Transcriptomics

Dataset Information

5

Quantitative Expression Profiling of RNA from Formalin-Fixed, Paraffin-Embedded (FFPE)and Fresh Frozen (FF) Breast Cancer samples


ABSTRACT: Unluckily, FFPE archival methods lead to partial RNA degradation, limiting the amount of derivable information. This study aims to evaluate if the DASL gene expression assay, designed to generate reproducible data from degraded RNAs, is a reliable method to apply on RNA from FFPE tissues. In order to do that, we analyzed 20 FFPE breast cancer samples and 20 FF (Fresh Frozen) matched samples with the Illumina Whole Genome DASL platform for a genome-wide expression profiling.

ORGANISM(S): Homo sapiens  

DISEASE(S): Breast Cancer

SUBMITTER: Mittempergher Lorenza  

PROVIDER: E-TABM-1081 | ArrayExpress | 2011-09-05

REPOSITORIES: ArrayExpress

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Publications

Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue.

Mittempergher Lorenza L   de Ronde Jorma J JJ   Nieuwland Marja M   Kerkhoven Ron M RM   Simon Iris I   Rutgers Emiel J Th EJ   Wessels Lodewyk F A LF   Van't Veer Laura J LJ  

PloS one 20110211 2


BACKGROUND AND METHODS: Formalin Fixed Paraffin Embedded (FFPE) samples represent a valuable resource for cancer research. However, the discovery and development of new cancer biomarkers often requires fresh frozen (FF) samples. Recently, the Whole Genome (WG) DASL (cDNA-mediated Annealing, Selection, extension and Ligation) assay was specifically developed to profile FFPE tissue. However, a thorough comparison of data generated from FFPE RNA and Fresh Frozen (FF) RNA using this platform is lack  ...[more]

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