8520.5 0.963 title: GSM8857042 NC206, normoxic (6-months post-hypercapnia) control female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "normoxic, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054566 Skeletal Muscle 0.730 20.0 43628 1082.3 1578 906.2 2244 7793.6 0.979 title: GSM8857043 NC207, normoxic (6-months post-hypercapnia) control female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "normoxic, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054567 Skeletal Muscle 0.709 18.6 41111 1117.5 1680 900.5 1846 8553.1 0.973 title: GSM8857044 NC208, normoxic (6-months post-hypercapnia) control female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "normoxic, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}
SRX28054568 Skeletal Muscle 0.721 21.4 43765 1163.1 1533 888.9 2149 8779.5 0.943 title: GSM8857045 NC209, normoxic (6-months post-hypercapnia) control female, Mus musculus, Bisulfite-Seq; {"source_name": "skeletal muscle", "tissue": "skeletal muscle", "sex": "female", "genotype": "WT", "treatment": "normoxic, 44 weeks aged", "age": "44 weeks", "geo_loc_name": "missing", "collection_date": "missing"}

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.

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.