Agilent Technologies Gene Expression Microarray Analysis of Archival FFPE Samples Application Note
Update: 01 October, 2023
Application Note Abstract Microarray-based gene expression hybridization is a powerful and proven technique for studying differential gene expression signatures in cancer. RNA extracted from freshly frozen tissues is optimal for microarray analysis; however, in many cases, formalin-fixed paraffi n-embedded (FFPE) tissues are the only samples available. To work with these diffi cult samples, Agilent has developed an FFPE sample protocol optimized for use with Agilent gene expression microarrays. To test the effectiveness of this protocol, total RNA was extracted from a quadruplicate set of colon tumor (adenocarcinoma), and matched normal colon FFPE and fresh frozen tissues. RNA purity and quality were determined, and the RNA was amplifi ed using a system in which a reverse transcription-generated cDNA library is subjected to limited PCR amplifi cation. The resulting cDNA target was chemically labeled. Analysis of the microarray results revealed a reduced sensitivity of detection for the FFPE-derived RNA samples; however, the lists of detected genes showed high overlap between the FFPE and frozen samples. Comparison of gene expression signals demonstrated excellent assay reproducibility between the technical repli- cates. Principal component analysis of array signals demonstrated clear separa- tion between the tumor and normal samples with grouping of replicate samples. Statistical analysis of the expression level variations between tumor and normal samples revealed that both the FFPE and frozen samples showed similar expression level changes.
Brand: Agilent
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MD5 Checksum: EE2954A2A75B4922C86FCB76525A230A
Publication date: 02 July, 2012
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