title: 121211-allmis-ms-meth-ux1
status: Public on Aug 27 2016
contact.city: Pullman
contact.first: Michael
contact.middle: K
contact.last: Skinner
contact.email: skinner@mail.wsu.edu
contact.state: WA
contact.address: Abelson 507
contact.department: SBS
contact.country: USA
contact.institute: WSU
organism: Alligator mississippiensis
description: The array used for the differential methylation analysis was a DNA methylated custom array by Roche Nimblegen that consisted of a Whole Genome Tiling Array of the American Alligator (Alligator mississippiensis) made of two chip set arrays with a 200bp resolution (121211-allmis-ms-meth-ux1). Probe sizes were 50-75mer in length and median probe spacing was 200bp.
  
  The December 2014 report of the Alligator mississippiensis genome produced by the Genome Sequencing Center was retrieved (http://crocgenome.hpc.msstate.edu/crocbase/gbrowsers.html, http://crocgenome.hpc.msstate.edu/gb2/gbrowse/gator/). A seed file was constructed and a BSgenome package was forged for using the Alligator DNA sequence in the R code (Herve Pages BSgenome: Infrastructure for Biostrings-based genome data packages. R package version 1.24.0). This sequence was used to design the custom tiling arrays and to perform the bioinformatics.
manufacture_protocol: see http://www.nimblegen.com/technology/manufacture.html