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E-GEOD-4045 - Transcription profiling of human colorectal serrated adenocarcinomas and conventional adenocarcinomas reveals they are a molecular subclass as well as morphologically distinct

Status
Submitted on 16 January 2006, released on 27 October 2007, last updated on 27 March 2012
Organism
Homo sapiens
Samples (37)
Array (1)
Protocols (7)
Description
Serrated adenocarcinomas are morphologically different from conventional adenocarcinomas. The serrated pathway has recently been proposed to represent a novel mechanism of colorectal cancer (CRC) formation. However, whether they are biologically different and truly form a distinct subclass of CRC, is not known. This study shows that the gene expression profile of serrated and conventional CRCs differs from each others and that serrated CRCs are not only morphologically novel, but also biologically distinct subclass of CRC. Experiment Overall Design: Total RNA was extracted from fresh frozen tumors with Trizol (GibcoBRL) and purified using RNeasy spin columns (Qiagen). The RNA quality was analyzed using a spectrophotometer and a Agilent 2100 Bioanalyzer (Agilent Technologies). Biotin labeled and fragmented cRNA was prepared from 8 micrograms of total RNA with procedures recommended for the HG-U133 GeneChip expression analysis (Affymetrix). The HG-U133A chips were hybridized, scanned and analyzed with Microarray Suite 5.0 software according to the manufacturer’s instructions (Affymetrix).
Experiment types
transcription profiling by array, co-expression, disease state
Contact
Antti Kokko
Citation
Serrated carcinomas form a subclass of colorectal cancer with distinct molecular basis. P Laiho, A Kokko, S Vanharanta, R Salovaara, H Sammalkorpi, H Järvinen, J-P Mecklin, T J Karttunen, K Tuppurainen, V Davalos, S Schwartz, D Arango, M J Mäkinen, L A Aaltonen. Oncogene 26(2):312-20 (2007)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-4045.idf.txt
Sample and data relationshipE-GEOD-4045.sdrf.txt
Raw data (1)E-GEOD-4045.raw.1.zip
Processed data (1)E-GEOD-4045.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-4045.eSet.r
Links