Mouse methylome studies SRP092540 Track Settings
 
WGBS assessment of global methylation alterations in hematopoietic stem and progenitor cells [methyl-seq] [Intermediate-Term Hematopoietic Stem Cell, Long-Term Hematopoietic Stem Cell, Multi-Potent Progenitor, Short-Term Hematopoeitic Stem Cell]

Track collection: Mouse methylome studies

+  All tracks in this collection (604)

Maximum display mode:       Reset to defaults   
Select views (Help):
PMD       HMR       AMR       CpG methylation ▾       CpG reads ▾      
Select subtracks by views and experiment:
 All views PMD  HMR  AMR  CpG methylation  CpG reads 
experiment
SRX2323930 
SRX2323931 
SRX2323932 
SRX2323933 
SRX2323934 
SRX2323936 
List subtracks: only selected/visible    all    ()
  experiment↓1 views↓2   Track Name↓3  
hide
 SRX2323930  PMD  Long-Term Hematopoietic Stem Cell / SRX2323930 (PMD)   Schema 
hide
 SRX2323930  HMR  Long-Term Hematopoietic Stem Cell / SRX2323930 (HMR)   Schema 
hide
 Configure
 SRX2323930  CpG methylation  Long-Term Hematopoietic Stem Cell / SRX2323930 (CpG methylation)   Schema 
hide
 Configure
 SRX2323930  CpG reads  Long-Term Hematopoietic Stem Cell / SRX2323930 (CpG reads)   Schema 
hide
 SRX2323931  PMD  Intermediate-Term Hematopoietic Stem Cell / SRX2323931 (PMD)   Schema 
hide
 SRX2323931  HMR  Intermediate-Term Hematopoietic Stem Cell / SRX2323931 (HMR)   Schema 
hide
 SRX2323931  AMR  Intermediate-Term Hematopoietic Stem Cell / SRX2323931 (AMR)   Schema 
hide
 Configure
 SRX2323931  CpG methylation  Intermediate-Term Hematopoietic Stem Cell / SRX2323931 (CpG methylation)   Schema 
hide
 Configure
 SRX2323931  CpG reads  Intermediate-Term Hematopoietic Stem Cell / SRX2323931 (CpG reads)   Schema 
hide
 SRX2323932  PMD  Intermediate-Term Hematopoietic Stem Cell / SRX2323932 (PMD)   Schema 
hide
 SRX2323932  HMR  Intermediate-Term Hematopoietic Stem Cell / SRX2323932 (HMR)   Schema 
hide
 SRX2323932  AMR  Intermediate-Term Hematopoietic Stem Cell / SRX2323932 (AMR)   Schema 
hide
 Configure
 SRX2323932  CpG methylation  Intermediate-Term Hematopoietic Stem Cell / SRX2323932 (CpG methylation)   Schema 
hide
 Configure
 SRX2323932  CpG reads  Intermediate-Term Hematopoietic Stem Cell / SRX2323932 (CpG reads)   Schema 
hide
 SRX2323933  HMR  Short-Term Hematopoeitic Stem Cell / SRX2323933 (HMR)   Schema 
hide
 SRX2323933  PMD  Short-Term Hematopoeitic Stem Cell / SRX2323933 (PMD)   Schema 
hide
 Configure
 SRX2323933  CpG methylation  Short-Term Hematopoeitic Stem Cell / SRX2323933 (CpG methylation)   Schema 
hide
 Configure
 SRX2323933  CpG reads  Short-Term Hematopoeitic Stem Cell / SRX2323933 (CpG reads)   Schema 
hide
 SRX2323934  PMD  Short-Term Hematopoeitic Stem Cell / SRX2323934 (PMD)   Schema 
hide
 SRX2323934  HMR  Short-Term Hematopoeitic Stem Cell / SRX2323934 (HMR)   Schema 
hide
 SRX2323934  AMR  Short-Term Hematopoeitic Stem Cell / SRX2323934 (AMR)   Schema 
hide
 Configure
 SRX2323934  CpG methylation  Short-Term Hematopoeitic Stem Cell / SRX2323934 (CpG methylation)   Schema 
hide
 Configure
 SRX2323934  CpG reads  Short-Term Hematopoeitic Stem Cell / SRX2323934 (CpG reads)   Schema 
hide
 SRX2323936  PMD  Multi-Potent Progenitor / SRX2323936 (PMD)   Schema 
hide
 SRX2323936  HMR  Multi-Potent Progenitor / SRX2323936 (HMR)   Schema 
hide
 SRX2323936  AMR  Multi-Potent Progenitor / SRX2323936 (AMR)   Schema 
hide
 Configure
 SRX2323936  CpG methylation  Multi-Potent Progenitor / SRX2323936 (CpG methylation)   Schema 
hide
 Configure
 SRX2323936  CpG reads  Multi-Potent Progenitor / SRX2323936 (CpG reads)   Schema 
    

Study title: WGBS assessment of global methylation alterations in hematopoietic stem and progenitor cells [methyl-seq]
SRA: SRP092540
GEO: GSE89490
Pubmed: 29727682

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
SRX2323930 Long-Term Hematopoietic Stem Cell 0.708 1.9 26931 1663.9 0 0.0 101 76381.5 0.965 title: GSM2373805 long-term hematopoietic stem cell rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "Hematopoietic stem cells", "strain": "C57BL/6", "age": "8-12 weeks old", "cell_type": "long-term hematopoietic stem cell"}
SRX2323931 Intermediate-Term Hematopoietic Stem Cell 0.760 2.0 28855 1449.8 2 1036.0 140 65755.8 0.962 title: GSM2373806 intermediate-term hematopoietic stem cell rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "Hematopoietic stem cells", "strain": "C57BL/6", "age": "8-12 weeks old", "cell_type": "intermediate-term hematopoietic stem cell"}
SRX2323932 Intermediate-Term Hematopoietic Stem Cell 0.758 2.8 31768 1349.7 1 733.0 234 44278.7 0.969 title: GSM2373807 intermediate-term hematopoietic stem cell rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "Hematopoietic stem cells", "strain": "C57BL/6", "age": "8-12 weeks old", "cell_type": "intermediate-term hematopoietic stem cell"}
SRX2323933 Short-Term Hematopoeitic Stem Cell 0.734 2.2 29224 1473.2 0 0.0 121 58934.8 0.965 title: GSM2373808 short-term hematopoeitic stem cell rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "Hematopoietic stem cells", "strain": "C57BL/6", "age": "8-12 weeks old", "cell_type": "short-term hematopoeitic stem cell"}
SRX2323934 Short-Term Hematopoeitic Stem Cell 0.741 2.0 30097 1420.5 2 1244.5 159 70795.4 0.971 title: GSM2373809 short-term hematopoeitic stem cell rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "Hematopoietic stem cells", "strain": "C57BL/6", "age": "8-12 weeks old", "cell_type": "short-term hematopoeitic stem cell"}
SRX2323936 Multi-Potent Progenitor 0.765 2.2 31140 1387.9 2 830.5 152 64957.6 0.967 title: GSM2373811 multi-potent progenitor rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "Hematopoietic stem cells", "strain": "C57BL/6", "age": "8-12 weeks old", "cell_type": "multi-potent progenitor"}

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.