Transcription profiling by array of formalin-fixed paraffin-embedded or fresh frozen human tumor samples

ABSTRACT: Background: To date, few studies have systematically characterized microarray gene expression signal performance with degraded RNA from formalin-fixed paraffin-embedded (FFPE) specimens in comparison to intact RNA from unfixed fresh-frozen (FF) specimens. Methodology: RNA was extracted and isolated from paired tumor and normal samples from both FFPE and FF kidney, lung and colon tissue specimens. Microarray signal dynamics on both the raw probe and probeset level were evaluated. A contrast metric was developed to directly compare microarray signal derived from RNA extracted from matched FFPE and FF specimens. Gene-level summaries were then compared to determine the degree of overlap in expression profiles. Results: RNA extracted from FFPE material was more degraded and fragmented than FF,

ORGANISM(S): Homo sapiens

SUBMITTER: Abdueva D 

PROVIDER: S-ECPF-GEOD-19249 | biostudies-other | 2010 Jul

REPOSITORIES: biostudies-other