Affymetrix GeneChip

RNA Expression: The core facility has the complete Affymetrix GeneChip system and can process RNA samples for a variety of organisms. This includes chips for all model organisms for which Affymetrix has a chip available including human, mouse, rat, drosophila, c. elegans, yeast and arabidopsis.

Whole Transcript Expression: Each gene on the Affymetrix Gene 1.0 ST array is represented by several probes spread across the length of the gene. Gene 1.0 ST arrays are available for human, mouse and rat.

miRNA Analysis: The Affymetrix GeneChip miRNA contains the most comprehensive microRNA (miRNA) coverage for human, mouse, rat, canine and monkey on one array. The array also contains human small nuclear RNAs (snoRNAs and scaRNAs).

Genome-wide SNP Analysis: In addition to expression analysis the Affymetrix system can be used to perform genome-wide SNP analysis. These arrays can also be used to determine genomic copy number alterations.

Spotted Microarray

Labeling and Hybridization: The core facility will label the RNA samples and perform the hybridizations to the slides for investigators.

Slides Available: 30k Human, 30k Mouse, 10k Human, 10k Mouse, 10k Rat and miRNA arrays

New! Genome-Wide spotted oligo microarrays for human and mouse experiments. The core facility can now offer you genome-wide expression profiling for your experiments involving human or mouse RNA samples at a reduced cost. The facility can compare the expression profile of ~ 30,000 genes between two samples in either mouse or human for a total cost of approximately $250.00. The slides used are from the company known as Phalanx Biotec.

Custom Array Printing: The core facility employs the use of a OmniGrid 100 spotting robot and will print custom oligo and cDNA arrays for users.

Scanning: The facility employs the use of an Axon 4000B Laser Scanner.

Image Analysis: GenePix is the image analysis software utilized for spotted microarray images.

Agilent Bioanalyzer - RNA Integrity Analysis

In our facility we employ the use of an Agilent Bioanalyzer which will assess the purity, potential degradation and genomic DNA contamination of RNA.


Statistical Analysis: The Microarray Core Facility can assist with initial analysis to determine fold-changes in genes. For in-depth statistical analysis the user is referred to statisticians and computer scientists at UNMC that routinely provide those services.

Pathway Analysis: The Microarray Core Facility has purchased access to the analysis program known as Ingenuity Systems. Users are encouraged to utilize this program to further analyze their microarray data.