This webpage serves to provide additional information, tutorials, and address feedback regarding the FigShare file set co-published with the manuscript:  Gavery MR, Roberts SB. (2013Predominant intragenic methylation is associated with gene expression characteristics in a bivalve molluscPeerJ  1:e215 http://dx.doi.org/10.7717/peerj.215

 

Crassostrea gigas high-throughput bisulfite sequencing (gill tissue).
Mackenzie Gavery, Steven Roberts. figshare.
http://dx.doi.org/10.6084/m9.figshare.749728

 

All files are associated with a MBD BS-seq effort targeting Crassostrea gigas gill tissue. Specific files include:

BiGill_CpG_methylation.igv - Location and proportion of methylation for all analyzed CpG dinucleotides with greater than 5x coverage.

BiGill_exon_clc_rpkm.igv - Exon-specific gene expression values (RPKM) from RNA-seq analysis.

BiGill_igv_charlie.xml - A session file, which loads methylation and RNA-seq feature tracks as well as the location of C.gigas genome features.

Query to derive_CG_AllData_IGV.txt - Query (SQLShare) used to derive the methylation feature track from the original methratio output (http://goo.gl/5LGq9Q


Quick Start

These data are developed to be easily visualized in the Integrative Genomics Viewer (IGV). I would suggest installing the downloadable version available here. When you open IGV you should see a browser window as shown.

emt

To load the gene and exon feature tracks (10.5524/100030) as well as exon specific gill gene expression (RPKM) and CpG DNA methylation data (10.6084/m9.figshare.749728) simply

  • Go to File > Load from url
  • paste http://eagle.fish.washington.edu/trilobite/Crassostrea_gigas_v9_tracks/BiGill_igv_charlie.xml

Then your browser should look like…

oyster

Have fun!