Mouse methylome studies SRP490016 Track Settings
 
Methylation status of CD4+ and CD11b+ cells from Dnmt3a+/+ or Dnmt3aR878/+ mice [Spleen]

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 SRX23642421  CpG methylation  Spleen / SRX23642421 (CpG methylation)   Schema 
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 SRX23642422  CpG methylation  Spleen / SRX23642422 (CpG methylation)   Schema 
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 SRX23642423  CpG methylation  Spleen / SRX23642423 (CpG methylation)   Schema 
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 SRX23642424  CpG methylation  Spleen / SRX23642424 (CpG methylation)   Schema 
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 SRX23642425  CpG methylation  Spleen / SRX23642425 (CpG methylation)   Schema 
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 SRX23642426  CpG methylation  Spleen / SRX23642426 (CpG methylation)   Schema 
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 SRX23642428  CpG methylation  Spleen / SRX23642428 (CpG methylation)   Schema 
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 SRX23642429  CpG methylation  Spleen / SRX23642429 (CpG methylation)   Schema 
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 SRX23642430  CpG methylation  Spleen / SRX23642430 (CpG methylation)   Schema 
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 SRX23642431  CpG methylation  Spleen / SRX23642431 (CpG methylation)   Schema 
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Study title: Methylation status of CD4+ and CD11b+ cells from Dnmt3a+/+ or Dnmt3aR878/+ mice
SRA: SRP490016
GEO: not found
Pubmed: not found

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
SRX23642418 Spleen 0.806 22.0 55456 952.5 858 1077.6 3507 7208.4 0.989 title: GSM8083224 01_WT-CD11b-1_S110_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD11b+ cells", "cell_type": "CD11b+ cells", "genotype": "Dnmt3a+/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642419 Spleen 0.804 22.0 55619 954.2 786 1075.3 2827 7904.1 0.989 title: GSM8083225 02_WT-CD11b-2_S111_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD11b+ cells", "cell_type": "CD11b+ cells", "genotype": "Dnmt3a+/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642420 Spleen 0.808 25.1 57488 948.3 889 1073.6 3167 7704.5 0.989 title: GSM8083226 03_WT-CD11b-3_S112_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD11b+ cells", "cell_type": "CD11b+ cells", "genotype": "Dnmt3a+/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642421 Spleen 0.809 21.9 56017 950.2 897 1069.9 3054 7661.0 0.989 title: GSM8083227 04_WT-CD11b-4_S113_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD11b+ cells", "cell_type": "CD11b+ cells", "genotype": "Dnmt3a+/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642422 Spleen 0.759 24.1 71993 904.9 600 1068.5 3460 8481.4 0.989 title: GSM8083228 05_DNMT3A-CD11b-1_S114_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD11b+ cells", "cell_type": "CD11b+ cells", "genotype": "Dnmt3aR878/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642423 Spleen 0.762 25.1 72755 900.0 641 1099.3 3907 8025.7 0.989 title: GSM8083229 06_DNMT3A-CD11b-2_S115_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD11b+ cells", "cell_type": "CD11b+ cells", "genotype": "Dnmt3aR878/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642424 Spleen 0.774 18.7 63831 982.6 753 1073.4 3644 8698.6 0.990 title: GSM8083230 07_DNMT3A-CD11b-3_S116_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD11b+ cells", "cell_type": "CD11b+ cells", "genotype": "Dnmt3aR878/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642425 Spleen 0.775 3.8 39978 1389.4 218 955.6 735 29744.8 0.961 title: GSM8083231 07_DNMT3A-CD11b-3_S201_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD11b+ cells", "cell_type": "CD11b+ cells", "genotype": "Dnmt3aR878/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642426 Spleen 0.777 19.2 64101 977.0 832 1102.2 3601 8629.1 0.989 title: GSM8083232 08_DNMT3A-CD11b-4_S117_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD11b+ cells", "cell_type": "CD11b+ cells", "genotype": "Dnmt3aR878/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642427 Spleen 0.778 4.0 40654 1370.9 315 1005.8 731 29994.0 0.959 title: GSM8083233 08_DNMT3A-CD11b-4_S202_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD11b+ cells", "cell_type": "CD11b+ cells", "genotype": "Dnmt3aR878/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642428 Spleen 0.811 25.7 55435 983.1 927 1079.2 2950 8304.6 0.988 title: GSM8083234 09_WT-CD4-1_S118_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD4+ cells", "cell_type": "CD4+ cells", "genotype": "Dnmt3a+/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642429 Spleen 0.821 23.5 54833 1005.4 604 1006.5 3223 7940.7 0.994 title: GSM8083235 10_WT-CD4-2_S203_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD4+ cells", "cell_type": "CD4+ cells", "genotype": "Dnmt3a+/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642430 Spleen 0.816 22.2 55702 985.9 814 1063.4 3128 8148.5 0.989 title: GSM8083236 11_WT-CD4-3_S119_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD4+ cells", "cell_type": "CD4+ cells", "genotype": "Dnmt3a+/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642431 Spleen 0.818 21.3 55080 986.7 882 1054.8 3483 7733.2 0.989 title: GSM8083237 12_WT-CD4-4_S120_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD4+ cells", "cell_type": "CD4+ cells", "genotype": "Dnmt3a+/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642432 Spleen 0.763 22.9 58292 1011.5 726 1045.2 3313 8403.2 0.989 title: GSM8083238 13_DNMT3A-CD4-1_S204_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD4+ cells", "cell_type": "CD4+ cells", "genotype": "Dnmt3aR878/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642433 Spleen 0.765 23.4 60115 1010.7 409 981.1 3203 8678.4 0.994 title: GSM8083239 14_DNMT3A-CD4-2_S205_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD4+ cells", "cell_type": "CD4+ cells", "genotype": "Dnmt3aR878/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642434 Spleen 0.785 33.5 68964 994.2 793 1066.2 4107 8647.6 0.994 title: GSM8083240 15_DNMT3A-CD4-3_S206_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD4+ cells", "cell_type": "CD4+ cells", "genotype": "Dnmt3aR878/+", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23642435 Spleen 0.786 33.8 69081 994.3 826 1064.3 3903 8784.9 0.993 title: GSM8083241 16_DNMT3A-CD4-4_S207_R1, Mus musculus, Bisulfite-Seq; {"source_name": "spleen", "tissue": "spleen", "cell_line": "CD4+ cells", "cell_type": "CD4+ cells", "genotype": "Dnmt3aR878/+", "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.