The Genomics Resource Lab will hybridize the biotin-labeled target overnight to the Affymetrix GeneChip array. Following hybridization, the GeneChip array undergoes an automated washing and streptavidin phycoerythrin conjugate staining protocol on the fluidics station. GeneChips are processed with strict adherence to the protocols outlined in the Affymetrix GeneChip manual specifically for the type of GeneChip being processed.
Once the GeneChip array has been processed, it is scanned by the Genomics Resource Lab with the GeneChip Scanner 3000 7G. Each image is stored as an image data file (.dat extension). The Affymetrix GeneChip Operating Software (GCOS) defines the probe cells and automatically computes a single intensity value for each probe cell, which it stores as a cell intensity file (.cel extension).
For 3' expression analysis, Genomics Resource staff use the GCOS expression analysis algorithm and the cell intensity file to compute a single-array expression analysis (.chp extension), from which an expression report (.rpt extension) may be generated and QC metrics determined.
For Genome-Wide SNP analysis, Genomics Resource staff use Affymetrix Genotyping Console Software, for SNP5.0 or SNP6.0 arrays, or the GeneChip Genotyping Analysis Software (GTYPE), for Mapping 10K 2.0, 100K or 500K arrays, to evaluate QC metrics and call rates.
While the lab will perform QC analysis of all microarrays processed, it is advisable that the investigator perform an assessment of microarray quality before proceeding to further analysis.
Data generated within the resource are transferred through automated pipelines to systems supported by the Hutchinson Center's Research Computing Support shared resource. Data is transferred to the user's 'fred' account, in the researcher's dnaarray folder. Researchers may transfer these flat files into GCOS by using the Affymetrix Data Transfer Tool (DTT).
If you do not currently have an account on the Research Computing server please fill out the User Account Application prior to the completion of your microarray experiment.
Affymetrix provides some analysis software specific to their microarrays. However, there are many third party software applications that can be used to further process and analyze your microarray data. Some of the software applications available to you can be found on the Genomics IT web page. (License agreements dictate that some of the software is available only from FHCRC based computers. If you are not at FHCRC and need access to the software, please contact Genomics and we will arrange access for you.)
Additional support is available to those requiring assistance with analyzing and interpreting their data. Please contact one of the following for guidance:
Jeff Delrow, Ph.D.
Director and Staff Scientist, Genomics Resource
voice : 206.667.2763
email : jdelrow@fhcrc.org
Martin Morgan, Ph.D.
Director and Staff Scientist, Bioinformatics Shared Resource
voice: 208.667-2793
email: mtmorgan@fhcrc.org
