Questioning the utility of pooling samples in microarray experiments with cell lines

Lara Lusa, V. Cappelletti, M. Gariboldi, C. Ferrario, L. De Cecco, J. F. Reid, S. Toffanin, G. Gallus, L. M. McShane, M. G. Daidone, M. A. Pierotti

Research output: Contribution to journalArticlepeer-review

Abstract

We describe a microarray experiment using the MCF-7 breast cancer cell line in two different experimental conditions for which the same number of independent pools as the number of individual samples was hybridized on Affymetrix GeneChips. Unexpectedly, when using individual samples, the number of probe sets found to be differentially expressed between treated and untreated cells was about three times greater than that found using pools. These findings indicate that pooling samples in microarray experiments where the biological variability is expected to be small might not be helpful and could even decrease one's ability to identify differentially expressed genes.

Original languageEnglish
Pages (from-to)67-73
Number of pages7
JournalInternational Journal of Biological Markers
Volume21
Issue number2
Publication statusPublished - Apr 2006

Keywords

  • Affymetrix GeneChips
  • Breast cancer
  • DNA microarrays
  • MCF-7 cell line
  • Sample pooling
  • Toremifene

ASJC Scopus subject areas

  • Immunology
  • Biochemistry

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