Mouse methylome studies SRP487827 Track Settings
 
Endocrine islet beta-cell subtypes with differential function are derived from biochemically distinct embryonic endocrine islet progenitors that are regulated by maternal nutrients [endocrine islets postnatal day-2 female mice, endocrine islets postnatal day-2 male mice, endocrine islets postnatal day-60 female mice, endocrine islets postnatal day-60 male mice]

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       HMR      
Select subtracks by views and experiment:
 All views AMR  CpG reads  CpG methylation  PMD  HMR 
experiment
SRX23511408 
SRX23511409 
SRX23511410 
SRX23511411 
SRX23511412 
SRX23511413 
SRX23511414 
SRX23511415 
SRX23511416 
SRX23511417 
SRX23511418 
SRX23511419 
List subtracks: only selected/visible    all    ()
  experiment↓1 views↓2   Track Name↓3  
hide
 Configure
 SRX23511408  CpG methylation  endocrine islets postnatal day-2 female mice / SRX23511408 (CpG methylation)   Schema 
hide
 SRX23511408  HMR  endocrine islets postnatal day-2 female mice / SRX23511408 (HMR)   Schema 
hide
 Configure
 SRX23511409  CpG methylation  endocrine islets postnatal day-2 female mice / SRX23511409 (CpG methylation)   Schema 
hide
 SRX23511409  HMR  endocrine islets postnatal day-2 female mice / SRX23511409 (HMR)   Schema 
hide
 SRX23511410  HMR  endocrine islets postnatal day-2 male mice / SRX23511410 (HMR)   Schema 
hide
 Configure
 SRX23511410  CpG methylation  endocrine islets postnatal day-2 male mice / SRX23511410 (CpG methylation)   Schema 
hide
 Configure
 SRX23511411  CpG methylation  endocrine islets postnatal day-2 male mice / SRX23511411 (CpG methylation)   Schema 
hide
 SRX23511411  HMR  endocrine islets postnatal day-2 male mice / SRX23511411 (HMR)   Schema 
hide
 Configure
 SRX23511412  CpG methylation  endocrine islets postnatal day-60 female mice / SRX23511412 (CpG methylation)   Schema 
hide
 SRX23511412  HMR  endocrine islets postnatal day-60 female mice / SRX23511412 (HMR)   Schema 
hide
 Configure
 SRX23511413  CpG methylation  endocrine islets postnatal day-60 male mice / SRX23511413 (CpG methylation)   Schema 
hide
 SRX23511413  HMR  endocrine islets postnatal day-60 male mice / SRX23511413 (HMR)   Schema 
hide
 Configure
 SRX23511414  CpG methylation  endocrine islets postnatal day-60 female mice / SRX23511414 (CpG methylation)   Schema 
hide
 SRX23511414  HMR  endocrine islets postnatal day-60 female mice / SRX23511414 (HMR)   Schema 
hide
 Configure
 SRX23511415  CpG methylation  endocrine islets postnatal day-60 male mice / SRX23511415 (CpG methylation)   Schema 
hide
 SRX23511415  HMR  endocrine islets postnatal day-60 male mice / SRX23511415 (HMR)   Schema 
hide
 Configure
 SRX23511416  CpG methylation  endocrine islets postnatal day-60 female mice / SRX23511416 (CpG methylation)   Schema 
hide
 SRX23511416  HMR  endocrine islets postnatal day-60 female mice / SRX23511416 (HMR)   Schema 
hide
 Configure
 SRX23511417  CpG methylation  endocrine islets postnatal day-60 male mice / SRX23511417 (CpG methylation)   Schema 
hide
 SRX23511417  HMR  endocrine islets postnatal day-60 male mice / SRX23511417 (HMR)   Schema 
hide
 SRX23511418  HMR  endocrine islets postnatal day-60 female mice / SRX23511418 (HMR)   Schema 
hide
 Configure
 SRX23511418  CpG methylation  endocrine islets postnatal day-60 female mice / SRX23511418 (CpG methylation)   Schema 
hide
 Configure
 SRX23511419  CpG methylation  endocrine islets postnatal day-60 male mice / SRX23511419 (CpG methylation)   Schema 
hide
 SRX23511419  HMR  endocrine islets postnatal day-60 male mice / SRX23511419 (HMR)   Schema 
    

Study title: Endocrine islet beta-cell subtypes with differential function are derived from biochemically distinct embryonic endocrine islet progenitors that are regulated by maternal nutrients
SRA: SRP487827
GEO: not found
Pubmed: not found

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
SRX23511408 endocrine islets postnatal day-2 female mice 0.649 11.8 53914 1002.5 174 1163.4 1172 12730.0 0.985 title: GSM8061312 WGBS of P2 M-N+ (eGFP-) sorted beta-cells from female mice - Rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "endocrine islets, postnatal day-2, female mice", "tissue": "endocrine islets, postnatal day-2, female mice", "cell_type": "all islet cells", "genotype": "Myt1cCre; Ngn3nCre; Rosa26eYFP, InsApple", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23511409 endocrine islets postnatal day-2 female mice 0.663 12.8 54880 1036.3 182 1149.9 1934 9591.6 0.980 title: GSM8061313 WGBS of P2 M+N+ (eGFP+) sorted beta-cells from female mice - Rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "endocrine islets, postnatal day-2, female mice", "tissue": "endocrine islets, postnatal day-2, female mice", "cell_type": "all islet cells", "genotype": "Myt1cCre; Ngn3nCre; Rosa26eYFP, InsApple", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23511410 endocrine islets postnatal day-2 male mice 0.656 10.1 49113 1092.2 162 1042.3 1127 13475.0 0.980 title: GSM8061314 WGBS of P2 M-N+ (eGFP-) sorted beta-cells from male mice - Rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "endocrine islets, postnatal day-2, male mice", "tissue": "endocrine islets, postnatal day-2, male mice", "cell_type": "all islet cells", "genotype": "Myt1cCre; Ngn3nCre; Rosa26eYFP, InsApple", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23511411 endocrine islets postnatal day-2 male mice 0.657 9.1 47750 1107.6 161 1115.7 1277 12308.3 0.983 title: GSM8061315 WGBS of P2 M+N+ (eGFP+) sorted beta-cells from male mice - Rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "endocrine islets, postnatal day-2, male mice", "tissue": "endocrine islets, postnatal day-2, male mice", "cell_type": "all islet cells", "genotype": "Myt1cCre; Ngn3nCre; Rosa26eYFP, InsApple", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23511412 endocrine islets postnatal day-60 female mice 0.632 10.2 41364 1054.7 207 1114.1 626 20215.2 0.985 title: GSM8061316 WGBS of P60 M-N+ (eGFP-) sorted beta-cells from female mice - Rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "endocrine islets, postnatal day-60, female mice", "tissue": "endocrine islets, postnatal day-60, female mice", "cell_type": "all islet cells", "genotype": "Myt1cCre; Ngn3nCre; Rosa26eYFP, InsApple", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23511413 endocrine islets postnatal day-60 male mice 0.641 12.8 46875 992.0 203 1079.5 925 16713.2 0.983 title: GSM8061317 WGBS of P60 M-N+ (eGFP-) sorted beta-cells from male mice - Rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "endocrine islets, postnatal day-60, male mice", "tissue": "endocrine islets, postnatal day-60, male mice", "cell_type": "all islet cells", "genotype": "Myt1cCre; Ngn3nCre; Rosa26eYFP, InsApple", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23511414 endocrine islets postnatal day-60 female mice 0.631 5.7 32632 1303.7 85 993.3 411 28545.2 0.982 title: GSM8061318 WGBS of P60 M-N+ (eGFP-) sorted beta-cells from female mice - Rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "endocrine islets, postnatal day-60, female mice", "tissue": "endocrine islets, postnatal day-60, female mice", "cell_type": "all islet cells", "genotype": "Myt1cCre; Ngn3nCre; Rosa26eYFP, InsApple", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23511415 endocrine islets postnatal day-60 male mice 0.649 12.4 43386 1024.5 283 1037.6 933 14536.1 0.987 title: GSM8061319 WGBS of P60 M-N+ (eGFP-) sorted beta-cells from male mice - Rep 4, Mus musculus, Bisulfite-Seq; {"source_name": "endocrine islets, postnatal day-60, male mice", "tissue": "endocrine islets, postnatal day-60, male mice", "cell_type": "all islet cells", "genotype": "Myt1cCre; Ngn3nCre; Rosa26eYFP, InsApple", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23511416 endocrine islets postnatal day-60 female mice 0.632 8.3 38860 1117.8 161 1012.4 798 16899.5 0.986 title: GSM8061320 WGBS of P60 M+N+ (eGFP+) sorted beta-cells from female mice - Rep 1, Mus musculus, Bisulfite-Seq; {"source_name": "endocrine islets, postnatal day-60, female mice", "tissue": "endocrine islets, postnatal day-60, female mice", "cell_type": "all islet cells", "genotype": "Myt1cCre; Ngn3nCre; Rosa26eYFP, InsApple", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23511417 endocrine islets postnatal day-60 male mice 0.629 10.8 41434 1068.9 178 1036.9 851 15388.2 0.982 title: GSM8061321 WGBS of P60 M+N+ (eGFP+) sorted beta-cells from male mice - Rep 2, Mus musculus, Bisulfite-Seq; {"source_name": "endocrine islets, postnatal day-60, male mice", "tissue": "endocrine islets, postnatal day-60, male mice", "cell_type": "all islet cells", "genotype": "Myt1cCre; Ngn3nCre; Rosa26eYFP, InsApple", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23511418 endocrine islets postnatal day-60 female mice 0.631 5.4 30856 1367.7 73 1039.9 402 30134.6 0.982 title: GSM8061322 WGBS of P60 M+N+ (eGFP+) sorted beta-cells from female mice - Rep 3, Mus musculus, Bisulfite-Seq; {"source_name": "endocrine islets, postnatal day-60, female mice", "tissue": "endocrine islets, postnatal day-60, female mice", "cell_type": "all islet cells", "genotype": "Myt1cCre; Ngn3nCre; Rosa26eYFP, InsApple", "geo_loc_name": "missing", "collection_date": "missing"}
SRX23511419 endocrine islets postnatal day-60 male mice 0.648 15.3 47588 963.5 179 1089.6 864 16449.6 0.987 title: GSM8061323 WGBS of P60 M+N+ (eGFP+) sorted beta-cells from male mice - Rep 4, Mus musculus, Bisulfite-Seq; {"source_name": "endocrine islets, postnatal day-60, male mice", "tissue": "endocrine islets, postnatal day-60, male mice", "cell_type": "all islet cells", "genotype": "Myt1cCre; Ngn3nCre; Rosa26eYFP, InsApple", "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.