The on-line version of this article (available at http://www.bambed.org) contains the step-by-step protocol for this experiment and a supplemental figure.
Microarrays for undergraduate classes†
Article first published online: 26 JAN 2007
Copyright © 2006 International Union of Biochemistry and Molecular Biology, Inc.
Biochemistry and Molecular Biology Education
Volume 34, Issue 6, pages 432–437, November 2006
How to Cite
Hancock, D., Nguyen, L. L., Denyer, G. S. and Johnston, J. M. (2006), Microarrays for undergraduate classes. Biochem. Mol. Biol. Educ., 34: 432–437. doi: 10.1002/bmb.2006.494034062682
- Issue published online: 26 JAN 2007
- Article first published online: 26 JAN 2007
- Manuscript Revised: 28 JUL 2006
- Manuscript Received: 25 MAY 2006
- Gene expression;
- undergraduate education;
- microarray technology;
A microarray experiment is presented that, in six laboratory sessions, takes undergraduate students from the tissue sample right through to data analysis. The model chosen, the murine erythroleukemia cell line, can be easily cultured in sufficient quantities for class use. Large changes in gene expression can be induced in these cells by erythropoietic agents such as DMSO over a 72-h time period. Students isolate total RNA from control (0 h) and 72-h DMSO-treated murine erythroleukemia cells. From this, they synthesize a cDNA copy incorporating amino-allyl dUTP, which is then coupled to either a Cy5 or a Cy3 dye. Equal amounts of the two labeled cDNA samples are then applied to a standard cDNA microarray, which is then hybridized, washed, and scanned. Up- and down-regulated genes are selected using an “in-house” user-friendly data base program. Quality control checks are included at various stages throughout the procedure and, as the process of erythropoiesis is well characterized, a number of erythroid sequences serve as internal controls on the validity of the array data. Through this experiment, students gain experience in a wide range of molecular biology techniques, the use of controls to check a multistep process, validation of results, and strategies to manage the large amount of data generated. Most importantly, it provides undergraduate students with an opportunity to carry out experiments using cutting edge techniques normally found only in research laboratories.