title: Elaeis Guineensis Tiling Microarray
status: Public on Sep 09 2015
contact.city: St. Louis
contact.first: Steve
contact.middle: W.
contact.last: smith
contact.email: curator@oriongenomics.com
contact.state: MO
contact.address: 4041 Forest Park Ave
contact.department: Bioinformatics
contact.country: USA
contact.institute: Orion Genomics
contact.phone: 3146156977
organism: Elaeis guineensis
description: EG5 Build
  RefSeq:GCF_000442705.1
  Note: Original array design was based on the early P1 build and remapped to EG5 for analysis. Genome coordinates in platform table reflect remapping to EG5.
manufacture_protocol: The microarray design was based on the E. guineensis genome (Singh, 2013, Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature 500, 335-339) and contains over 1 million 60 base probes.   Probes were selected from non-overlapping 1.5 kb windows across all scaffolds of the P1 pisifera genome build, choosing the 60mer with the lowest composite 15mer frequency count within the genome.  When compared to the publically available EG5 genome assembly (Singh, 2013, Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature 500, 335-339), 860,861 probes from the microarray match at 100% stringency (81,194 probes falling on exons and the remaining covering intronic and intergenic regions of the genome). The microarrays were manufactured by Roche NimbleGen using the HX1 platform.  Among the ~860,000 microarray probes matching the oil palm genome with 100% sequence stringency, a subset of ~460,000 uniquely mapped probes was selected to reduce noise from non-specific hybridizations.