E-GEOD-51655 - Transcriptional profiling of the rust fungus Cronartium quercuum f. sp. fusiforme (Cqf) during vegetative growth on 2 different hosts

Status
Released on 25 October 2013, last updated on 3 June 2014
Organism
Cronartium quercuum
Samples (16)
Array (1)
Protocols (11)
Description
The purpose of this study was to make a single comparison between Cqf genes expressed during the vegetative stages of infection on the telial host (oak leaf) versus the aecial host (pine stem). A large proportion of genes were expressed in both hosts and significantly differentially expressed genes were enriched for candidate fungal effectors (small secreted proteins). These results suggest that the Cqf rust fungus uses a largely common set of genes to create two very different infection phenotypes. This study was based on hybridizations to custom microarrays containing features representing 8692 gene models from a Cqf genome sequencing project midpoint assembly. Two Agilent 4 X 44K microarray slides were populated with 60-mer probes (1 to 5 per transcript), designed using Agilent’s web-based eArray software. Labeled target cRNA (complementary RNA) was generated using Agilent’s Low Input Quick Amp Labeling Kit, such that oak and pine samples were labeled with either cy3 or cy5 an equal number of times across the experiment. Each microarray was hybridized with labeled cRNA target derived from a single oak sample and labeled cRNA target derived from a single pine sample. There were a total of eight oak sample replications and eight pine sample replications. Target hybridization and scanning were performed by the University of Florida’s Interdisciplinary Center for Biotechnology Research using standard procedures and an Agilent G250B Scanner.
Experiment type
transcription profiling by array 
Contacts
John Davis <geo@ncbi.nlm.nih.gov>, John M Davis, Katherine E Smith
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-51655.idf.txt
Sample and data relationshipE-GEOD-51655.sdrf.txt
Processed data (1)E-GEOD-51655.processed.1.zip
Array designA-GEOD-17836.adf.txt
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