Both microarray and RNA-seq are powerful methods to analyze the transcriptome at a given point in time. While microarrays are less expensive, faster, and easier to interpret, sequencing of mRNA has the important advantage of providing unbiased information about the entire transcriptome, which can be used to determine mutations, splice variants, gene fusions and other unanticipated events, though at a higher cost. Both techniques are highly useful and the choice should depend on the exact goals of the research. We strongly recommend that you consult with the lab at the earliest stage of planning your study so that we can assure that you are using the best approach to meet your objectives.
Example applications include:
• Differences between normal and diseased tissues
• Deregulated cellular pathways following experimental treatment
• Genetic pathways (e.g. knock-out mouse)
Microarray services: All methods use fluoresce Cy-dye labeling and long oligo (60 mer) Agilent high density microarrays
RNA expression analysis
One color arrays (Cy3 only) use a labeled sample or reference hybridize on separate microarray and a digital comparison is performed. All samples are amplified, so small sample sizes can be accommodated.
Two color arrays (Cy3 and Cy5) use separately labeled (amplified) sample and reference hybridize on the same microarray. Note that while it is possible to run the older 2 dye method on microarrays, we strong discourage use of this method. Current array printing technologies have improved so that there is essentially a negligible difference between spots on an array, unlike older methods. Cy5 is extremely sensitive to environmental degradation (complete oxidation by ozone at a level of 1-2 parts per billion) which can lead to substantial signal artifacts. For these and other reasons, we rarely recommend use of the two color method with the current generation of technology.
microRNA expression analysis
1 color Cy-dye labeled small RNA sample hybridized on each microarray printed with 20-40 repeats of each microRNA feature. No sample amplification is used so very small samples are not possible.
Gene dosage using comparative genomic hybridization (CGH)
Using direct labeling method, 2 color separately labeled sample genomic DNA and reference genomic DNA hybridize on a same microarray.
Library preparation for Illumina sequencing platforms for high throughput sequencing now offered through the High Throughput Sequencing Facility (HTSF).
Total RNA to final mRNA library
Total RNA (including total RNA isolated from FFPE tissue) to final total stranded RNA library
Total RNA (including total RNA isolated from FFPE tissue) to final small RNA library