Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

38 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Serpula lacrymans gene expression on different substrates

ABSTRACT: Transcript profiles of Serpula lacrymans grown on different substrates were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Serpula lacrymans 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 Serpula lacrymans grown on liquid MMN medium and on wood. We performed 9 hybridizations (NimbleGen) with samples derived fromfrom Serpula lacrymans grown on liquid MMN medium and on wood.

ORGANISM(S): Serpula lacrymans var. lacrymans S7.9

SUBMITTER: Annegret Kohler

PROVIDER: E-GEOD-27839 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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.

2012-03-15 | E-GEOD-30230 | biostudies-arrayexpress

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

Gene expression changes in Cenococcum geophilum-Pinus sylvestris ectomycorrhizal roots compared to Cenococcum geophilum free-living mycelium

Project description:Illumina HiSeq technology was used to generate mRNA profiles from Cenococcum geophilum ectomycorrhizal roots compared to free-living mycelium . Mycorrhizal roots were harvested after 3 months, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Cenococcum geophilum (http://genome.jgi.doe.gov/Cenge3/Cenge3.home.html) reference transcripts using CLC Genomics Workbench 6. mRNA profiles from Cenococcum geophilum ectomycorrhizal roots and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.

2016-08-01 | E-GEOD-83909 | biostudies-arrayexpress

Gene expression changes in Suillus luteus- Pinus sylvestris ectomycorrhizal roots compared to Suillus luteus free-living mycelium

Project description:Illumina HiSeq technology was used to generate mRNA profiles from Suillus luteus ectomycorrhizal roots compared to free-living mycelium . Mycorrhizal roots were harvested after 40 days, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Suillus luteus (http://genome.jgi-psf.org/Suilu1/Suilu1.home.html) using CLC Genomics Workbench 6. mRNA profiles from Suillus luteus ectomycorrhizal roots and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Two biological replicates were sequenced for mycorrhizal and mycelium samples.

2015-02-06 | E-GEOD-63926 | biostudies-arrayexpress

Gene expression of Laccaria bicolor S238N free-living mycelium grown on different media

Project description:Transcript profiles of Laccaria bicolor S238N mycelium on various media were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Laccaria bicolor genome sequence version 1. One goal was to evaluate the effect of nutrient deprivation on the transcriptome of Laccaria bicolor. We performed 15 hybridizations (Roche-NimbleGen) with samples derived from Laccaria bicolor free-living mycelium grown on MMN medium, on MMN with a 10 times reduction in all major macro-elements, on MMN with a 10 times reduction in the quantity of glucose or onto agar medium supplemented with the same nutrients used to fertilize our mycorrhization experiments.

2012-03-01 | E-GEOD-35556 | biostudies-arrayexpress

Serpula lacrymans gene expression on different substrates

Project description:Transcript profiles of Serpula lacrymans grown on different substrates were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Serpula lacrymans 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 Serpula lacrymans grown on liquid MMN medium and on wood.

2011-07-01 | GSE27839 | GEO

Scots pine (Pinus sylvestris) differentially interacts with Cenococcum geophilum and other simultaneously inoculated mycorrhizal (ECM) fungi

Project description:To identify specific gene networks induced in host roots by C. geophilum, we inoculated seedlings of Scots pine simultaneously with C. geophilum and either Suillus granulatus or Rhizopogon roseolus, two common ECM fungi associated to pines. We then measured the differential expression of Scots pine genes in the respective mycorrhizas using oligoarrays. We performed 14 hybridizations (NimbleGen) with samples derived from Pinus sylvestris mycorrhiza with Cenococcum geophilum, Rhizopogon roseolus or Suillus granulatus (3 biological replicates each), as well as from non-mycorrhizal control roots (two replicates). Only the Pinus-derived sequences from the array were considered for this analysis. All samples were labeled with Cy3.

2016-08-01 | E-GEOD-80549 | biostudies-arrayexpress

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

2012-03-15 | GSE30230 | GEO

Sepula lacrymans interacting with tree roots

Project description:This study characterizes the transcriptomic alterations of Serpula lacrymans in contact with tree roots compared to the transcriptome of free-living mycelium. We performed 6 hybridizations (NimbleGen) with samples derived from Picea sylvestris root tips inoculated with Serpula lacrymans (three biological replicates). These samples were compared to free-living mycelium from Serpula lacrymans (three biological replicates). All samples were labeled with Cy3.

2015-02-06 | E-GEOD-63929 | biostudies-arrayexpress

Activation of defense pathways in Scots pine bark after feeding by Pine Weevil (Hylobius abietis)

Project description:Coniferous trees use the oleoresin, a mixture of non-volatile non-volatile diterpene acids and a large (20-50%) volatile fraction of mono- and sesquiterpenes, as a defence tool against damaging herbivores and pathogens. Volatilization of monoterpenes increases viscosity of oleoresin and finally leading to polymerization of resin and a formation of protective solid plug. Resin storing conifers form an important source of volatile organic compounds (VOCs) mainly dominated by volatile monoterpenes. In the atmosphere, conifer VOCs react with ozone and OH and nitrous oxide radicals forming secondary organic compounds. This project seeks a better understanding of the genetic control of conifer defences and the role of monoterpenoid compounds under biotic stresses. Two separate samples were analysed (control-unchallenged and treatment-infected with the insect). There were a total of 3 biological replicates for the control samples and another set of three biological replicates for the treatment samples.

2015-04-01 | E-GEOD-60383 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data