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Heterobasidion annosum gene expression from mycelium grown on different substrates

ABSTRACT: Transcript profiles of H. annosum from mycelium grown on different substrates and under different stresses were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) H. irregulare genome sequence version 1. One aim of this study was to compare gene expression profiles of H. annosum pre-grown on secondary metabolites from the biocontrol agent Phlebiopsis gigantea.

ORGANISM(S): Heterobasidion annosum

PROVIDER: GSE41301 | GEO | 2013/11/01

SECONDARY ACCESSION(S): PRJNA176693

REPOSITORIES: GEO

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Heterobasidion annosum gene expression from mycelium grown on different substrates

Project description:Transcript profiles of H. annosum from mycelium grown on different substrates and under different stresses were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) H. irregulare genome sequence version 1. One aim of this study was to compare gene expression profiles of H. annosum pre-grown on secondary metabolites from the biocontrol agent Phlebiopsis gigantea. We performed six hybridizations with samples derived from H. annosum grown in either liquid Malt Extract Medium (three biological replicates) or on secondary metabolite from Phlebiopsis gigantea (three biological replicates). The Heterobasidion irregulare custom-exon expression array (4 x 72K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products/exp/index.html) contained five independent, non-identical, 60-mer probes per gene model coding sequence. For 12,199 of the 12,299 annotated protein-coding gene models, probes could be designed. For 19 gene models, no probes could be generated, and 81 gene models shared all five probes with other gene models. Included in the array were 916 random 60-mer control probes and labelling controls. For 2032 randomly chosen gene models, technical duplicates were included on the array.

2013-11-01 | E-GEOD-41301 | biostudies-arrayexpress

Heterobasidion annosum gene expression from different tissues and mycelium grown on different substrates and under different biotic and abiotic stresses

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Heterobasidion annosum gene expression from different tissues and mycelium grown on different substrates and under different biotic and abiotic stresses

Project description:Transcript profiles of H. annosum from different tissues and mycelium grown on different substrates and under different stresses were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) H. irregulare genome sequence version 1. One aim of this study was to compare gene expression profiles of H. annosum grown on different substrates and under different biotic and abiotic stresses. We performed hybridizations (NimbleGen) with samples derived from H. annosum grown in either liquid Malt Extract Medium at 20Â°C (three biological replicates), under NaCl stress (three biological replicates), under CaCl2 stress (three biological replicates), at 8Â°C (three biological replicates), at 27Â°C (three biological replicates), saprotrophic growth on Scots pine sapwood (three biological replicates), bark (three biological replicates) or heartwood (three biological replicates). Additional hybridizations were performed with RNA from necrotrophic growth of Heterobasidion on Scots pine xylem (three biological replicates), necrotrophic growth on Scots pine phloem (three biological replicates), under nutrient starvation (three biological replicates) or under oxidative stress (three biological replicates). The Heterobasidion irregulare custom-exon expression array (4 x 72K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products/exp/index.html) contained five independent, non-identical, 60-mer probes per gene model coding sequence. For 12,199 of the 12,299 annotated protein-coding gene models, probes could be designed. For 19 gene models, no probes could be generated, and 81 gene models shared all five probes with other gene models. Included in the array were 916 random 60-mer control probes and labelling controls. For 2032 randomly chosen gene models, technical duplicates were included on the array.

2013-11-01 | E-GEOD-39805 | biostudies-arrayexpress

Heterobasidion irregulare gene expression from different tissues and mycelium grown on different substrates

Project description:Transcript profiles of Heterobasion irregulare from different tissues and mycelium grown on different substrates were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Heterobasidion annosum genome sequence version 1. One aim of this study was to verify the expression of the automatically annotated gene models under various conditions. Another goal was to compare gene expression profiles from different tissues of Heterobasidion irregulare and from mycelium grown on liquid MMN medium, liquid medium amended with lignin or cellulose and on wood. The Heterobasidion annosum custom-exon expression array (4 x 72K) manufactured byRoche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products /exp/index.html) contained five independent, nonidentical, 60-mer probes per gene model coding sequence. For 12,199 of the 12,299 annotated protein-coding gene models probes could be designed. For 19 gene models no probes could be generated and 81 gene models shared all five probes with other gene models. Included in the array were 916 random 60-mer control probes and labelling controls. For 2032 randomly chosen gene models, technical duplicates were included on the array. We performed 18 hybridizations (NimbleGen) with samples derived from Heterobasidion irregulare fruiting bodies (four biological replicates) , from necrotic bark of pines inoculated with H. irregulare (21dpi; three biological replicates), from H. irregulare mycelium grown in liquid MMN medium (three biological replicates) as well as from H. irregulare grown on wood shavings from pine (four biological replicates), grown in liquid medium amended with lignin (2 biological replicates) and growth in liquid medium amended with cellulose from Spruce (2 biological replicates). Cultures were harvested after 3 weeks of incubation 22°C in darkness. All samples were labeled with Cy3.

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