Thai Cancer Journal
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Browsing Thai Cancer Journal by Author "Anchalee Tantiwetrueangdet"
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Item Assessment of the Relationship Between RNA Integrity and Post-Chip QC Variables of Affymetrix GeneChip Human Genome U133 Plus 2.0 Array Experiments(Thai Cancer Journal, 2010-04-07) Anchalee Tantiwetrueangdet; Ravat Panvichian; Sansanee Wongwaisayawan; Koset Pinpradap; Surasak LeelaudomlipiRNA purity and integrity are important factors for reliability and reproducibility of downstream applications, especially for microarray analysis. However, it is difficult in practice to obtain perfect RNA from cancerous tissues and thus microarray experiments of gene expression are very expensive. So, it would be very useful to be able to predict, based on their RNA integrity, which RNA samples should be proceeded and will give interpretable results after hybridization. To assess the relationship between the RNA integrity and post-chip quality control variables of Affymetrix GeneChip Human Genome U133 Plus 2.0 Array experiments, total cellular RNA was isolate from 13 snap-frozen tissues including 7 breast tissues (2 tissues of normal breast, 2 tissues of primary breast cancer without metastasis and 3 tissues of primary breast cancer with metastasis) and 6 axillary lymph node tissues (3 tissues of normal axillary lymph node and 3 tissues of metastatic axillary lymph node). All samples were verified and confirmed by pathologist. RNA samples with RNA integrity number (RIN) between 5.5 and 7.9 were selected as starting material for conducting 13 chips of Affmetrix GeneChip Human U133 Plus 2.0 Array. Pearson correlation test was used to determine the correlation between RIN and post-chip quality control variables of Affymetrix GeneChip Human Genome U133 Plus 2.0 Array experiments. The assessed variables include the followings: background, noise (RawQ), scaling factor, percentage of present genes (%P), as well as 3’/5’ ratio of GAPDH (Sig3’/5’). We found that post-chip quality control variables after hybridizing RNA samples with RIN 5.8-7.9 to Affmetrix GeneChip Human Genome U133 Plus 2.0 Array were acceptable. We also observed a significant negative correlation between RIN and scale factor (r =-0.593, p=0.033, n=13) but no correlation between RIN and others variables. Based on this study, our data suggested that RNA samples with RIN not lower than 5.8 could be processed to conduct AFFmetrix GeneChip Human Genome U133 Plus 2.0 Array experiments.