DNA Methylation Track Settings
 
DNA methylation in cow tissues (bosTau6)

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            placenta4
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 Oocytes Methyl  DNA methylation in cow oocytes (bam)   Schema 
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 Oocytes Methyl 2  DNA methylation in cow oocytes (bigWig)   Schema 
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 Placenta2 Methyl  DNA methylation in cow placenta tissue (biological replicate 2) (bam)   Schema 
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 Placenta2 Methyl 2  DNA methylation in cow placenta (biological replicate 2) (bigWig)   Schema 
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 Placenta3 Methyl  DNA methylation in cow placenta tissue (biological replicate 3) (bam)   Schema 
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 Placenta3 Methyl 2  DNA methylation in cow placenta (biological replicate 3) (bigWig)   Schema 
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 Placenta4 Methyl  DNA methylation in cow placenta tissue (biological replicate 4) (bam)   Schema 
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 Placenta4 Methyl 2  DNA methylation in cow placenta (biological replicate 4) (bigWig)   Schema 
    

Description

This track shows low-coverage DNA methylation (MethylC-seq) data in cow cells and tissues.


Display Conventions and Configuration

Methylation data are available in two formats:

Methyl (BAM format)

In dense mode, each bar represents a single CpG site.

  • Red = 80-100% methylation
  • Green = 60-80% methylation
  • Blue = 1-60% methylation
  • Black = 0% methylation

In pack mode, the color-coding is the same but each CpG site is labeled by the percent methylation at that site.

Note that, due to low coverage, a CpG site may be colored red or black simply because there was only one read that covered that site. Therefore this data is most useful when viewed over larger genomic distances.

Methyl2 (bigWig format)

In dense mode, each bar represents a single CpG site, color-coded as a gradient from light gray (low methylation) to black (high methylation).

In full mode, methylation is graphed as a black curve with percent methylation on the y axis. Properties of this track can be modified by pressing the wrench symbol above.


Methods

MII oocytes were produced by in vitro maturation of GV oocytes collected from ovaries according to standard protocols. Oocyte maturation was confirmed by the presence of a polar body. Then, zona pellucida and first polar body were removed by incubation in 0.5% pronase solution for 2 minutes and vigorous pipetting. Zona-free oocytes were snap frozen in liquid nitrogen and stored at -80°C until DNA extraction.

For all samples, MethylC-seq read were aligned to the genome using BS Seeker, allowing two mismatches (not including those at CpG sites). Only one read per genomic position was kept to prevent clonal PCR amplification biases. CpG site methylation data were combined from both DNA strands.


Credits

All data provided by:
Diane Schroeder, Dr. Pablo Ross, and Dr. Janine LaSalle from UC Davis.

For questions, contact Dr. Janine LaSalle: jmlasalle@ucdavis.edu


References

Schroeder DI, Blair JD, Lott P, Yu HO, Hong D, Crary F, Ashwood P, Walker C, Korf I, Robinson WP, LaSalle JM. (2013) The human placenta methylome. Proc Natl Acad Sci U S A. 110(15):6037-42.

Schroeder DI, Jayashankar K, Douglas KC, Thirkill TL, York D, Dickinson PJ, Williams LE, Samollow PB, Ross PJ, Bannasch DL, Douglas GC, LaSalle JM. (2015) Early developmental and evolutionary origins of gene body DNA methylation patterns in mammalian placentas. PLoS Genet. 11(8):e1005442.