Description

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

Display Conventions and Configuration

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

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, Kartika Jayashankar, Daniel York, Dr. Pete Dickinson, Dr. Danika Bannasch, 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.