Transcriptomics

Dataset Information

38

Comparison of gene expression in roots from Populus trichocarpa and Populus deltoides colonized with Laccaria bicolor


ABSTRACT: The majority of trees live in association with symbiotic fungi, which facilitate their access to soil nutrients. The ectomycorrhizal symbiosis represents a complex biological system involving multifaceted interactions between the two partners. The establishment of the symbiosis depends on various conditions (e.g. climate), but also on the genetic traits of the partners. To evaluate the impact of the genetic predisposition on the development and functioning of ectomycorrhizas, we compared the transcriptome of roots from Populus trichocarpa and Populus deltoides colonized with Laccaria bicolor. Overall design: The Populus whole-genome expression array version 2.0 (S. DiFazio, A. Brunner, P. Dharmawardhana, and K. Munn, unpublished data) manufactured by NimbleGen Systems Limited (Madison, WI) contains in duplicates three independent, non-identical, 60-mer probes per whole gene model plus control probes and labeling controls. Included in the microarray are 65,965 probe sets corresponding to 55,970 gene models predicted on the P.trichocarpa genome sequence version 1.0 and 9,995 aspen cDNA sequences (Populus tremula, Populus tremuloides, and P. tremula x P. tremuloides). NimbleGen whole genome microarray analyses were performed in triplicate as per manufacturer's instructions. We carried out six hybridizations (NimbleGen) with samples derived from Populus trichocarpa and Populus deltoides mycorrhizal root tips. Three samples (biological replicates) originated from Populus trichocarpa (GSM648401, GSM648403, GSM648405) and three biological replicates from Populus deltoides (GSM648408, GSM648411, GSM648414). cDNA was synthesized using CLONTECH Super Smart cDNA Synthesis kit containing an amplification step on the cDNA level. All samples were labeled with Cy3.

INSTRUMENT(S): Populus 2.0

SUBMITTER: Annegret Kohler  

PROVIDER: GSE26416 | GEO | 2011-01-15

SECONDARY ACCESSION(S): PRJNA136793

REPOSITORIES: GEO

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