Mouse methylome studies SRP469968 Track Settings
 
FTDC1/2, oocyte-specific cofactors of DNMT1 required for epigenetic regulation and embryonic development (Bisulfite-Seq) [Blastula, Four, Oocyte]

Track collection: Mouse methylome studies

+  All tracks in this collection (604)

Maximum display mode:       Reset to defaults   
Select views (Help):
CpG reads ▾       CpG methylation ▾       PMD       AMR      
Select subtracks by views and experiment:
 All views CpG reads  CpG methylation  PMD  AMR 
experiment
SRX22359322 
SRX22359323 
SRX22359324 
SRX22359325 
SRX22359326 
SRX22359327 
SRX22359328 
SRX22359329 
SRX22359330 
SRX22359331 
SRX22359332 
SRX22359333 
SRX22359334 
SRX22359335 
SRX22359336 
SRX22359337 
SRX22359338 
SRX22359339 
SRX22359340 
SRX22359341 
SRX22359342 
SRX22359343 
SRX22359344 
SRX22359345 
SRX22359346 
SRX22359347 
SRX22359348 
SRX22359349 
SRX22359350 
SRX22359351 
SRX22359352 
SRX22359353 
experiment
 All views CpG reads  CpG methylation  PMD  AMR 
List subtracks: only selected/visible    all    ()
  experiment↓1 views↓2   Track Name↓3  
hide
 Configure
 SRX22359322  CpG methylation  Four / SRX22359322 (CpG methylation)   Schema 
hide
 Configure
 SRX22359323  CpG methylation  Four / SRX22359323 (CpG methylation)   Schema 
hide
 Configure
 SRX22359324  CpG methylation  Blastula / SRX22359324 (CpG methylation)   Schema 
hide
 Configure
 SRX22359325  CpG methylation  Blastula / SRX22359325 (CpG methylation)   Schema 
hide
 Configure
 SRX22359326  CpG methylation  Blastula / SRX22359326 (CpG methylation)   Schema 
hide
 Configure
 SRX22359327  CpG methylation  Oocyte / SRX22359327 (CpG methylation)   Schema 
hide
 Configure
 SRX22359328  CpG methylation  Oocyte / SRX22359328 (CpG methylation)   Schema 
hide
 Configure
 SRX22359329  CpG methylation  Oocyte / SRX22359329 (CpG methylation)   Schema 
hide
 Configure
 SRX22359330  CpG methylation  Four / SRX22359330 (CpG methylation)   Schema 
hide
 Configure
 SRX22359331  CpG methylation  Four / SRX22359331 (CpG methylation)   Schema 
hide
 Configure
 SRX22359332  CpG methylation  Blastula / SRX22359332 (CpG methylation)   Schema 
hide
 Configure
 SRX22359333  CpG methylation  Blastula / SRX22359333 (CpG methylation)   Schema 
hide
 Configure
 SRX22359334  CpG methylation  Blastula / SRX22359334 (CpG methylation)   Schema 
hide
 Configure
 SRX22359335  CpG methylation  Oocyte / SRX22359335 (CpG methylation)   Schema 
hide
 Configure
 SRX22359336  CpG methylation  Oocyte / SRX22359336 (CpG methylation)   Schema 
hide
 Configure
 SRX22359337  CpG methylation  Oocyte / SRX22359337 (CpG methylation)   Schema 
hide
 Configure
 SRX22359338  CpG methylation  Four / SRX22359338 (CpG methylation)   Schema 
hide
 Configure
 SRX22359339  CpG methylation  Four / SRX22359339 (CpG methylation)   Schema 
hide
 Configure
 SRX22359340  CpG methylation  Blastula / SRX22359340 (CpG methylation)   Schema 
hide
 Configure
 SRX22359341  CpG methylation  Blastula / SRX22359341 (CpG methylation)   Schema 
hide
 Configure
 SRX22359342  CpG methylation  Blastula / SRX22359342 (CpG methylation)   Schema 
hide
 Configure
 SRX22359343  CpG methylation  Oocyte / SRX22359343 (CpG methylation)   Schema 
hide
 Configure
 SRX22359344  CpG methylation  Oocyte / SRX22359344 (CpG methylation)   Schema 
hide
 Configure
 SRX22359345  CpG methylation  Oocyte / SRX22359345 (CpG methylation)   Schema 
hide
 Configure
 SRX22359346  CpG methylation  Four / SRX22359346 (CpG methylation)   Schema 
hide
 Configure
 SRX22359347  CpG methylation  Four / SRX22359347 (CpG methylation)   Schema 
hide
 Configure
 SRX22359348  CpG methylation  Blastula / SRX22359348 (CpG methylation)   Schema 
hide
 Configure
 SRX22359349  CpG methylation  Blastula / SRX22359349 (CpG methylation)   Schema 
hide
 Configure
 SRX22359350  CpG methylation  Blastula / SRX22359350 (CpG methylation)   Schema 
hide
 Configure
 SRX22359351  CpG methylation  Oocyte / SRX22359351 (CpG methylation)   Schema 
hide
 Configure
 SRX22359352  CpG methylation  Oocyte / SRX22359352 (CpG methylation)   Schema 
hide
 Configure
 SRX22359353  CpG methylation  Oocyte / SRX22359353 (CpG methylation)   Schema 
    

Study title: FTDC1/2, oocyte-specific cofactors of DNMT1 required for epigenetic regulation and embryonic development (Bisulfite-Seq)
SRA: SRP469968
GEO: not found
Pubmed: not found

Experiment Label Methylation Coverage HMRs HMR size AMRs AMR size PMDs PMD size Conversion Details
SRX22359322 Four 0.275 5.0 20 199376.8 2483 955.3 54 1404243.8 0.987 title: GSM7880620 Dnmt1_KO_4C_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "four cell", "tissue": "four cell", "cell_type": "four cell", "treatment": "Dnmt1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359323 Four 0.271 5.1 13 171076.2 2479 961.8 25 1214324.7 0.986 title: GSM7880621 Dnmt1_KO_4C_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "four cell", "tissue": "four cell", "cell_type": "four cell", "treatment": "Dnmt1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359324 Blastula 0.095 3.1 1 1168208.0 48 1261.2 1 87324461.0 0.989 title: GSM7880622 Dnmt1_KO_Blastocyst_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "blastula", "tissue": "blastula", "cell_type": "blastula", "treatment": "Dnmt1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359325 Blastula 0.098 3.2 0 0.0 55 1142.2 0 0.0 0.989 title: GSM7880623 Dnmt1_KO_Blastocyst_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "blastula", "tissue": "blastula", "cell_type": "blastula", "treatment": "Dnmt1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359326 Blastula 0.093 3.1 1 795055.0 53 1307.8 0 0.0 0.989 title: GSM7880624 Dnmt1_KO_Blastocyst_rep3, Mus musculus, Bisulfite-Seq; {"source_name": "blastula", "tissue": "blastula", "cell_type": "blastula", "treatment": "Dnmt1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359327 Oocyte 0.346 2.8 7341 44720.0 141 947.6 2869 379533.2 0.927 title: GSM7880625 Dnmt1_KO_MII_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "oocyte", "tissue": "oocyte", "cell_type": "MII", "treatment": "Dnmt1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359328 Oocyte 0.345 2.7 6450 46935.7 140 962.4 2833 385206.7 0.928 title: GSM7880626 Dnmt1_KO_MII_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "oocyte", "tissue": "oocyte", "cell_type": "MII", "treatment": "Dnmt1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359329 Oocyte 0.345 2.8 7610 43303.6 130 990.8 2848 370939.8 0.929 title: GSM7880627 Dnmt1_KO_MII_rep3, Mus musculus, Bisulfite-Seq; {"source_name": "oocyte", "tissue": "oocyte", "cell_type": "MII", "treatment": "Dnmt1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359330 Four 0.253 6.1 54 186951.9 4215 974.0 732 479940.7 0.987 title: GSM7880628 Ftdc1_KO_4C_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "four cell", "tissue": "four cell", "cell_type": "four cell", "treatment": "Ftdc1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359331 Four 0.286 5.0 93 150284.0 3067 970.2 71 1155270.1 0.984 title: GSM7880629 Ftdc1_KO_4C_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "four cell", "tissue": "four cell", "cell_type": "four cell", "treatment": "Ftdc1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359332 Blastula 0.062 3.6 1 838820.0 34 1235.7 1 118815053.0 0.989 title: GSM7880630 Ftdc1_KO_Blastocyst_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "blastula", "tissue": "blastula", "cell_type": "blastula", "treatment": "Ftdc1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359333 Blastula 0.069 3.6 1 838820.0 25 1566.2 2 131336197.0 0.989 title: GSM7880631 Ftdc1_KO_Blastocyst_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "blastula", "tissue": "blastula", "cell_type": "blastula", "treatment": "Ftdc1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359334 Blastula 0.044 3.5 1 838635.0 8 751.4 1 118813868.0 0.990 title: GSM7880632 Ftdc1_KO_Blastocyst_rep3, Mus musculus, Bisulfite-Seq; {"source_name": "blastula", "tissue": "blastula", "cell_type": "blastula", "treatment": "Ftdc1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359335 Oocyte 0.321 2.9 11451 34630.0 325 953.0 3017 347015.2 0.944 title: GSM7880633 Ftdc1_KO_MII_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "oocyte", "tissue": "oocyte", "cell_type": "MII", "treatment": "Ftdc1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359336 Oocyte 0.325 2.7 10233 35409.1 274 943.0 2790 370496.2 0.945 title: GSM7880634 Ftdc1_KO_MII_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "oocyte", "tissue": "oocyte", "cell_type": "MII", "treatment": "Ftdc1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359337 Oocyte 0.329 2.8 10838 34912.1 246 1027.5 2911 354515.3 0.944 title: GSM7880635 Ftdc1_KO_MII_rep3, Mus musculus, Bisulfite-Seq; {"source_name": "oocyte", "tissue": "oocyte", "cell_type": "MII", "treatment": "Ftdc1KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359338 Four 0.298 5.3 555 115153.2 2993 978.7 162 941292.0 0.986 title: GSM7880636 Ftdc2_KO_4C_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "four cell", "tissue": "four cell", "cell_type": "four cell", "treatment": "Ftdc2KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359339 Four 0.300 5.8 718 106050.7 3747 975.9 101 950334.7 0.986 title: GSM7880637 Ftdc2_KO_4C_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "four cell", "tissue": "four cell", "cell_type": "four cell", "treatment": "Ftdc2KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359340 Blastula 0.057 3.3 1 838798.0 9 1245.4 0 0.0 0.990 title: GSM7880638 Ftdc2_KO_Blastocyst_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "blastula", "tissue": "blastula", "cell_type": "blastula", "treatment": "Ftdc2KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359341 Blastula 0.062 3.2 2 894107.0 13 2008.0 1 109671250.0 0.988 title: GSM7880639 Ftdc2_KO_Blastocyst_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "blastula", "tissue": "blastula", "cell_type": "blastula", "treatment": "Ftdc2KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359342 Blastula 0.049 3.2 0 0.0 12 2138.9 1 118816319.0 0.988 title: GSM7880640 Ftdc2_KO_Blastocyst_rep3, Mus musculus, Bisulfite-Seq; {"source_name": "blastula", "tissue": "blastula", "cell_type": "blastula", "treatment": "Ftdc2KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359343 Oocyte 0.274 3.3 10221 34154.5 294 968.1 2760 370586.7 0.955 title: GSM7880641 Ftdc2_KO_MII_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "oocyte", "tissue": "oocyte", "cell_type": "MII", "treatment": "Ftdc2KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359344 Oocyte 0.300 3.8 11389 35848.4 396 975.8 3371 324012.1 0.948 title: GSM7880642 Ftdc2_KO_MII_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "oocyte", "tissue": "oocyte", "cell_type": "MII", "treatment": "Ftdc2KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359345 Oocyte 0.290 3.6 10620 36430.5 319 971.5 3081 339806.5 0.949 title: GSM7880643 Ftdc2_KO_MII_rep3, Mus musculus, Bisulfite-Seq; {"source_name": "oocyte", "tissue": "oocyte", "cell_type": "MII", "treatment": "Ftdc2KO", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359346 Four 0.327 5.9 1710 85957.0 4157 994.8 111 957031.6 0.985 title: GSM7880644 WT-4C-rep1, Mus musculus, Bisulfite-Seq; {"source_name": "four cell", "tissue": "four cell", "cell_type": "four cell", "treatment": "WT", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359347 Four 0.337 5.7 1571 77998.9 4278 988.1 65 1122589.6 0.985 title: GSM7880645 WT-4C-rep2, Mus musculus, Bisulfite-Seq; {"source_name": "four cell", "tissue": "four cell", "cell_type": "four cell", "treatment": "WT", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359348 Blastula 0.183 3.2 0 0.0 207 932.2 0 0.0 0.988 title: GSM7880646 WT-Blastocyst_rep1, Mus musculus, Bisulfite-Seq; {"source_name": "blastula", "tissue": "blastula", "cell_type": "blastula", "treatment": "WT", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359349 Blastula 0.160 3.2 0 0.0 145 934.5 1 118815080.0 0.988 title: GSM7880647 WT-Blastocyst_rep2, Mus musculus, Bisulfite-Seq; {"source_name": "blastula", "tissue": "blastula", "cell_type": "blastula", "treatment": "WT", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359350 Blastula 0.171 3.1 0 0.0 189 970.7 0 0.0 0.988 title: GSM7880648 WT-Blastocyst_rep3, Mus musculus, Bisulfite-Seq; {"source_name": "blastula", "tissue": "blastula", "cell_type": "blastula", "treatment": "WT", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359351 Oocyte 0.282 3.5 8675 39974.6 230 1002.6 3026 346181.7 0.953 title: GSM7880649 WT-MII-rep1, Mus musculus, Bisulfite-Seq; {"source_name": "oocyte", "tissue": "oocyte", "cell_type": "MII", "treatment": "WT", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359352 Oocyte 0.289 3.5 9107 39165.9 262 973.3 3058 347848.0 0.950 title: GSM7880650 WT-MII-rep2, Mus musculus, Bisulfite-Seq; {"source_name": "oocyte", "tissue": "oocyte", "cell_type": "MII", "treatment": "WT", "geo_loc_name": "missing", "collection_date": "missing"}
SRX22359353 Oocyte 0.293 3.7 9524 39595.8 294 1020.5 3219 334599.7 0.950 title: GSM7880651 WT-MII-rep3, Mus musculus, Bisulfite-Seq; {"source_name": "oocyte", "tissue": "oocyte", "cell_type": "MII", "treatment": "WT", "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.