Affymetrix GeneChips
- Set up a meeting with Drs. Alekseyev and Lenburg to plan your experiment, discuss RNA isolation methods, costs and/or have them order the GeneChips that you need. If you are familiar with microarray analysis, you may want to simply have us order GeneChips for you.
- Isolate either total RNA (most common) or polyA-selected RNA and deliver the sample to Dr. Alekseyev. See our list of RNA Isolation protocols.
- Wait about 3 days while the microarray resource team labels your RNA, hybridizes it to the GeneChips, collects the data using a laser scanner and presents you with electronic and hard copies of the results.
- Go over basic data analysis on our in-house work stations with a member of the microarray resource or on your own once you learn how to do it.
Custom Oligo Arrays
- Decide which genes you wish to analyze. This can be done
by any combination of:
- defining a set of genes of interest from an Affymetrix GeneChip experiment
- consulting our pre-designed gene sets (eg. "cancer genes", "immunology genes") available soon
- using published data sets
- searching the NCBI or other genome websites
- or simply listing the genes of interest
- The microarray resource will then design appropriate oligos taking into account parameters such as melting temperature, sequence uniqueness, and secondary structure.
- The oligos will be synthesized in house and spotted on derivatized glass slides. We will synthesize roughly 100 oligos/day to start with.
- Isolate either total RNA (most common) or polyA-selected RNA and deliver the sample to Dr. Alekseyev.
- Wait about 3 days while the microarray resource team labels your RNA, hybridizes it to the custom slides, collects the data using a laser scanner and presents you with electronic and hard copies of the results.
- Go over basic data analysis on our in-house work stations with a member of the microarray resource or on your own once you learn how to do it.
When you're ready to start either an Affymetrix or custom array project, contact us with questions, or if you want to set up a time to meet about your project.
links
Primer on microarrays (link to NCBI website)
Affymetrix Technical Manual (PDF format, 6.6MB)
This document contains a variety of interesting technical information about the Affymetrix system.
