- The GFC provides four microarray platforms and the associated technologies necessary to use them.
- The four platforms are: 5,760-gene human and mouse cDNA microarrays, 20,000-gene human oligonucleotide microarrays, the Affymetrix GeneChip system, and the GE HealthCare Codelink Bioarrays.
- The oligonucleotide microarrays manufactured on-site by the GFC are made using Sigma/Compugen 60-mers on Corning's ultraGAPS II slides with a GeneMachine OmniGrid and Stealth printing tips from Telechem International. The cDNA arrays are made the same way using cDNA clones produced by the IMAGE consortium.
- The GFC provides quality control analysis of RNA samples using the Agilent Bioanalyzer and real time PCR confirmation of microarray results using an Applied Biosystems Prism 7000 and 7300 Sequence Detection Systems.
- The GFC also manufactures CpG island microarrays that are made available for purchase to researchers. More detailed descriptions of these platforms are provided.
The Genomics Facility Core can provide next-generation RNAseq solutions through the Ion Torrent Proton platform. Here, an overview of a RNA sequencing run is shown with the loading of the sequencing chip, number of reads obtained, and a read length histogram.
The Genomics Facility Core can provide microbiome analysis through 16S rRNA gene sequencing or whole genome sequencing. Here the results of a study on the microbiome of diabetic foot ulcers that resulted in an operating room visit is shown. Of interest was the species of bacteria in the
center of the heatmap which were only present in the samples at the right side. These bacteria were found to be soil-based, and present only on the seven out-patients at the far right. In contrast the wounds of in-patients, who we hospitalized and non-ambulatory, were nearly devoid of soil-derived bacteria.
Genomics Facility Core, Room 3933
The University of Arizona Cancer Center
1515 N. Campbell Ave.
Tucson AZ 85724