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Gene Expression Assay and Data Analysis

Frequently Asked Questions

  1. Where can I get information on gene expression sample preparation?

  2. What are the different target labeling assays for GeneChip® expression arrays?

  3. What are the steps of the GeneChip® eukaryotic expression assay?

  4. How long does the GeneChip® eukaryotic expression assay take from sample preparation to obtaining the array image?

  5. What is the sensitivity of the GeneChip® expression assay?

  6. How long can I store a eukaryotic hybridization cocktail after the first hybridization?

  7. How long can I keep my GeneChip® expression arrays in a low-stringency wash buffer before scanning?

  8. How many times can I scan a GeneChip® expression array before the data is affected?

  9. What are the safe stopping points in the GeneChip® expression assay?

  10. What is the minimum amount of total RNA I can use for each microarray experiment?

  11. What is the least amount of labeled eukaryotic cRNA target I can put on an array?

  12. What parameters should I use to QC my GeneChip probe array data?

  13. When I follow your recommended protocol of isolating total RNA from mammalian tissues, first using Trizol reagents, then with RNeasy columns, I sometimes see a reduced recovery off the RNeasy columns.

  14. Does the GeneChip Sample Cleanup Module generate comparable results relative to the previously recommended phenol/chloroform extraction for cDNA purification?

  15. What happens if the hybridization time is extended beyond 16 hours?

  16. I have observed on occasion that multiple _at probe sets are mapped to the same gene but give different expression results. How do I reconcile the difference?

  17. What 3'/5' ratio for control genes, for example GAPDH and Actin, should I anticipate to obtain on GeneChip probe arrays?

  18. Can results from different laboratories and different times be compared with each other directly and how do you control the variables in this type of experiment?

  19. Should I always anticipate the hybridization controls, bioB, bioC, bioD, and cre, to be called as Present?