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E-GEOD-36870 - Laser capture microdissection and microarray analysis of ectomycorrhizas formed by the ascomycete Tuber melanosporum reveal functional heterogeneity between mantle and Hartig net compartments

Status
Released on 1 March 2013, last updated on 19 March 2013
Organism
, Corylus avellana, Tuber melanosporum
Samples (6)
Array (1)
Protocols (7)
Description
The aim of this analysis was to better understand the complex symbiotic stage of Tuber melanosporum by combining the use of laser capture microdissection and microarray gene expression analysis. We isolated the fungal/soil (i.e. the mantle) and the fungal/plant (i.e. the Hartig net) interfaces from transverse sections of T. melanosporum/Corylus avellana ectomycorrhizas and identified the transcriptional landscape associated with each compartment. We compared these data to the transcriptome of ectomycorrhizal root tips, free-living mycelium and fruiting bodies of Tuber melanosporum (Series GSE17529). The T. melanosporum custom-exon expression array (4 x 72K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) contained five independent, nonidentical, 60-mer probes per gene model coding sequence. Included in the oligoarray were 12,232 annotated gene models, 3,913 random 60-mer control probes and labelling controls. Sequences used for the oligonucleotide design were from an early draft of the gene catalog containing several TE families. For 1,876 gene models, technical duplicates were included on the array. We performed 6 hybridizations (NimbleGen) with samples derived from microdissected mantles (3 biological replicates) and Hartig nets ((3 biological replicates each) from T. melanosporum/Corylus avellana ectomycorrhizal root tips . All samples were labeled with Cy3.
Experiment type
transcription profiling by array 
Contacts
Annegret Kohler, Annick Brun, Emilie Tisserant, Francis Martin, Stéphane Hacquard, Valérie Legué
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-36870.idf.txt
Sample and data relationshipE-GEOD-36870.sdrf.txt
Raw data (1)E-GEOD-36870.raw.1.zip
Processed data (1)E-GEOD-36870.processed.1.zip
Array designA-GEOD-8982.adf.txt
Links