Mouse methylome studies SRP292265 Track Settings
 
Cell type-specific transcriptomic and eipgenome analysis of diabetic cardiomyopathy [Heart]

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Study title: Cell type-specific transcriptomic and eipgenome analysis of diabetic cardiomyopathy
SRA: SRP292265
GEO: not found
Pubmed: not found

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
SRX9489442 Heart 0.670 2.3 28447 1984.6 17 975.5 244 46329.6 0.994 title: Endothelialcell_STZ_03_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Endothelial cell", "treatment": "STZ", "biological_replicate": "replicate 3"}
SRX9489443 Heart 0.664 1.6 24639 2231.1 7 761.9 142 73452.1 0.994 title: Endothelialcell_STZ_04_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Endothelial cell", "treatment": "STZ", "biological_replicate": "replicate 4"}
SRX9489444 Heart 0.618 3.0 24176 2277.9 20 1333.2 159 43568.0 0.984 title: Fibroblast_CTRL_01_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Fibroblast", "treatment": "control", "biological_replicate": "replicate 1"}
SRX9489445 Heart 0.619 6.0 42277 1367.6 62 1054.9 628 17529.5 0.987 title: Fibroblast_CTRL_02_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Fibroblast", "treatment": "control", "biological_replicate": "replicate 2"}
SRX9489446 Heart 0.621 3.5 28021 1969.2 19 1241.4 281 30856.9 0.984 title: Fibroblast_STZ_01_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Fibroblast", "treatment": "STZ", "biological_replicate": "replicate 1"}
SRX9489448 Heart 0.645 15.3 66075 987.0 214 1011.7 1685 9219.3 0.992 title: Fibroblast_STZ_02_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Fibroblast", "treatment": "STZ", "biological_replicate": "replicate 2"}
SRX9489456 Heart 0.707 1.6 24848 1887.9 9 1060.7 110 61792.1 0.989 title: Macrophage_STZ_04_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Macrophage", "treatment": "STZ", "biological_replicate": "replicate 4"}
SRX9489493 Heart 0.642 7.1 32579 1275.5 81 1206.2 803 17225.7 0.987 title: Cardiacmyocyte_CTRL_01_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Cardiac myocyte", "treatment": "control", "biological_replicate": "replicate 1"}
SRX9489494 Heart 0.690 8.9 43336 1129.3 237 990.9 1875 42604.2 0.990 title: Cardiacmyocyte_CTRL_03_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Cardiac myocyte", "treatment": "control", "biological_replicate": "replicate 3"}
SRX9489495 Heart 0.654 7.4 37301 1273.2 81 1091.8 1079 23825.0 0.987 title: Cardiacmyocyte_CTRL_02_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Cardiac myocyte", "treatment": "control", "biological_replicate": "replicate 2"}
SRX9489496 Heart 0.687 11.1 49533 1028.2 214 1029.6 2478 32340.6 0.989 title: Cardiacmyocyte_CTRL_04_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Cardiac myocyte", "treatment": "control", "biological_replicate": "replicate 4"}
SRX9489497 Heart 0.667 10.5 37211 1158.7 228 978.8 1199 17542.6 0.988 title: Cardiacmyocyte_STZ_01_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Cardiac myocyte", "treatment": "STZ", "biological_replicate": "replicate 1"}
SRX9489498 Heart 0.689 10.2 46497 1070.7 229 1051.7 2395 30916.0 0.991 title: Cardiacmyocyte_STZ_02_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Cardiac myocyte", "treatment": "STZ", "biological_replicate": "replicate 2"}
SRX9489499 Heart 0.682 6.8 41827 1193.2 91 954.8 1694 35389.8 0.990 title: Cardiacmyocyte_STZ_03_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Cardiac myocyte", "treatment": "STZ", "biological_replicate": "replicate 3"}
SRX9489500 Heart 0.667 2.0 25602 2211.2 12 974.8 221 46495.2 0.994 title: Endothelialcell_CTRL_01_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Endothelial cell", "treatment": "control", "biological_replicate": "replicate 1"}
SRX9489502 Heart 0.666 2.2 27050 2064.9 25 1118.6 164 52429.7 0.993 title: Endothelialcell_CTRL_02_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Endothelial cell", "treatment": "control", "biological_replicate": "replicate 2"}
SRX9489503 Heart 0.670 2.0 27078 2089.3 15 828.3 129 61548.5 0.994 title: Endothelialcell_CTRL_03_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Endothelial cell", "treatment": "control", "biological_replicate": "replicate 3"}
SRX9489504 Heart 0.670 2.2 27481 2048.3 5 795.8 215 47276.5 0.994 title: Endothelialcell_CTRL_04_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Endothelial cell", "treatment": "control", "biological_replicate": "replicate 4"}
SRX9489505 Heart 0.667 1.9 25297 2141.6 13 822.4 146 56424.9 0.994 title: Endothelialcell_STZ_01_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Endothelial cell", "treatment": "STZ", "biological_replicate": "replicate 1"}
SRX9489506 Heart 0.673 2.1 26163 2063.6 18 1141.2 141 52716.4 0.994 title: Endothelialcell_STZ_02_WGBS; {"strain": "C57BL/6", "dev_stage": "adult", "sex": "male", "tissue": "heart", "cell_type": "Endothelial cell", "treatment": "STZ", "biological_replicate": "replicate 2"}

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.