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We currently use Affymetrix GeneChip Technology to generate
mouse, rat and human expression profiles for our projects. The GeneChip platform consists of oligonucleotide arrays,
instruments to process and analyze the arrays, and software tools to manage and
mine the data. So far, expression profiles have been generated using the
GeneChip® Murine Genome 11K and U74 Set. The 11K set consists of 2 probe arrays
(Mu11KsubA, Mu11KsubB) which allow one to monitor the relative abundance of
greater than 11,000 genes from mRNA transcripts and EST clusters. Out of the
three probe arrays of the U74 set, we use the MGU74A GeneChip containing 12,654
elements. It was discovered that 25% of the probes on the MgU74 array set were incorrectly oriented and therefore unusable. A mask file that could be interpreted by MAS to leave blank fields for incorrect probe sets was generated and this mask file has been applied to all our text files that have been generated by these arrays. A revised chip with corrected sequences, MgU74Av2, was generated and used for separate experiments.
The GeneChip Instrument System consisting of the workstation, GeneArrayTM Scanner, Fluidics
Station 400, and Hybridization Oven 640 is available to us through the Harvard
Center of Genomic Research.
Previous scanner versions used a photon multiplier tube (PMT) gain of 100%, which allowed for fluorescent intensities to become easily saturated. New scanner settings use a PMT of 10%, which increases the range of intensity values that are detected. Values from arrays that have been scanned at different settings can no longer be directly compared. The scanner setting and array type will be noted on each experiment's downloadable data page.
Over the past years,
Affymetrix technology has been proven to be highly reproducible and
standardized, and is therefore widely used in the scientific community. An
investigator elsewhere who wishes to compare his experimental mouse model to our
database of expression profiles can simply download the raw data from this
website and generate a new series of gene expression changes.
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