Description
This track shows low-coverage DNA methylation (MethylC-seq) data in rhesus macaque 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
Trophoblast cells were isolated from rhesus placental tissue (Gestation Day: 40–65 days) using procedures previously described. All procedures involving animals were performed in accordance with the NIH Guide for the Care and Use of Laboratory Animals and under the approval of the University of California Davis, Animal Care and Use Committee. These cells are 95% cytokeratin 7-positive and 5% vimentin-positive, consistent with a predominantly trophoblast population.
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, Twanda Thirkill, Dr. Gordon Douglas, 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.
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