Microarray

Transcript profiling experiments aim to characterize the expression of known mRNA transcripts in samples. Usually, there is little discovery of novel transcripts expected, unlike in transcript discovery. The GSL offers transcript profiling by arrays or next-gen sequencing. Arrays are often a good choice when the analysis of many samples or groups of samples is required, as it is usually cheaper to run a well-designed array experiment with replicates than to run RNA-Seq. RNA-Seq can be more advantageous if there are only a small number of samples of interest and splice variant detection is desired.

Platform Information

Affymetrix GeneChips

Affymetrix GeneChips are the most widely used microarray in both research and clinical settings. Affymetrix has overhauled the design of their GeneChips in recent years, resulting in several choices for the arrays used in whole-genome analysis.

Cartridge GeneChip Options:

• 3' Expression Arrays are the classic Affymetrix array in which probes are designed for the 3' end of the gene. These are older arrays (ca 2001) and are more expensive than their newer counterparts. (many non-standard research organisms including plants)
• Gene Arrays are the most common arrays used for new projects. The probes are designed to hit most, if not all, of the exons in a gene. The content is updated to a newer version of the genome (ca 2006) and the arrays are cheaper, costing about half the price of the 3' arrays. (human, mouse, and rat)
• Exon Arrays allow detection of splice variants and expression calculations on the exon level rather than the gene level. (human, mouse, and rat)

GeneTitan GeneChip Options:

• The Affymetrix GeneTitan completely automates microarray processing from hybridization to data generation. Samples are processed in a plate format and can be run in batches of 16, 24, or 96. (human, mouse, rat: Gene arrays and 3' arrays)

Illumina BeadArrays

Illumina's BeadArray technology is based on 3-micron silica beads that self-assemble in microwells on the array substrate. Hundreds of thousands of copies of a specific oligonucleotide cover each bead. Expression arrays contain more than 48K probes on each array with either 6, 8, or 12 arrays per BeadChip. (human, mouse, and rat)

Sample Submission Requirements

Cartridge arrays are only run in batches of 30. A user may submit less than 30 samples but there will be a delay until other samples arrive to fill the batch. Users may opt to purchase their own reagents and arrays. Most cartridge arrays are sold in packs of 2, 6, or 30; reagents are sold as either 10 reactions or 30 reactions. GeneTitan projects are usually a minimum of 96 samples; however, projects of other sizes may be considered if samples from other projects are able to fill the plate. Minimum array orders from Illumina require either 12 or 24 samples to be run, depending on the array type. Samples may be diluted in water, 10mM Tris, or Qiagen EB. Large numbers of samples should be submitted in a plate (non-deep well). Any samples submitted that do not meet the requirements below will be subjected to a $25 surcharge per sample.