Mouse methylome studies SRP337411 Track Settings
 
Examining age-dependent DNA methylation patterns and gene expression in the male and female mouse hippocampus [Dorsal Hippocampus]

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 SRX12204111  CpG methylation  Dorsal Hippocampus / SRX12204111 (CpG methylation)   Schema 
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 SRX12204113  CpG methylation  Dorsal Hippocampus / SRX12204113 (CpG methylation)   Schema 
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 SRX12204114  CpG methylation  Dorsal Hippocampus / SRX12204114 (CpG methylation)   Schema 
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 SRX12204115  CpG methylation  Dorsal Hippocampus / SRX12204115 (CpG methylation)   Schema 
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 SRX12204117  CpG methylation  Dorsal Hippocampus / SRX12204117 (CpG methylation)   Schema 
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 SRX12204118  CpG methylation  Dorsal Hippocampus / SRX12204118 (CpG methylation)   Schema 
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Study title: Examining age-dependent DNA methylation patterns and gene expression in the male and female mouse hippocampus
SRA: SRP337411
GEO: GSE184267
Pubmed: 34598831

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
SRX12204088 Dorsal Hippocampus 0.716 3.9 28675 1907.5 144 1014.9 602 34639.2 0.975 title: GSM5582924 20 Month Female 02 (L2-P02), Mus musculus, Bisulfite-Seq; {"source_name": "Mouse dorsal hippocampus", "strain": "C57BL/6", "age": "20 month", "sex": "female", "tissue": "Mouse dorsal hippocampus"}
SRX12204090 Dorsal Hippocampus 0.716 2.8 24017 2095.9 63 1189.4 453 51591.6 0.974 title: GSM5582926 20 Month Female 04 (L2-P04), Mus musculus, Bisulfite-Seq; {"source_name": "Mouse dorsal hippocampus", "strain": "C57BL/6", "age": "20 month", "sex": "female", "tissue": "Mouse dorsal hippocampus"}
SRX12204106 Dorsal Hippocampus 0.675 2.9 25088 1967.3 131 1039.2 368 48081.9 0.974 title: GSM5582942 2 Month Female 01 (L2-P11), Mus musculus, Bisulfite-Seq; {"source_name": "Mouse dorsal hippocampus", "strain": "C57BL/6J", "age": "2 month", "sex": "female", "tissue": "Mouse dorsal hippocampus"}
SRX12204110 Dorsal Hippocampus 0.672 3.4 25626 2046.8 219 977.9 455 46567.1 0.975 title: GSM5582946 2 Month Female 05 (L3-P12), Mus musculus, Bisulfite-Seq; {"source_name": "Mouse dorsal hippocampus", "strain": "C57BL/6J", "age": "2 month", "sex": "female", "tissue": "Mouse dorsal hippocampus"}
SRX12204111 Dorsal Hippocampus 0.670 3.7 27527 1975.9 261 1067.8 246 49288.8 0.976 title: GSM5582947 2 Month Female 06 (L3-P13), Mus musculus, Bisulfite-Seq; {"source_name": "Mouse dorsal hippocampus", "strain": "C57BL/6J", "age": "2 month", "sex": "female", "tissue": "Mouse dorsal hippocampus"}
SRX12204112 Dorsal Hippocampus 0.704 3.9 28664 1974.8 127 979.5 659 36500.3 0.975 title: GSM5582948 2 Month Female 07 (L3-P14), Mus musculus, Bisulfite-Seq; {"source_name": "Mouse dorsal hippocampus", "strain": "C57BL/6J", "age": "2 month", "sex": "female", "tissue": "Mouse dorsal hippocampus"}
SRX12204113 Dorsal Hippocampus 0.696 3.0 27500 2021.5 82 1245.4 578 40530.9 0.976 title: GSM5582949 2 Month Female 08 (L3-P15), Mus musculus, Bisulfite-Seq; {"source_name": "Mouse dorsal hippocampus", "strain": "C57BL/6J", "age": "2 month", "sex": "female", "tissue": "Mouse dorsal hippocampus"}
SRX12204114 Dorsal Hippocampus 0.657 3.7 27597 2074.7 284 1013.7 471 43561.6 0.975 title: GSM5582950 2 Month Female 09 (L3-P16), Mus musculus, Bisulfite-Seq; {"source_name": "Mouse dorsal hippocampus", "strain": "C57BL/6J", "age": "2 month", "sex": "female", "tissue": "Mouse dorsal hippocampus"}
SRX12204115 Dorsal Hippocampus 0.693 3.9 27866 1962.5 138 1120.2 483 36938.0 0.972 title: GSM5582951 2 Month Male 01 (L2-P14), Mus musculus, Bisulfite-Seq; {"source_name": "Mouse dorsal hippocampus", "strain": "C57BL/6J", "age": "2 month", "sex": "male", "tissue": "Mouse dorsal hippocampus"}
SRX12204117 Dorsal Hippocampus 0.674 4.6 27397 1968.5 249 1048.8 581 34392.7 0.974 title: GSM5582953 2 Month Male 03 (L2-P16), Mus musculus, Bisulfite-Seq; {"source_name": "Mouse dorsal hippocampus", "strain": "C57BL/6J", "age": "2 month", "sex": "male", "tissue": "Mouse dorsal hippocampus"}
SRX12204118 Dorsal Hippocampus 0.686 4.5 29119 1959.2 184 1047.0 528 37977.2 0.975 title: GSM5582954 2 Month Male 04 (L2-P17), Mus musculus, Bisulfite-Seq; {"source_name": "Mouse dorsal hippocampus", "strain": "C57BL/6J", "age": "2 month", "sex": "male", "tissue": "Mouse dorsal hippocampus"}
SRX12204119 Dorsal Hippocampus 0.708 3.0 25894 2042.2 71 1044.3 511 42667.4 0.974 title: GSM5582955 2 Month Male 05 (L2-P18), Mus musculus, Bisulfite-Seq; {"source_name": "Mouse dorsal hippocampus", "strain": "C57BL/6J", "age": "2 month", "sex": "male", "tissue": "Mouse dorsal hippocampus"}
SRX12204121 Dorsal Hippocampus 0.688 3.1 26300 1960.0 93 1073.0 235 53443.5 0.973 title: GSM5582957 2 Month Male 07 (L3-P17), Mus musculus, Bisulfite-Seq; {"source_name": "Mouse dorsal hippocampus", "strain": "C57BL/6J", "age": "2 month", "sex": "male", "tissue": "Mouse dorsal hippocampus"}
SRX12204122 Dorsal Hippocampus 0.685 3.4 27761 2004.0 128 1122.5 474 44478.9 0.974 title: GSM5582958 2 Month Male 08 (L3-P18), Mus musculus, Bisulfite-Seq; {"source_name": "Mouse dorsal hippocampus", "strain": "C57BL/6J", "age": "2 month", "sex": "male", "tissue": "Mouse dorsal hippocampus"}

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.