Mouse methylome studies SRP511364 Track Settings
 
Maternal loss-of-function of Nlrp2 results in failure of epigenetic reprogramming in mouse oocytes [Ovary]

Track collection: Mouse methylome studies

+  All tracks in this collection (604)

Maximum display mode:       Reset to defaults   
Select views (Help):
AMR       CpG reads ▾       CpG methylation ▾       PMD      
Select subtracks by views and experiment:
 All views AMR  CpG reads  CpG methylation  PMD 
experiment
SRX24781899 
SRX24781900 
SRX24781901 
SRX24781902 
SRX24781904 
SRX24781905 
SRX24781906 
List subtracks: only selected/visible    all    ()
  experiment↓1 views↓2   Track Name↓3  
hide
 SRX24781899  AMR  Ovary / SRX24781899 (AMR)   Schema 
hide
 Configure
 SRX24781899  CpG reads  Ovary / SRX24781899 (CpG reads)   Schema 
hide
 Configure
 SRX24781899  CpG methylation  Ovary / SRX24781899 (CpG methylation)   Schema 
hide
 SRX24781899  PMD  Ovary / SRX24781899 (PMD)   Schema 
hide
 SRX24781900  AMR  Ovary / SRX24781900 (AMR)   Schema 
hide
 SRX24781900  PMD  Ovary / SRX24781900 (PMD)   Schema 
hide
 Configure
 SRX24781900  CpG reads  Ovary / SRX24781900 (CpG reads)   Schema 
hide
 Configure
 SRX24781900  CpG methylation  Ovary / SRX24781900 (CpG methylation)   Schema 
hide
 SRX24781901  AMR  Ovary / SRX24781901 (AMR)   Schema 
hide
 Configure
 SRX24781901  CpG reads  Ovary / SRX24781901 (CpG reads)   Schema 
hide
 Configure
 SRX24781901  CpG methylation  Ovary / SRX24781901 (CpG methylation)   Schema 
hide
 SRX24781901  PMD  Ovary / SRX24781901 (PMD)   Schema 
hide
 SRX24781902  AMR  Ovary / SRX24781902 (AMR)   Schema 
hide
 Configure
 SRX24781902  CpG reads  Ovary / SRX24781902 (CpG reads)   Schema 
hide
 Configure
 SRX24781902  CpG methylation  Ovary / SRX24781902 (CpG methylation)   Schema 
hide
 SRX24781902  PMD  Ovary / SRX24781902 (PMD)   Schema 
hide
 SRX24781904  AMR  Ovary / SRX24781904 (AMR)   Schema 
hide
 Configure
 SRX24781904  CpG reads  Ovary / SRX24781904 (CpG reads)   Schema 
hide
 Configure
 SRX24781904  CpG methylation  Ovary / SRX24781904 (CpG methylation)   Schema 
hide
 SRX24781904  PMD  Ovary / SRX24781904 (PMD)   Schema 
hide
 SRX24781905  AMR  Ovary / SRX24781905 (AMR)   Schema 
hide
 Configure
 SRX24781905  CpG reads  Ovary / SRX24781905 (CpG reads)   Schema 
hide
 Configure
 SRX24781905  CpG methylation  Ovary / SRX24781905 (CpG methylation)   Schema 
hide
 SRX24781905  PMD  Ovary / SRX24781905 (PMD)   Schema 
hide
 SRX24781906  AMR  Ovary / SRX24781906 (AMR)   Schema 
hide
 Configure
 SRX24781906  CpG reads  Ovary / SRX24781906 (CpG reads)   Schema 
hide
 Configure
 SRX24781906  CpG methylation  Ovary / SRX24781906 (CpG methylation)   Schema 
hide
 SRX24781906  PMD  Ovary / SRX24781906 (PMD)   Schema 
    

Study title: Maternal loss-of-function of Nlrp2 results in failure of epigenetic reprogramming in mouse oocytes
SRA: SRP511364
GEO: not found
Pubmed: not found

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
SRX24781899 Ovary 0.379 4.9 12587 42481.9 1182 948.7 5964 212074.5 0.956 title: PBAT of mus musculus ovary; {"strain": "C57BL/6N", "isolate": "44", "breed": "not applicable", "cultivar": "not applicable", "ecotype": "not applicable", "age": "26-28 days", "dev_stage": "mature", "collection_date": "2021-09-27", "geo_loc_name": "USA", "sex": "female", "tissue": "ovary", "genotype": "WT"}
SRX24781900 Ovary 0.490 3.4 4085 44153.9 2767 925.0 1161 658767.6 0.972 title: PBAT of mus musculus ovary; {"strain": "C57BL/6N", "isolate": "47", "breed": "not applicable", "cultivar": "not applicable", "ecotype": "not applicable", "age": "26-28 days", "dev_stage": "mature", "collection_date": "2021-11-04", "geo_loc_name": "USA", "sex": "female", "tissue": "ovary", "genotype": "WT"}
SRX24781901 Ovary 0.472 4.3 2197 75041.0 5753 1023.8 1836 498480.6 0.970 title: PBAT of mus musculus ovary; {"strain": "C57BL/6N", "isolate": "48", "breed": "not applicable", "cultivar": "not applicable", "ecotype": "not applicable", "age": "26-28 days", "dev_stage": "mature", "collection_date": "2021-11-09", "geo_loc_name": "USA", "sex": "female", "tissue": "ovary", "genotype": "WT"}
SRX24781902 Ovary 0.357 5.4 16545 37941.3 1111 952.7 5812 223034.8 0.961 title: PBAT of mus musculus ovary; {"strain": "C57BL/6N", "isolate": "49", "breed": "not applicable", "cultivar": "not applicable", "ecotype": "not applicable", "age": "26-28 days", "dev_stage": "mature", "collection_date": "2021-11-09", "geo_loc_name": "USA", "sex": "female", "tissue": "ovary", "genotype": "WT"}
SRX24781904 Ovary 0.480 5.4 2595 80017.0 10120 973.2 2723 366565.4 0.968 title: PBAT of mus musculus ovary; {"strain": "C57BL/6N", "isolate": "50", "breed": "not applicable", "cultivar": "not applicable", "ecotype": "not applicable", "age": "26-28 days", "dev_stage": "mature", "collection_date": "2021-11-10", "geo_loc_name": "USA", "sex": "female", "tissue": "ovary", "genotype": "WT"}
SRX24781905 Ovary 0.453 2.6 3412 52124.9 857 871.0 2924 384594.0 0.948 title: PBAT of mus musculus ovary; {"strain": "C57BL/6N", "isolate": "23122", "breed": "not applicable", "cultivar": "not applicable", "ecotype": "not applicable", "age": "26-28 days", "dev_stage": "mature", "collection_date": "2020-11-18", "geo_loc_name": "USA", "sex": "female", "tissue": "ovary", "genotype": "WT"}
SRX24781906 Ovary 0.407 3.0 7303 47269.4 345 917.0 3940 302793.6 0.944 title: PBAT of mus musculus ovary; {"strain": "C57BL/6N", "isolate": "23123", "breed": "not applicable", "cultivar": "not applicable", "ecotype": "not applicable", "age": "26-28 days", "dev_stage": "mature", "collection_date": "2020-11-18", "geo_loc_name": "USA", "sex": "female", "tissue": "ovary", "genotype": "WT"}

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.