The GPSR maintains array technology platforms for:
genotyping, cytogenetics, and expression and methylation profiling
The GeneChip system offers multiple array designs to interrogate genome-wide expression profiles of mRNA, lncRNA, and miRNA of human and widely-used model species, as well as many agricultural species. View information on available expression array options. The GeneChip system operated in the GPSR supports the GeneChip cartridge format which analyzes one labeled sample target per array hybridization. Please note the Affymetrix brand has recently been purchased by ThermoFisher Scientific and is being marketed under their Applied Biosystems product line. Visit cytogenetic analysis with microarrays for information about GeneChip array solutions for human cytogenetic analysis. Please contact the core if you are interested in these options.
Free Affymetrix analysis software - Transcriptome Analysis Console (TAC)
Transcriptome Analysis software 4.0 - features include:
- Streamlined QC and data analysis with integration of EC software and TAC software into a single tool
- Ability to analyze large data sets of 1,000 samples or more
- Integration of established LIMMA package
- Improved alternative splicing analysis
Illumina BeadChip arrays
Infinium BeadChip assays are designed for whole-genome and targeted genotyping and DNA methylation profiling. The GPSR is able to advise on platform options and coordinate services available through the Knight Diagnostic Lab for Infinium MethylationEPIC array assays or external Illumina service providers for all Infinium microarray options. The GPSR can assist with genomic DNA isolation for array assay and with bisulfite conversion for DNA methylation array assays. The BeadChip system is designed with multiple arrays per BeadChip so that sample number minimums are based on BeadChip format and minimum pack sizes. View array options for genotyping and epigenetics analysis.