E-MEXP-522 - Transcription profiling of Mycosphaerella graminicola in different nutritional environments

Status
Submitted on 5 January 2006, released on 28 February 2006, last updated on 3 May 2014
Organism
Mycosphaerella graminicola
Samples (4)
Array (1)
Protocols (8)
Description
In order to gain a first insight into the Mycosphaerella graminicola global transcriptome in different nutritional environments, we performed initial experiments on two in vitro growth conditions during log-phase growth and on infected plant material twenty-eight days after inoculation. In vitro log phase growth in nutrient-rich Potato Dextrose Broth (PDB) was used as a control in independent comparisons with 1) log phase growth in nutrient-limiting Czapek-Dox Broth (CDB) and 2) twenty-eight days of plant infection. Growth in PDB results in a rapid “budding” type growth of the M. graminicola sporidia. Growth in CDB is phenotypically similar in that the fungus continues to grow as budding sporidia but this occurs at approximately 20% of the rate in PDB. In contrast, late stage infected plant material contains fungus growing as filamentous hyphae, generating pycnidia and sporulating. At this stage the plant material is completely senesced and the RNA isolated from this tissue is entirely of fungal origin. The complete lack of plant RNA enabled the microarray comparison to be made against growth in PDB. In order to generate statistically significant data for further analysis sixteen independent microarray blocks were hybridised for each experiment. Within these sixteen replicates were three biological repeats. For data analysis we employed limits of a two-fold cut-off in expression based upon statistical analysis of the replicate hybridisations (P <0.01).
Experiment types
transcription profiling by array, growth condition
Contacts
John Keon <john.keon@bbsrc.ac.uk>, Jason J Rudd, John Antoniw, John Hargreaves, Kim Hammond-Kosack, Wendy Skinner
Citation
Metabolic and stress adaptation by Mycosphaerella graminicola during sporulation in its host revealed through microarray transcription profiling. John Keon; Jason Rudd; John Antoniw; Wendy Skinner; John Hargreaves; Kim Hammond-Kosack. Mol Plant Pathol 6:527-540 (2005)
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-MEXP-522.idf.txt
Sample and data relationshipE-MEXP-522.sdrf.txt
Raw data (1)E-MEXP-522.raw.1.zip
Array designA-MEXP-293.adf.txt
R ExpressionSetE-MEXP-522.eSet.r
Links