GEO DataSets

(Submitter supplied) Illumina technology was used to generate mRNA profiles of leaves, roots and Laccaria bicolor mycorrhiza of Poplar treated with ozone or stopped watering. Total RNA was extracted separately from each plant and pooled to 4 biological replicates per condition.TruSeq mRNA Stranded libraries were constructed and and sequenced using Illumina HiSeq 3000 at the Genotoul sequencing facilities (Toulouse, France). more...

Organism:

Laccaria bicolor; Populus trichocarpa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30192 GPL30193

60 Samples

Download data: TXT

(Submitter supplied) We analyzed oxidized 5-methylcytosine derivatives 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine in nucleic acids of multicellular fungi Laccaria bicolor and Coprinopsis cinerea which have been used as models to study DNA methylation, developmental processes and symbiotic interactions. All three cytosine derivatives were detected in the genomes of both fungi, and importantly, we discovered 5carC in the RNA fractions, potentially including large non-coding, messenger RNAs and small RNA molecules, indicating gene regulatory functions of 5carC.

Organism:

Laccaria bicolor; Coprinopsis cinerea

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL30834 GPL30833

27 Samples

Download data: COV

(Submitter supplied) We performed whole transcriptome sequencing of L. bicolor mycelium cultivated under normal and elevated vitamin C conditions.

Organism:

Laccaria bicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30831

4 Samples

Download data: GTF

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Laccaria bicolor; Coprinopsis cinerea

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL30833 GPL30831 GPL30834

31 Samples

Download data: COV, GTF

(Submitter supplied) Illumina technology was used to generate mRNA profiles of Laccaria bicolor mycelium grown under different nutrien conditions. Total RNA was extracted.TruSeq mRNA Stranded libraries were constructed and and sequenced (2 x 150 bp Illumina HiSeq3000) at the Genotoul sequencing facilities (Toulouse, France). Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the L. more...

Organism:

Laccaria bicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31043

20 Samples

Download data: TXT

(Submitter supplied) Illumina technology was used to generate mRNA profiles of three stages of L. bicolor basidiocarps. Total RNA was extracted separately from cap and stipe.TruSeq mRNA Stranded libraries were constructed and and 2 x 100 bp sequenced using Illumina HiSeq 2000 at the Genotoul sequencing facilities (Toulouse, France). Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the L. more...

Organism:

Laccaria bicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19637

18 Samples

Download data: TXT

(Submitter supplied) Illumina technology was used to generate mRNA profiles of a time course of Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro ectomycorrhizal development. Total RNA was extracted, TruSeq mRNA Stranded libraries were constructed and and sequenced in triplicates (2 x 150 bp Illumina HiSeq3000) at the Genotoul sequencing facilities (Toulouse, France). Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the L. more...

Organism:

Laccaria bicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31043

37 Samples

Download data: TXT

(Submitter supplied) Cytosine methylation is a conserved base modification, but explanations for its interspecific variation remain elusive. Only through taxonomic sampling of disparate groups can unifying explanations for interspecific variation be thoroughly tested. Here we leverage phylogenetic resolution of cytosine DNA methyltransferases (DNA MTases) and genome evolution to better understand widespread interspecific variation across 40 diverse fungal species. more...

Organism:

Plenodomus lingam; Candida albicans; Coemansia reversa; Coemansia spiralis; Kirkomyces cordensis; Metarhizium robertsii; Pseudogymnoascus destructans; Saccharomyces cerevisiae; Aspergillus flavus; Coprinopsis cinerea; Clavispora lusitaniae; Lobosporangium transversale; Radiomyces spectabilis; Flammula alnicola; Cryptococcus neoformans var. grubii; Candidozyma auris; Pyricularia oryzae KJ201; Syncephalis fuscata; Podospora anserina; Phanerodontia chrysosporium; Agaricus bisporus; Mixia osmundae; Sporobolomyces roseus; Cordyceps militaris; Wolfiporia cocos; Spinellus fusiger; Hesseltinella vesiculosa; Rhodonia placenta; Microbotryum lychnidis-dioicae; Heterobasidion irregulare; Phycomyces blakesleeanus; Fusarium fujikuroi; Neurospora crassa; Pleurotus ostreatus; Aureobasidium pullulans; Laccaria bicolor; Uncinocarpus reesii; Parasitella parasitica; Botrytis cinerea; Tilletiopsis washingtonensis

Type:

Methylation profiling by high throughput sequencing; Third-party reanalysis

29 related Platforms

31 Samples

Download data: TSV, TXT, XLS

(Submitter supplied) Many trees form ectomycorrhizal symbiosis with fungi. During symbiosis, the tree roots supply sugar to the fungi in exchange for nitrogen, and this process is critical for the nitrogen and carbon cycles in forest ecosystems. However, the extents to which ectomycorrhizal fungi can liberate nitrogen and modify the soil organic matter and the mechanisms by which they do so remain unclear since they have lost many enzymes for litter decomposition that were present in their free-living, saprotrophic ancestors. more...

Organism:

Paxillus involutus; Laccaria bicolor

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19511 GPL19637

24 Samples

Download data: TAB

(Submitter supplied) Illumina HiSeq2000 technology was used to generate mRNA profiles from the ectomycorrhizal fungi Laccaria bicolor colonizing roots of Populus trichocarpa. Samples were taken after 3 months of contact in order to identify mycorrhiza-regulated transcripts. 100bp reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) reference genome.

Organism:

Laccaria bicolor; Populus trichocarpa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17415 GPL21175

2 Samples

Download data: TXT

(Submitter supplied) Decomposition of soil organic matter in forest soils is thought to be controlled by the activity of saprotrophic fungi, while biotrophic fungi including ectomycorrhizal fungi act as vectors for input of plant carbon. The limited decomposing ability of ectomycorrhizal fungi is supported by recent findings showing that they have lost many of the genes that encode hydrolytic plant cell-wall degrading enzymes in their saprophytic ancestors. more...

Organism:

Hebeloma cylindrosporum; Piloderma croceum; Leucogyrophana pinastri; Suillus luteus; Serpula lacrymans; Jaapia argillacea; Paxillus involutus; Laccaria bicolor; Coniophora puteana

Type:

Expression profiling by high throughput sequencing

9 related Platforms

54 Samples

Download data: TAB

(Submitter supplied) This study characterizes the transcriptomic alterations of Laccaria bicolor S238N during interaction with Pseudotsuga menziesii. Three time-points were analyzed, two weeks, four weeks and six weeks after inoculation and compared to the transcriptome of free-living mycelium from Laccaria bicolor S238N.

Organism:

Laccaria bicolor S238N-H82; Laccaria bicolor; Pseudotsuga menziesii

Type:

Expression profiling by array

Platform:

GPL14641

12 Samples

Download data: PAIR

(Submitter supplied) This study characterizes the transcriptomic alterations of Laccaria bicolor S238N during interaction with P. trichocarpa. Four time-points were analyzed, two weeks, four weeks , six weeks and twelve weeks after inoculation and compared to the transcriptome of free-living mycelium from Laccaria bicolor S238N

Organism:

Populus trichocarpa; Laccaria bicolor S238N-H82; Laccaria bicolor

Type:

Expression profiling by array

Platform:

GPL14641

19 Samples

Download data: PAIR

(Submitter supplied) In order to get insights into the ability of ectomycorrhizal fungi to perceive their biotic environment as well as into the mechanisms of the interactions between ectomycorrhizal fungi and soil bacteria, we analysed the transcriptomic response of the ectomycorrhizal fungus L. bicolor and one detrimental bacterial strain during their interactions in vitro.

Organism:

Laccaria bicolor

Type:

Expression profiling by array

Platform:

GPL9465

6 Samples

Download data: TXT

(Submitter supplied) In order to get insights into the ability of ectomycorrhizal fungi to perceive their biotic environment as well as into the mechanisms of the interactions between ectomycorrhizal fungi and soil bacteria, we analysed the transcriptomic response of the ectomycorrhizal fungus L. bicolor and of two beneficial, and neutral soil bacteria during their interactions in vitro.

Organism:

Laccaria bicolor

Type:

Expression profiling by array

Platform:

GPL9465

9 Samples

Download data: TXT

(Submitter supplied) Illumina GAIIx technology was used to generate mRNA profiles from the ectomycorrhizal fungi Laccaria bicolor colonizing roots of Populus trichocarpa. Samples were taken after two, four and 12 weeks of contact in order to identify mycorrhiza-regulated transcripts. 37bp reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) and the Laccaria bicolor (http://genome.jgi-psf.org/Lacbi2/Lacbi2.home.html) reference genomes using CLC Genomics Workbench 6.

Organism:

Populus trichocarpa; Laccaria bicolor

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18263 GPL17579 GPL18265

7 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Laccaria bicolor; Laccaria bicolor S238N-H82

Type:

Expression profiling by array

Platform:

GPL14641

15 Samples

Download data: PAIR

(Submitter supplied) Laccaria bicolor transcript profiles of different tissues and mycorrhizal root tips from different host trees 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 compare gene expression profiles from ectomycorrhizal root tips with different host plants.

Organism:

Laccaria bicolor S238N-H82; Pseudotsuga menziesii; Populus deltoides; Populus trichocarpa

Type:

Expression profiling by array

Platform:

GPL14641

12 Samples

Download data: PAIR

(Submitter supplied) Mycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the soil and in return the fungus receives photosynthetically-derived carbohydrates. This union of plant and fungal metabolisms is the mycorrhizal metabolome. Understanding this symbiotic relationship at a molecular level provides important contributions to the understanding of forest ecosystems and global carbon cycling. more...

Organism:

Laccaria bicolor; Populus tremuloides

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13325

2 Samples

Download data: TXT

(Submitter supplied) Bacteria use small diffusible molecules to communicate and to coordinate population response by a cell density-depend mechanism named quorum sensing (QS). If such a cross-talk was first described between bacterial species, it was recently evidenced that bacterial QS signal molecules can also be sensed by eukaryotic organisms thus playing as inter-kingdom signalling molecules. Although ectomycorrhizal fungi interact physically and metabolically with myriads of bacterial species in soils, nothing is known about the ability of ectomycorrhiza-associated bacteria to produce QS molecules and the potential impact of these molecules in the interaction. more...

Organism:

Laccaria bicolor; Laccaria bicolor S238N-H82

Type:

Expression profiling by array

Platform:

GPL9465

8 Samples

Download data: TXT