Expression data from human osteosarcoma cells treated with CDK11 siRNA

The U-2OS and KHOS osteosarcoma cell lines where seeded onto the 100mm cell culture plate, then treated with CDK11 siRNA (40nM) or nonspecificsiRNA (40nM). Change with regular medium 24 hour later. Total RNA was collected from these cells using TRIzol Reagent (GIBCO Grand Island, NY) according to the manufacturers instructions. To account for and eliminate biologic noise, RNA was isolated from three distinct flasks of each cell line and pooled together. RNA quality was determined via ethidium bromide staining following agarose/formaldehyde gel electrophoresis. Total RNA was processed and hybridized to Affymetrix Genechip HG-U95Av2 arrays (Affymetrix, Santa Clara, CA) by the Gene Array Technology Center at Harvard Medical School (http://genome.med.harvard.edu). Affymetrix Gene Chip U133 Plus 2.0 in the first and most comprehensive whole human genome expression array. This array completes coverage of the whole human Genome with over 47,000 transcripts. The expression level of each mRNA is quantified by measuring its hybridization to these 23-mers in comparison to its hybridization to a one-base mismatch oligonucleotide. GeneSifter and Qlucore were used to analyze the microarray data (http://www.genesifter.net/web/; http://www.qlucore.com). Fold change in expression between CDK11 siRNA treated cell lines and control cell lines were evaluated using the Mann-Whitney test. A tenfold or greater change in intensity combined with a Mann-Whitney associated P value less than 0.05 was used as the criterion for inclusion in our filtered data set.

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