Mouse methylome studies SRP401089 Track Settings
 
Dual gene activating and repressive functions of TET1 in germ layer lineage bifurcation distinguished by genomic context and dependence on 5-methylcytosine oxidation [oxWGBS] [mESC B6129S6F1 Tet1, mESC B6129S6F1 Tet1 CRISPR HDR]

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 SRX17803019  HMR  mESC B6129S6F1 Tet1 CRISPR HDR / SRX17803019 (HMR)   Schema 
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 SRX17803019  CpG methylation  mESC B6129S6F1 Tet1 CRISPR HDR / SRX17803019 (CpG methylation)   Schema 
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 SRX17803020  HMR  mESC B6129S6F1 Tet1 / SRX17803020 (HMR)   Schema 
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 SRX17803020  CpG methylation  mESC B6129S6F1 Tet1 / SRX17803020 (CpG methylation)   Schema 
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 SRX17803021  HMR  mESC B6129S6F1 Tet1 / SRX17803021 (HMR)   Schema 
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 SRX17803021  CpG methylation  mESC B6129S6F1 Tet1 / SRX17803021 (CpG methylation)   Schema 
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 SRX17803022  HMR  mESC B6129S6F1 Tet1 / SRX17803022 (HMR)   Schema 
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 SRX17803022  CpG methylation  mESC B6129S6F1 Tet1 / SRX17803022 (CpG methylation)   Schema 
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 SRX17803023  HMR  mESC B6129S6F1 Tet1 / SRX17803023 (HMR)   Schema 
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 SRX17803023  CpG methylation  mESC B6129S6F1 Tet1 / SRX17803023 (CpG methylation)   Schema 
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 SRX17803024  HMR  mESC B6129S6F1 Tet1 CRISPR HDR / SRX17803024 (HMR)   Schema 
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 SRX17803024  CpG methylation  mESC B6129S6F1 Tet1 CRISPR HDR / SRX17803024 (CpG methylation)   Schema 
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 SRX17803025  HMR  mESC B6129S6F1 Tet1 / SRX17803025 (HMR)   Schema 
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 SRX17803025  CpG methylation  mESC B6129S6F1 Tet1 / SRX17803025 (CpG methylation)   Schema 
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 SRX17803026  HMR  mESC B6129S6F1 Tet1 / SRX17803026 (HMR)   Schema 
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 SRX17803026  CpG methylation  mESC B6129S6F1 Tet1 / SRX17803026 (CpG methylation)   Schema 
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 SRX17803027  HMR  mESC B6129S6F1 Tet1 / SRX17803027 (HMR)   Schema 
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 SRX17803027  CpG methylation  mESC B6129S6F1 Tet1 / SRX17803027 (CpG methylation)   Schema 
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 SRX17803028  HMR  mESC B6129S6F1 Tet1 CRISPR HDR / SRX17803028 (HMR)   Schema 
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 SRX17803028  CpG methylation  mESC B6129S6F1 Tet1 CRISPR HDR / SRX17803028 (CpG methylation)   Schema 
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 SRX17803029  HMR  mESC B6129S6F1 Tet1 / SRX17803029 (HMR)   Schema 
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 SRX17803029  CpG methylation  mESC B6129S6F1 Tet1 / SRX17803029 (CpG methylation)   Schema 
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 SRX17803030  HMR  mESC B6129S6F1 Tet1 / SRX17803030 (HMR)   Schema 
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 SRX17803030  CpG methylation  mESC B6129S6F1 Tet1 / SRX17803030 (CpG methylation)   Schema 
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 SRX17803031  HMR  mESC B6129S6F1 Tet1 CRISPR HDR / SRX17803031 (HMR)   Schema 
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 SRX17803031  CpG methylation  mESC B6129S6F1 Tet1 CRISPR HDR / SRX17803031 (CpG methylation)   Schema 
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 SRX17803032  HMR  mESC B6129S6F1 Tet1 / SRX17803032 (HMR)   Schema 
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 SRX17803032  CpG methylation  mESC B6129S6F1 Tet1 / SRX17803032 (CpG methylation)   Schema 
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 SRX17803033  HMR  mESC B6129S6F1 Tet1 / SRX17803033 (HMR)   Schema 
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 SRX17803033  CpG methylation  mESC B6129S6F1 Tet1 / SRX17803033 (CpG methylation)   Schema 
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 SRX17803034  HMR  mESC B6129S6F1 Tet1 / SRX17803034 (HMR)   Schema 
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 SRX17803034  CpG methylation  mESC B6129S6F1 Tet1 / SRX17803034 (CpG methylation)   Schema 
    

Study title: Dual gene activating and repressive functions of TET1 in germ layer lineage bifurcation distinguished by genomic context and dependence on 5-methylcytosine oxidation [oxWGBS]
SRA: SRP401089
GEO: not found
Pubmed: not found

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
SRX17803019 mESC B6129S6F1 Tet1 CRISPR HDR 0.702 8.2 25431 1133.2 398 1086.5 520 18052.4 0.979 title: GSM6616451 BS - CM59 - day 2, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1; CRISPR HDR", "tissue": "mESC B6129S6F1 Tet1; CRISPR HDR", "cell_type": "CM59", "genotype": "MUT", "treatment": "day 2", "molecule_type": "BS DNA"}
SRX17803020 mESC B6129S6F1 Tet1 0.811 8.0 27936 1173.1 169 1079.0 837 16885.4 0.979 title: GSM6616453 BS - KO1 - day 2, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1", "tissue": "mESC B6129S6F1 Tet1", "cell_type": "KO1", "genotype": "KO", "treatment": "day 2", "molecule_type": "BS DNA"}
SRX17803021 mESC B6129S6F1 Tet1 0.806 8.1 27582 1197.4 188 976.9 924 14699.8 0.980 title: GSM6616455 BS - WT70 - day 2, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1", "tissue": "mESC B6129S6F1 Tet1", "cell_type": "WT70", "genotype": "WT", "treatment": "day 2", "molecule_type": "BS DNA"}
SRX17803022 mESC B6129S6F1 Tet1 0.807 8.9 24717 1131.9 243 1070.2 778 15589.7 0.984 title: GSM6616462 oxBS - KO15 - day 5 + XAV, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1", "tissue": "mESC B6129S6F1 Tet1", "cell_type": "KO15", "genotype": "KO", "treatment": "day 5 + XAV", "molecule_type": "oxBS DNA"}
SRX17803023 mESC B6129S6F1 Tet1 0.787 7.8 29465 1155.3 240 3022.3 929 14002.3 0.987 title: GSM6616464 oxBS - WT7 - day 5 + XAV, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1", "tissue": "mESC B6129S6F1 Tet1", "cell_type": "WT7", "genotype": "WT", "treatment": "day 5 + XAV", "molecule_type": "oxBS DNA"}
SRX17803024 mESC B6129S6F1 Tet1 CRISPR HDR 0.816 7.8 25579 1168.6 158 1000.3 1155 13752.2 0.980 title: GSM6616452 BS - CM69 - day 2, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1; CRISPR HDR", "tissue": "mESC B6129S6F1 Tet1; CRISPR HDR", "cell_type": "CM69", "genotype": "MUT", "treatment": "day 2", "molecule_type": "BS DNA"}
SRX17803025 mESC B6129S6F1 Tet1 0.698 7.1 27373 1153.6 350 1209.2 734 16252.5 0.978 title: GSM6616454 BS - KO15 - day 2, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1", "tissue": "mESC B6129S6F1 Tet1", "cell_type": "KO15", "genotype": "KO", "treatment": "day 2", "molecule_type": "BS DNA"}
SRX17803026 mESC B6129S6F1 Tet1 0.794 6.9 28525 1193.0 163 1076.7 901 14075.8 0.986 title: GSM6616463 oxBS - WT34 - day 5 + XAV, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1", "tissue": "mESC B6129S6F1 Tet1", "cell_type": "WT34", "genotype": "WT", "treatment": "day 5 + XAV", "molecule_type": "oxBS DNA"}
SRX17803027 mESC B6129S6F1 Tet1 0.786 7.1 27830 1202.4 177 1053.8 1009 14136.3 0.980 title: GSM6616465 oxBS - WT70 - day 2, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1", "tissue": "mESC B6129S6F1 Tet1", "cell_type": "WT70", "genotype": "WT", "treatment": "day 2", "molecule_type": "oxBS DNA"}
SRX17803028 mESC B6129S6F1 Tet1 CRISPR HDR 0.702 6.5 24654 1150.6 391 2181.6 389 21071.5 0.980 title: GSM6616457 oxBS - CM59 - day 2, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1; CRISPR HDR", "tissue": "mESC B6129S6F1 Tet1; CRISPR HDR", "cell_type": "CM59", "genotype": "MUT", "treatment": "day 2", "molecule_type": "oxBS DNA"}
SRX17803029 mESC B6129S6F1 Tet1 0.744 4.7 25088 1267.0 286 1258.0 481 20521.3 0.979 title: GSM6616466 oxBS - WT72 - day 2, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1", "tissue": "mESC B6129S6F1 Tet1", "cell_type": "WT72", "genotype": "WT", "treatment": "day 2", "molecule_type": "oxBS DNA"}
SRX17803030 mESC B6129S6F1 Tet1 0.523 12.1 27721 1112.0 731 1777.6 739 17378.2 0.982 title: GSM6616456 BS - WT72 - day 2, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1", "tissue": "mESC B6129S6F1 Tet1", "cell_type": "WT72", "genotype": "WT", "treatment": "day 2", "molecule_type": "BS DNA"}
SRX17803031 mESC B6129S6F1 Tet1 CRISPR HDR 0.808 7.0 25339 1167.8 144 1001.3 810 15334.8 0.980 title: GSM6616458 oxBS - CM69 - day 2, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1; CRISPR HDR", "tissue": "mESC B6129S6F1 Tet1; CRISPR HDR", "cell_type": "CM69", "genotype": "MUT", "treatment": "day 2", "molecule_type": "oxBS DNA"}
SRX17803032 mESC B6129S6F1 Tet1 0.798 8.6 28200 1163.8 226 1062.5 1051 15657.3 0.979 title: GSM6616459 oxBS - KO1 - day 2, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1", "tissue": "mESC B6129S6F1 Tet1", "cell_type": "KO1", "genotype": "KO", "treatment": "day 2", "molecule_type": "oxBS DNA"}
SRX17803033 mESC B6129S6F1 Tet1 0.810 7.3 23968 1154.3 180 1060.8 759 13738.5 0.984 title: GSM6616460 oxBS - KO1 - day 5 + XAV, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1", "tissue": "mESC B6129S6F1 Tet1", "cell_type": "KO1", "genotype": "KO", "treatment": "day 5 + XAV", "molecule_type": "oxBS DNA"}
SRX17803034 mESC B6129S6F1 Tet1 0.714 6.5 27013 1166.8 346 1189.4 668 17128.3 0.978 title: GSM6616461 oxBS - KO15 - day 2, Mus musculus, Bisulfite-Seq; {"source_name": "mESC B6129S6F1 Tet1", "tissue": "mESC B6129S6F1 Tet1", "cell_type": "KO15", "genotype": "KO", "treatment": "day 2", "molecule_type": "oxBS DNA"}

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.