Arrays for Gene Expression analysis:
Arrays from Agilent and Illumina can be run in the Genomics Facility. Information on the available arrays and formats can be obtained from the manufacturer's websites (www.agilent.com or www.illumina.com). The Genomics Facility offers services for RNA QC, sample labeling, hybridization, and scanning of the arrays. For Agilent arrays, users may perform the initial steps and the Genomics Facility offers hybridization and/or scanning services only. For Affymetrix arrays, we may be able to outsource the arrays to another, nearby facility. Please contact the Director of the Genomics Facility for Affymetrix arrays.
Arrays for SNP genotyping:
The Genomics Facility can run SNP arrays from Illumina or Agilent. However, Illumina BeadChip arrays using either the GoldenGate or Infinium chemistries are the preferred kits for SNP genotyping, because of their ease of use and superior performance. Illumina has stock arrays for many species, but also can create custom content arrays. More information can be found on the Illumina website (www.illumina.com) for what arrays are currently available, and information about designing custom SNP genotyping arrays. The Genomics Facility cannot scan some of the higher-density arrays available from Illumina. Therefore, before initiating any SNP genotyping project, it's strongly advised to consult with the Director of the Genomics Facility about the different options available.
Arrays for CGH, ChIP-on-chip, microRNA expression, etc.:
Arrays for applications other than gene expression or SNP genotyping are less frequently done in the Genomics Facility and it's strongly advised to consult with the Director of the Genomics Facility before initiating such projects.
Software for data analysis:
Several softwares are available through the Biotechnology Resource Center for analyzing microarray data. In addition to free softwares available directly from the array manufacturers, we have several licensed softwares available by remote access on BRC servers. For gene expression analysis, GeneSpring is available, and for analyzing Illumina SNP genotyping array data, Illumina's GenomeStudio is available. These softwares are made available, free of charge, to anyone generating their data in the Genomics Facility.