Mouse methylome studies SRP116373 Track Settings
 
Early-life gene expression in neurons modulates lasting epigenetic states. [Bisulfite-seq] [Cortex, Hippocampus]

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Study title: Early-life gene expression in neurons modulates lasting epigenetic states. [Bisulfite-seq]
SRA: SRP116373
GEO: GSE103213
Pubmed: 29056337

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
SRX3142662 Cortex 0.725 10.6 49101 1202.9 49 1306.6 1393 13154.3 0.993 title: GSM2757470 Cortex_BS_1wk, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "wild type", "background": "C57BL/6", "age": "1 week"}
SRX3142663 Cortex 0.734 12.3 38987 1206.0 71 1169.4 3093 8414.3 0.988 title: GSM2757471 Cortex_BS_2wk, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "wild type", "background": "C57BL/6", "age": "2 week"}
SRX3142664 Cortex 0.753 11.5 38523 1210.0 90 1030.0 2807 9581.4 0.984 title: GSM2757472 Cortex_BS_8wk, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "wild type", "background": "C57BL/6", "age": "8 week"}
SRX3142665 Hippocampus 0.717 9.2 54290 1239.0 35 1288.1 1255 14947.8 0.993 title: GSM2757473 Hippocampus_BS_1wk, Mus musculus, Bisulfite-Seq; {"source_name": "Hippocampus", "genotype": "wild type", "background": "C57BL/6", "age": "1 week"}
SRX3142666 Hippocampus 0.715 13.4 51992 1175.3 63 1354.2 2780 9313.2 0.990 title: GSM2757474 Hippocampus_BS_2wk, Mus musculus, Bisulfite-Seq; {"source_name": "Hippocampus", "genotype": "wild type", "background": "C57BL/6", "age": "2 week"}
SRX3142667 Hippocampus 0.738 12.5 46678 1171.4 82 1072.2 2978 9355.8 0.987 title: GSM2757475 Hippocampus_BS_8wk, Mus musculus, Bisulfite-Seq; {"source_name": "Hippocampus", "genotype": "wild type", "background": "C57BL/6", "age": "8 week"}
SRX3142668 Cortex 0.695 32.9 32712 1154.9 901 882.9 1639 9049.7 0.984 title: GSM2757476 Dnmt3aWT_Cortex_BS_10wk_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Dnmt3a flx/flx", "background": "C57BL/6", "age": "10 week"}
SRX3142669 Cortex 0.492 4.3 23647 1734.6 1061 1105.8 187 24349.9 0.981 title: GSM2757477 Dnmt3aWT_Cortex_BS_10wk_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Dnmt3a flx/flx", "background": "C57BL/6", "age": "10 week"}
SRX3142670 Cortex 0.621 21.6 54910 1312.1 567 952.3 2068 9425.1 0.994 title: GSM2757478 Dnmt3acKO_Cortex_BS_10wk_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Dnmt3a flx/flx Tg(Nes-cre)1Kln/J", "background": "C57BL/6", "age": "10 week"}
SRX3142671 Cortex 0.555 10.8 44077 1410.8 705 977.5 1300 13174.5 0.992 title: GSM2757479 Dnmt3acKO_Cortex_BS_10wk_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Dnmt3a flx/flx Tg(Nes-cre)1Kln/J", "background": "C57BL/6", "age": "10 week"}
SRX3142672 Cortex 0.699 7.8 35884 1261.2 45 1167.0 1032 13305.6 0.992 title: GSM2757480 Pv_BS_1wk_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Pv-cre; Sun1", "background": "C57BL/6", "age": "1 week"}
SRX3142673 Cortex 0.700 8.2 35794 1242.9 47 1399.7 1117 13101.5 0.991 title: GSM2757481 Pv_BS_1wk_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Pv-cre; Sun1", "background": "C57BL/6", "age": "1 week"}
SRX3142674 Cortex 0.792 12.5 67969 1262.8 80 1325.9 4753 18387.5 0.973 title: GSM2757482 Pv_BS_3wk, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Pv-cre; Sun1", "background": "C57BL/6", "age": "3 week"}
SRX3142675 Cortex 0.810 8.7 61308 1220.7 49 1478.3 3283 28916.5 0.968 title: GSM2757483 Pv_BS_8wk_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Pv-cre; Sun1", "background": "C57BL/6", "age": "8 week"}
SRX3142676 Cortex 0.812 8.7 60497 1225.0 44 1252.5 3325 28672.7 0.968 title: GSM2757484 Pv_BS_8wk_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Pv-cre; Sun1", "background": "C57BL/6", "age": "8 week"}
SRX3142677 Cortex 0.726 16.3 53211 1115.1 119 1145.1 2692 8668.2 0.993 title: GSM2757485 Vip_BS_1wk, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Vip-cre; Sun1", "background": "C57BL/6", "age": "1 week"}
SRX3142678 Cortex 0.780 10.2 57618 1182.6 42 1442.6 2017 19199.4 0.979 title: GSM2757486 Vip_BS_3wk_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Vip-cre; Sun1", "background": "C57BL/6", "age": "3 week"}
SRX3142679 Cortex 0.782 11.1 60471 1163.5 50 1515.8 2080 19903.7 0.978 title: GSM2757487 Vip_BS_3wk_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Vip-cre; Sun1", "background": "C57BL/6", "age": "3 week"}
SRX3142680 Cortex 0.801 7.9 55422 1160.2 36 1389.0 2103 17719.9 0.975 title: GSM2757488 Vip_BS_8wk_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Vip-cre; Sun1", "background": "C57BL/6", "age": "8 week"}
SRX3142681 Cortex 0.803 8.1 55546 1163.6 39 1234.0 2245 17284.4 0.975 title: GSM2757489 Vip_BS_8wk_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Vip-cre; Sun1", "background": "C57BL/6", "age": "8 week"}
SRX3239278 Cortex 0.727 2.4 26626 1928.0 13 1555.9 525 40397.5 0.987 title: GSM2802788 Ezh2WT_Cortex_BS_2wk, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Ezh2 fl/fl", "background_strain": "C57BL/6", "tissue": "Cortex", "age": "2 week"}
SRX3239279 Cortex 0.726 2.6 29734 1787.8 7 1760.7 554 40895.8 0.986 title: GSM2802789 Ezh2cKO_Cortex_BS_2wk, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Nes-cre; Ezh2 fl/fl", "background_strain": "C57BL/6", "tissue": "Cortex", "age": "2 week"}
SRX3239280 Hippocampus 0.728 3.7 36530 1601.0 6 1103.3 647 33305.0 0.989 title: GSM2802790 WT_Hippocampus_BS_8wk_DailyKA_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "Hippocampus", "genotype": "wild type", "background_strain": "C57BL/6", "tissue": "Hippocampus", "age": "8 week", "treatment": "Injection of kainic acid (Sigma Aldrich K0250) daily from postnatal day10 (P10) to P20"}
SRX3239281 Hippocampus 0.736 3.5 33314 1683.6 1 1008.0 738 31256.2 0.989 title: GSM2802791 WT_Hippocampus_BS_8wk_DailyKA_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "Hippocampus", "genotype": "wild type", "background_strain": "C57BL/6", "tissue": "Hippocampus", "age": "8 week", "treatment": "Injection of kainic acid (Sigma Aldrich K0250) daily from postnatal day10 (P10) to P20"}
SRX3239282 Hippocampus 0.740 3.6 34668 1609.4 5 980.6 751 26857.3 0.988 title: GSM2802792 WT_Hippocampus_BS_8wk_DailyKA_rep3, Mus musculus, Bisulfite-Seq; {"source_name": "Hippocampus", "genotype": "wild type", "background_strain": "C57BL/6", "tissue": "Hippocampus", "age": "8 week", "treatment": "Injection of kainic acid (Sigma Aldrich K0250) daily from postnatal day10 (P10) to P20"}
SRX3239283 Hippocampus 0.738 3.6 36873 1566.7 4 1698.0 660 32569.7 0.988 title: GSM2802793 WT_Hippocampus_BS_8wk_Control_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "Hippocampus", "genotype": "wild type", "background_strain": "C57BL/6", "tissue": "Hippocampus", "age": "8 week", "treatment": "Control"}
SRX3239284 Hippocampus 0.742 3.7 34395 1638.0 3 897.0 624 34745.2 0.988 title: GSM2802794 WT_Hippocampus_BS_8wk_Control_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "Hippocampus", "genotype": "wild type", "background_strain": "C57BL/6", "tissue": "Hippocampus", "age": "8 week", "treatment": "Control"}
SRX3239285 Hippocampus 0.741 4.1 37130 1484.3 8 1400.6 996 24070.4 0.988 title: GSM2802795 WT_Hippocampus_BS_8wk_Control_rep3, Mus musculus, Bisulfite-Seq; {"source_name": "Hippocampus", "genotype": "wild type", "background_strain": "C57BL/6", "tissue": "Hippocampus", "age": "8 week", "treatment": "Control"}
SRX3239286 Hippocampus 0.739 3.9 35138 1541.3 1 750.0 787 25345.3 0.988 title: GSM2802796 WT_Hippocampus_BS_8wk_Control_rep4, Mus musculus, Bisulfite-Seq; {"source_name": "Hippocampus", "genotype": "wild type", "background_strain": "C57BL/6", "tissue": "Hippocampus", "age": "8 week", "treatment": "Control"}
SRX3239288 Cortex 0.660 1.8 25307 2010.2 2 822.5 373 59789.6 0.988 title: GSM2802798 Cortex_BS_12wk, Mus musculus, Bisulfite-Seq; {"source_name": "Cortex", "genotype": "Dnmt3a fl/fl", "background_strain": "C57BL/6", "tissue": "Cortex", "age": "12 week"}

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.