Affymetrix Sample Preparation

RNA Isolation Techniques	Affymetrix Eukaryotic Recommendations Affymetrix Prokaryotic Recommendations Blood Affymetrix technical note Zebrafish Arabidopsis - Carrington Lab Protocol Small Sample Extraction
RNA Quality	Free of DNA, salt, phenol and other contaminants that could interfere with enzymatic reactions A260/A280 ratio between 1.9-2.1 measured in 10 mm Tris ph 7.6 Agilent 2100 Bioanalyzer shows no degradation of RNA. RIN 7.0 or above.
RNA Quantity	2 - 5 µg Eukaryotic total RNA for Regular Sample Prep 10 - 100 ng Eukaryotic total RNA for Small Sample Prep 50-500 ng Eukaryotic total RNA for MessageAmp Premier Prep 10 µg Prokaryotic total RNA Inquire for Eukaryotic total RNA for WT-cDNA synthesis
Information about Pooling	Affymetrix Technical report on Pooling [1] Kerr, M.K., Design considerations for efficient and effective microarray studies. Biometrics, 59, 822-828 (2003). Kendziorski, C.M., Zhang, Y., Lan, H., and Attie, A.D., The efficiency of pooling mRNA in microarray experiments. Biostatistics, 4, 465-477 (2003). Peng, X., Wood, C.L., Blalock, E.M., Chen, K.C., Landfield, P.W., and Stromberg, A.J., Statistical implications of pooling RNA samples for microarray experiments. BMC Bioinformatics, 4, 26 (2003). C. Kendziorski , R. A. Irizarry , K.-S. Chen , J. D. Haag and M. N. Gould, On the utility of pooling biological samples in microarray experiments . PNAS \| March 22, 2005 \| vol. 102 \| no. 12 \| 4252-4257
How many replicates?	The more replicates, the lower the false positive rate (FDR) (Wolfinger et al.) Fewer replicates will identify a smaller percentage of the differentially expressed genes. See how increasing replicates can dramatically affect your data
Biological or Technical Replicates?	Affymetrix Arrays are technically quite reproducible (0.99) so the expense does not usually justify technical reps. Biological replicates give much more information about your system.