Mouse methylome studies SRP590085 Track Settings
 
NAD+-dependent Sirt6 is a key regulator involved in telomere shortening of in vitro-cultured preimplantation embryos [Bisulfite-Seq] [Muscle tissue and Connective]

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
SRX29059735 
SRX29059736 
SRX29059737 
SRX29059738 
SRX29059739 
SRX29059740 
SRX29059741 
SRX29059742 
SRX29059743 
SRX29059744 
SRX29059745 
SRX29059746 
List subtracks: only selected/visible    all    ()
  experiment↓1 views↓2   Track Name↓3  
hide
 SRX29059735  HMR  Muscle tissue and Connective / SRX29059735 (HMR)   Schema 
hide
 Configure
 SRX29059735  CpG methylation  Muscle tissue and Connective / SRX29059735 (CpG methylation)   Schema 
hide
 SRX29059736  HMR  Muscle tissue and Connective / SRX29059736 (HMR)   Schema 
hide
 Configure
 SRX29059736  CpG methylation  Muscle tissue and Connective / SRX29059736 (CpG methylation)   Schema 
hide
 SRX29059737  HMR  Muscle tissue and Connective / SRX29059737 (HMR)   Schema 
hide
 Configure
 SRX29059737  CpG methylation  Muscle tissue and Connective / SRX29059737 (CpG methylation)   Schema 
hide
 SRX29059738  HMR  Muscle tissue and Connective / SRX29059738 (HMR)   Schema 
hide
 Configure
 SRX29059738  CpG methylation  Muscle tissue and Connective / SRX29059738 (CpG methylation)   Schema 
hide
 SRX29059739  HMR  Muscle tissue and Connective / SRX29059739 (HMR)   Schema 
hide
 Configure
 SRX29059739  CpG methylation  Muscle tissue and Connective / SRX29059739 (CpG methylation)   Schema 
hide
 SRX29059740  HMR  Muscle tissue and Connective / SRX29059740 (HMR)   Schema 
hide
 Configure
 SRX29059740  CpG methylation  Muscle tissue and Connective / SRX29059740 (CpG methylation)   Schema 
hide
 SRX29059741  HMR  Muscle tissue and Connective / SRX29059741 (HMR)   Schema 
hide
 Configure
 SRX29059741  CpG methylation  Muscle tissue and Connective / SRX29059741 (CpG methylation)   Schema 
hide
 SRX29059742  HMR  Muscle tissue and Connective / SRX29059742 (HMR)   Schema 
hide
 Configure
 SRX29059742  CpG methylation  Muscle tissue and Connective / SRX29059742 (CpG methylation)   Schema 
hide
 SRX29059743  HMR  Muscle tissue and Connective / SRX29059743 (HMR)   Schema 
hide
 Configure
 SRX29059743  CpG methylation  Muscle tissue and Connective / SRX29059743 (CpG methylation)   Schema 
hide
 SRX29059744  HMR  Muscle tissue and Connective / SRX29059744 (HMR)   Schema 
hide
 Configure
 SRX29059744  CpG methylation  Muscle tissue and Connective / SRX29059744 (CpG methylation)   Schema 
hide
 SRX29059745  HMR  Muscle tissue and Connective / SRX29059745 (HMR)   Schema 
hide
 Configure
 SRX29059745  CpG methylation  Muscle tissue and Connective / SRX29059745 (CpG methylation)   Schema 
hide
 SRX29059746  HMR  Muscle tissue and Connective / SRX29059746 (HMR)   Schema 
hide
 Configure
 SRX29059746  CpG methylation  Muscle tissue and Connective / SRX29059746 (CpG methylation)   Schema 
    

Study title: NAD+-dependent Sirt6 is a key regulator involved in telomere shortening of in vitro-cultured preimplantation embryos [Bisulfite-Seq]
SRA: SRP590085
GEO: not found
Pubmed: not found

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
SRX29059735 Muscle tissue and Connective 0.680 2.0 25447 2030.5 65 1048.2 91 90918.4 0.993 title: GSM9031915 Invivo_W1_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "Tail DNA of 1-week-old mice born from in vivo blastocyst transfer", "tissue": "Muscle tissue and Connective tissue", "cell_type": "somatic cell", "treatment": "in vivo embryo tranfer", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29059736 Muscle tissue and Connective 0.653 3.3 30601 1648.1 191 1010.4 221 48511.0 0.992 title: GSM9031916 Invivo_W1_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "Tail DNA of 1-week-old mice born from in vivo blastocyst transfer", "tissue": "Muscle tissue and Connective tissue", "cell_type": "somatic cell", "treatment": "in vivo embryo tranfer", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29059737 Muscle tissue and Connective 0.656 2.1 25930 2318.5 106 1059.0 151 80730.1 0.993 title: GSM9031917 Invivo_W1_rep3, Mus musculus, Bisulfite-Seq; {"source_name": "Tail DNA of 1-week-old mice born from in vivo blastocyst transfer", "tissue": "Muscle tissue and Connective tissue", "cell_type": "somatic cell", "treatment": "in vivo embryo tranfer", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29059738 Muscle tissue and Connective 0.530 2.8 23008 2303.5 572 930.8 196 38817.1 0.977 title: GSM9031918 Invitro_W1_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "Tail DNA of 1-week-old mice born from in vitro blastocyst transfer", "tissue": "Muscle tissue and Connective tissue", "cell_type": "somatic cell", "treatment": "in vitro embryo tranfer", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29059739 Muscle tissue and Connective 0.581 2.8 21832 2273.8 426 971.6 112 60863.4 0.933 title: GSM9031919 Invitro_W1_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "Tail DNA of 1-week-old mice born from in vitro blastocyst transfer", "tissue": "Muscle tissue and Connective tissue", "cell_type": "somatic cell", "treatment": "in vitro embryo tranfer", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29059740 Muscle tissue and Connective 0.673 2.3 27951 1820.5 123 1052.1 67 87206.2 0.977 title: GSM9031920 Invitro_W1_rep3, Mus musculus, Bisulfite-Seq; {"source_name": "Tail DNA of 1-week-old mice born from in vitro blastocyst transfer", "tissue": "Muscle tissue and Connective tissue", "cell_type": "somatic cell", "treatment": "in vitro embryo tranfer", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29059741 Muscle tissue and Connective 0.645 2.8 26795 1851.1 198 1047.8 176 50512.4 0.974 title: GSM9031921 Invivo_W7_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "Tail DNA of 7-week-old mice born from in vivo blastocyst transfer", "tissue": "Muscle tissue and Connective tissue", "cell_type": "somatic cell", "treatment": "in vivo embryo tranfer", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29059742 Muscle tissue and Connective 0.637 3.2 29116 1778.1 295 993.5 230 43588.0 0.992 title: GSM9031922 Invivo_W7_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "Tail DNA of 7-week-old mice born from in vivo blastocyst transfer", "tissue": "Muscle tissue and Connective tissue", "cell_type": "somatic cell", "treatment": "in vivo embryo tranfer", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29059743 Muscle tissue and Connective 0.652 2.5 25489 1975.8 159 1024.3 110 66789.9 0.992 title: GSM9031923 Invivo_W7_rep3, Mus musculus, Bisulfite-Seq; {"source_name": "Tail DNA of 7-week-old mice born from in vivo blastocyst transfer", "tissue": "Muscle tissue and Connective tissue", "cell_type": "somatic cell", "treatment": "in vivo embryo tranfer", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29059744 Muscle tissue and Connective 0.592 2.5 21887 2225.3 532 1804.9 55 64773.8 0.985 title: GSM9031924 Invitro_W7_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "Tail DNA of 7-week-old mice born from in vitro blastocyst transfer", "tissue": "Muscle tissue and Connective tissue", "cell_type": "somatic cell", "treatment": "in vitro embryo tranfer", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29059745 Muscle tissue and Connective 0.627 3.8 28130 1580.5 522 1021.5 146 44483.1 0.987 title: GSM9031925 Invitro_W7_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "Tail DNA of 7-week-old mice born from in vitro blastocyst transfer", "tissue": "Muscle tissue and Connective tissue", "cell_type": "somatic cell", "treatment": "in vitro embryo tranfer", "geo_loc_name": "missing", "collection_date": "missing"}
SRX29059746 Muscle tissue and Connective 0.632 2.6 24191 2102.5 117 1049.3 171 53851.3 0.992 title: GSM9031926 Invitro_W7_rep3, Mus musculus, Bisulfite-Seq; {"source_name": "Tail DNA of 7-week-old mice born from in vitro blastocyst transfer", "tissue": "Muscle tissue and Connective tissue", "cell_type": "somatic cell", "treatment": "in vitro embryo tranfer", "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.