E-GEOD-19020 - Analysis of DNA strand-specific differential expression with high density tiling microarrays

Status
Submitted on 13 November 2009, released on 14 May 2010, last updated on 10 June 2011
Organism
Schizosaccharomyces pombe 972h-
Samples (8)
Arrays (2)
Protocols (10)
Description
DNA microarray technology allows the analysis of genome structure and dynamics at genome-wide scale. Expression microarrays (EMA) contain probes for annotated open reading frames (ORF) and are widely used for the analysis of differential gene expression. By contrast, tiling microarrays (TMA) have a much higher probe density and provide unbiased genome-wide coverage. The purpose of this study was to develop a protocol that would take advantage of the high resolution of TMAs for quantitative measurement of DNA strand-specific differential expression of annotated and non-annotated transcripts. We extensively filtered probes present in Affymetrix Genechip Yeast Genome 2.0 expression and GeneChip S. pombe 1.0FR tiling microarrays to generate custom Chip Description Files (CDF) in order to compare the efficiency of both platforms. We experimentally tested the potential of our approach by measuring the differential expression of 4904 genes in the yeast Schizosaccharomyces pombe growing under conditions of oxidative stress. The results afforded a Pearson correlation coefficient of 0.943, indicating that TMAs are as reliable as EMAs for quantitative expression analysis. A significant advantage of TMAs over EMAs is the possibility of detecting non-annotated transcripts generated only under specific physiological conditions. We combined this property with a target-labelling protocol that preserves the original polarity of the transcripts with a view to determining the differential expression of non-annotated transcriptionally active regions. We have generated custom Chip Description Files (CDF) from Affymetrix Genechip Yeast Genome 2.0 expression and GeneChip S. pombe 1.0FR tiling microarrays to compare the efficiency of both platforms. We have experimentally tested the potential of our approach by measuring differential expression of the yeast Schizosaccharomyces pombe growing under conditions of oxidative stress.
Experiment types
transcription profiling by array, transcription profiling by tiling array 
Contacts
Luis Quintales, Francisco Antequera, Mar Sánchez
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-19020.idf.txt
Sample and data relationshipE-GEOD-19020.sdrf.txt
Raw data (1)E-GEOD-19020.raw.1.zip
Processed data (1)E-GEOD-19020.processed.1.zip
Array designsA-GEOD-9671.adf.txt, A-GEOD-9672.adf.txt
R ExpressionSetE-GEOD-19020.eSet.r
Links