Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-11875 - Transcriptome analysis of potato tubers: Effects of different agricultural practices

Status
Submitted on 23 June 2008, released on 1 February 2009, last updated on 1 May 2014
Organism
Solanum tuberosum
Samples (96)
Array (1)
Protocols (8)
Description
The use of profiling techniques such as transcriptomics, proteomics, and metabolomics has been proposed to improve the detection of side effects of plant breeding processes. This paper describes the construction of a food safety-oriented potato cDNA microarray (FSPM). Microarray analysis was performed on a well-defined set of tuber samples of two different potato varieties, grown under different, well-recorded environmental conditions. Data were analyzed to assess the potential of transcriptomics to detect differences in gene expression due to genetic differences or environmental conditions. The most pronounced differences were found between the varieties Sante and Lady Balfour, whereas differences due to growth conditions were less significant. Transcriptomics results were confirmed by quantitative PCR. Furthermore, the bandwidth of natural variation of gene expression was explored to facilitate biological and/or toxicological evaluation in future assessments. Keywords: experiment with factorial design factorial design; 2 potato cultivars (Sante, Lady Balfour); 2 fertilizers (dairy manure compost, chicken manure pellets); 3 plant protection treatments (copper oxychloride, comcat, water), 3 biological replicates, 48 samples
Experiment type
transcription profiling by array 
Contacts
Jeroen van Dijk <jeroen.vandijk@wur.nl>, Jeroen P van Dijk, Katarina Cankar, Kok J Esther
Citation
Transcriptome analysis of potato tubers--effects of different agricultural practices. van Dijk JP, Cankar K, Scheffer SJ, Beenen HG, Shepherd LV, Stewart D, Davies HV, Wilkockson SJ, Leifert C, Gruden K, Kok EJ.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-11875.idf.txt
Sample and data relationshipE-GEOD-11875.sdrf.txt
Raw data (1)E-GEOD-11875.raw.1.zip
Processed data (1)E-GEOD-11875.processed.1.zip
Experiment designE-GEOD-11875.biosamples.png, E-GEOD-11875.biosamples.svg
Array designA-GEOD-6993.adf.txt
Links