Functional Genomics Core - Microarray Information
General Information
Microarray analysis is a highly complex process requiring the work of a team of experienced scientists. We have developed routine procedures for analysis and evaluation of microarray data. The Core can do two types of microarray analysis:
- Agilent dual color expression analysis for direct comparison design: Keep the design of your experiment as simple as possible, with the preferred method being a direct comparison. If this is your first attempt at a microarray analysis experiment do not be tempted to include multiple conditions or time points. Rather, if it is possible, just compare two conditions (e.g. treated vs. untreated or KO vs. WT) or focus on the single time point that would likely answer the question you are most interested in. The more complex the design of your experiment, the greater is the potential for being overwhelmed with the output produced. When a single direct comparison is not possible a common control reference design should always be used over a loop design.
- Agilent single color expression analysis for multiple treatment groups: When looking at gene profiles over multiple time points or in multiple treatment groups a direct comparison design is not possible. Traditionally this type of question was approached by using a common control or reference design on two-color arrays. However, Agilent has developed a protocol in which their arrays can be processed with a single sample, allowing for comparisons of more than two conditions, with only a slight loss in sensitivity.
Our Agilent DNA Microarray Scanner can handle the new denser arrays from Agilent. All our microarray hybridization and scanning is done with SureScan technology that comes with Agilent Technologies' automated, dual-laser microarray scanner. Its dynamic autofocus technique constantly adjusts the focus of the scanner to compensate for glass-warp and curvature found in most glass slides. This delivers vast improvements in sensitivity and overall confidence in scanned results.
Agilent Gene Expression Arrays
We are currently are using Agilent Technologies commercially available long-oligo arrays. These arrays may be of particular interest to investigators looking at tissues or systems other than the pancreas and liver, such as brain, muscle, fat, kidney, etc. These arrays compete directly with Affymetrix arrays in terms of having genome-wide coverage, but offer greater sensitivity for a lower cost.
Agilent-designed 60-mer oligonucleotide microarrays are processed through a powerful combination of probe design algorithms coupled with Agilent's probe selection process. We can do a wide range of Agilent Gene Expression Arrays:
- Whole Mouse Genome Oligo Microarray 4x44k or 8x60k
- Whole Human Genome Oligo Microarray 4x44k or 8x60k
- Many other Whole Genome Oligo Microarrays
Human and Mouse Arrays contain 44,000 elements, with over 41,000 transcripts on each. The 8x60 denser gene expression arrays have approximately the same number of transcripts, just with more lncRNA and more replicates of each transcript.
Agilent Comparative Genomic Hybridization Arrays
Microarray-based Comparative Genomic Hybridization (aCGH) is a powerful technique used to identify and characterize DNA copy number variations across the genome. Agilent’s oligonucleotide aCGH platform is an integrated solution that gives you the resolution and flexibility to perform genome-wide as well as customized zoom-in profiling of genomic aberrations on a single chip. This service is only by special request and one needs to have 10 or more replicates. We can do:
Agilent ChIP on chip Arrays
The Agilent's Human Promoter and Mouse Promoter microarrays allow the monitoring of binding events of DNA-binding proteins to areas around the human and mouse promoters. They allow for the rapid screening of over 17,000 best defined transcripts using the powerful ChIP-on-Chip assay. Both sets cover -5.5kb upstream to +2.5kb downstream of the transcriptional start sites.
