Mouse methylome studies SRP522281 Track Settings
 
Early Moderate Prenatal Alcohol Exposure and Maternal Diet Impact Offspring DNA Methylation Across Species [Brain, Liver]

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 SRX25478908  CpG methylation  Liver / SRX25478908 (CpG methylation)   Schema 
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 SRX25478914  CpG methylation  Brain / SRX25478914 (CpG methylation)   Schema 
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 SRX25478915  CpG methylation  Liver / SRX25478915 (CpG methylation)   Schema 
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 SRX25478916  CpG methylation  Liver / SRX25478916 (CpG methylation)   Schema 
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 SRX25478918  CpG methylation  Liver / SRX25478918 (CpG methylation)   Schema 
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 SRX25478919  CpG methylation  Liver / SRX25478919 (CpG methylation)   Schema 
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 SRX25478920  CpG methylation  Liver / SRX25478920 (CpG methylation)   Schema 
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 SRX25478921  CpG methylation  Liver / SRX25478921 (CpG methylation)   Schema 
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 SRX25478925  CpG methylation  Liver / SRX25478925 (CpG methylation)   Schema 
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 SRX25478926  CpG methylation  Brain / SRX25478926 (CpG methylation)   Schema 
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 SRX25478928  CpG methylation  Brain / SRX25478928 (CpG methylation)   Schema 
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 SRX25478929  CpG methylation  Brain / SRX25478929 (CpG methylation)   Schema 
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 SRX25478930  CpG methylation  Brain / SRX25478930 (CpG methylation)   Schema 
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 SRX25478931  CpG methylation  Brain / SRX25478931 (CpG methylation)   Schema 
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 SRX25478932  HMR  Liver / SRX25478932 (HMR)   Schema 
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 SRX25478932  CpG methylation  Liver / SRX25478932 (CpG methylation)   Schema 
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 SRX25478933  CpG methylation  Liver / SRX25478933 (CpG methylation)   Schema 
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 SRX25478934  CpG methylation  Liver / SRX25478934 (CpG methylation)   Schema 
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 SRX25478935  CpG methylation  Liver / SRX25478935 (CpG methylation)   Schema 
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 SRX25478936  CpG methylation  Liver / SRX25478936 (CpG methylation)   Schema 
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 SRX25478937  CpG methylation  Liver / SRX25478937 (CpG methylation)   Schema 
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Study title: Early Moderate Prenatal Alcohol Exposure and Maternal Diet Impact Offspring DNA Methylation Across Species
SRA: SRP522281
GEO: not found
Pubmed: not found

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
SRX25478906 Brain 0.754 10.6 49683 1135.0 196 1079.9 1683 13008.1 0.996 title: GSM8423156 Brain, PAE+HMD,Male,Dam 25, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478907 Brain 0.764 8.8 45234 1215.9 126 1168.9 1873 11713.7 0.994 title: GSM8423157 Brain,PAE+Normal,Female,Dam 4, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478908 Liver 0.647 10.6 30029 1212.8 229 975.3 1164 9901.3 0.995 title: GSM8423158 Liver,PAE+HMD,Male,Dam 25, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478909 Brain 0.750 11.4 50632 1151.3 259 1077.8 3140 8203.6 0.995 title: GSM8423159 Brain,H2O+Normal,Female,Dam 3, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Water + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478910 Brain 0.741 10.4 54079 1137.0 207 1083.2 1338 13723.0 0.995 title: GSM8423160 Brain,PAE+Normal,Male,Dam 2, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478911 Brain 0.751 11.4 54761 1162.3 236 1112.9 1600 13087.7 0.989 title: GSM8423161 Brain,PAE+HMD,Male,Dam 26, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478912 Brain 0.753 10.8 46512 1168.1 190 1107.1 1732 12318.0 0.990 title: GSM8423162 Brain,PAE+Normal,Male,Dam 26, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478913 Brain 0.779 7.5 41916 1303.6 106 1181.1 1566 12319.7 0.993 title: GSM8423163 Brain,H2O+HMD,Female,Dam 11, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Water + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478914 Brain 0.767 9.5 45247 1247.5 172 1105.3 1508 12924.9 0.989 title: GSM8423164 Brain,H2O+Normal,Female,Dam 13, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Water + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478915 Liver 0.747 10.7 54616 1134.3 201 1150.4 1680 12559.2 0.994 title: GSM8423165 Brain,H2O+HMD,Male,Dam 11, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Water + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478916 Liver 0.619 12.2 31225 1163.9 289 954.2 2141 6419.9 0.996 title: GSM8423166 Liver,PAE+Normal,Female,Dam 4, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478917 Liver 0.658 12.2 31087 1181.9 345 937.0 986 11435.6 0.996 title: GSM8423167 Liver,H2O+HMD,Male,Dam 11, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Water + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478918 Liver 0.673 13.1 32626 1131.2 407 922.7 2704 6296.9 0.995 title: GSM8423168 Liver,H2O+Normal,Female,Dam 3, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Water + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478919 Liver 0.651 8.5 28614 1263.2 142 1014.6 961 11162.0 0.995 title: GSM8423169 Liver,PAE+HMD,Female,Dam 25, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478920 Liver 0.681 13.0 32301 1170.6 382 940.3 2614 6460.4 0.989 title: GSM8423170 Liver,PAE+Normal,Female,Dam 2, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478921 Liver 0.627 10.1 29326 1234.8 192 1075.3 871 11410.4 0.996 title: GSM8423171 Liver,H2O+Normal,Male,Dam 3, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Water + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478922 Liver 0.649 13.4 32461 1157.2 339 957.3 1071 10744.3 0.991 title: GSM8423172 Liver,H2O+HMD,Male,Dam 6, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Water + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478923 Brain 0.745 9.2 49162 1181.0 192 1084.4 1666 12456.3 0.994 title: GSM8423173 Brain,H2O+HMD,Female,Dam 6, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Water + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478924 Brain 0.751 10.8 47203 1156.6 274 1069.2 1764 12102.7 0.995 title: GSM8423174 Brain,PAE+HMD,Female,Dam 25, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478925 Liver 0.599 11.0 31188 1166.0 365 940.5 1117 10128.6 0.994 title: GSM8423175 Liver,PAE+HMD,Female,Dam 26, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478926 Brain 0.754 13.2 57678 1120.2 250 1089.2 3034 8733.9 0.995 title: GSM8423176 Brain,H2O+Normal,Male,Dam 3, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Water + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478927 Liver 0.683 11.7 31945 1171.2 351 906.9 1262 10562.8 0.995 title: GSM8423177 Liver,H2O+Normal,Male,Dam 13, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Water + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478928 Brain 0.745 7.7 46160 1225.1 130 1171.2 1201 17611.8 0.995 title: GSM8423178 Brain,PAE+Normal,Female, Dam 2, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478929 Brain 0.765 8.5 44676 1209.4 126 1158.1 1521 12365.3 0.995 title: GSM8423179 Brain,H2O+HMD,Male,Dam 6, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Water + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478930 Brain 0.749 12.5 52285 1142.7 321 1097.8 3505 7961.9 0.995 title: GSM8423180 Brain,PAE+HMD,Female,Dam 26, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478931 Brain 0.761 10.3 45601 1158.8 194 1071.1 1774 12114.4 0.994 title: GSM8423181 Brain,H2O+Normal,Male,Dam 13, Mus musculus, Bisulfite-Seq; {"source_name": "Brain", "tissue": "Brain", "genotype": "C57BL/6J", "treatment": "Water + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478932 Liver 0.636 10.1 29089 1249.5 170 996.4 850 11434.1 0.995 title: GSM8423182 Liver,PAE+Normal,Male,Dam 4, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478933 Liver 0.667 10.3 29768 1243.2 189 1027.5 1128 10587.0 0.995 title: GSM8423183 Liver,H2O+HMD,Female,Dam 11, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Water + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478934 Liver 0.646 12.9 32590 1124.5 457 899.2 1094 11032.5 0.996 title: GSM8423184 Liver,PAE+Normal,Male,Dam 2, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + normal diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478935 Liver 0.643 13.0 32717 1135.8 349 937.8 2525 6126.3 0.995 title: GSM8423185 Liver,H2O+HMD,Female,Dam 6, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Water + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478936 Liver 0.630 10.6 29882 1208.9 233 975.2 1032 10352.5 0.996 title: GSM8423186 Liver,PAE+HMD,Male,Dam 26, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Prenatal alcohol exposure + high methyl donor diet", "geo_loc_name": "missing", "collection_date": "missing"}
SRX25478937 Liver 0.675 10.3 30902 1211.3 254 974.4 1141 11069.3 0.991 title: GSM8423187 Liver,H2O+Normal,Female,Dam 13, Mus musculus, Bisulfite-Seq; {"source_name": "Liver", "tissue": "Liver", "genotype": "C57BL/6J", "treatment": "Water + normal diet", "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.