Laccaria bicolor S238N gene expression in different tissues

The Transcriptome of different tissues and developmental stages of Laccaria bicolor S238N was analyzed. The array probes were designed from gene models taken from the Joint Genome institute Laccaria bicolor genome sequence version1. One aim of this study was to verify the expression of the automatically annotated gene models in various tissues and to use this transcriptional information to confirm, to correct or to reject gene models. Another goal was to identify tissue-specific gene expression, e.g. mycorrhiza up-regulated transcripts or fruiting body up-regulated transcripts, or treatment specific gene expression for further detailed analyses. Keywords: Tissue comparison The Laccaria whole-genome expression array manufactured by NimbleGen (Madison, WI) contains in duplicates eight independent, non-identical, 60-mer probes per whole gene model (taken from the Joint Genome Institute Laccaria bicolor genome sequence version 1.0). We performed 11 hybridizations (NimbleGen) with samples derived from various tissues and treatments. Four samples were originated from ectomycorrhizae, two of them derived from the symbiosis with poplar roots (GSM245987 and GSM245992), the others from the interaction with Douglas fir (GSM245993 and GSM245994). Two samples derived from fruiting bodies (GSM245995 and GSM245996) and two samples from free-living mycelium (GSM245997 and GSM247052). The two free-living mycelium (GSM245997 and GSM247052) as well as the two Douglas fir mycorrhizae samples (GSM245993 and GSM245994) were biological replicates. In addition, free-living mycelium inoculated with sterile deionized water (GSM292146) or a bacterial suspension (GSM292155 and GSM292658) were analyzed. All samples were labeled with Cy3.