Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq analysis of Coprinopsis cinerea mycelium challenged with gram negative and gram positive bacteria

ABSTRACT: During growth in their ecological niche fungi encounter many (micro)organisms that compete for nutrients and /or have antagonistic activity. However, little is known about responses of fungi upon exposure to other microbes. In this project we want to gain insight in induced responses of C. cinerea towards bacteria through comparison of the transcriptome of vegetative C. cinerea mycelium either grown alone or exposed to the bacterial species Escherichia coli or Bacillus subtilis

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Coprinopsis cinerea

SUBMITTER: Annageldi Tayyrov

PROVIDER: E-MTAB-6876 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Inducible defense response of C. cinerea against its fungiverous nematode A. avenae in microfluidics device

Project description:The fungal toxin-encoding genes are highly upregulated in the vegetative mycelium upon challenge with the predator. Our recent studies in microfluidics have shown that latter induction is spatially restricted to parts of the vegetative mycelium that is in direct contact with the predator. In order to dissect the defensome of a multicellular fungus against a predator, here, we performed RNA - sequencing of mushroom Coprinopsis cinerea upon challenged with fungivorous nematode Aphelenchus avenae in Microfluidics device at three different time points. We analyzed hyphae that were collected from a microfluidics device where they have been in direct contact with or cultivated without A. avenae.

2018-11-30 | E-MTAB-7005 | biostudies-arrayexpress

Phosphoproteome profiles of the phytopathogenic fungi Alternaria brassicicola and Botrytis cinerea

Project description:This study describes the gel-free phosphoproteomic analysis the phytopathogenic fungi Alternaria brassicicola and Botrytis cinerea grown in vitro under non-limiting conditions.

2014-06-09 | PXD000817 | Pride

5'-Serial Analysis of Gene Expression of the transcriptomes of Coprinopsis cinerea during fruiting body initiation

Project description:Large scale assessment of the transcriptomes of the vegetative mycelium and primordium will facilitate the generation of a more comprehensive picture of the fruiting process in basidiomycetes. We coupled 5'-Serial Analysis of Gene Expression (5'-SAGE) to high-throughput pyrosequencing from 454 Life Sciences to analyze the transcriptomes and identify up-regulated genes (URGs) among vegetative mycelium (Myc) and stage 1 primordium (S1-Pri) of Coprinopsis cinerea during fruiting body development. We evaluated the expression of >3,000 genes in the two respective growth stages and demonstrated that almost one-third of these genes were preferentially expressed in either stage, which implicated a significant transcriptomic switch during fruiting body initiation. We annotated >34,000 and >45,000 transcription start sites (TSSs) in the transcriptomes of Myc and S1-Pri respectively. We identified a wealth of potential URGs related to early fruiting events, although their functions and roles are not exactly known. This study serves to advance our understanding of the molecular mechanisms of fruiting body development in the model mushroom C. cinerea. 5'-SAGE analysis of the transcriptomes of vegetative mycelium and primordium of C. cinerea by 454 GS20 high-throughput pyrosequencer

2013-01-10 | E-GEOD-40722 | biostudies-arrayexpress

5mC oxidation products in the nucleic acids of the Basidiomycete fungi Laccaria bicolor and Coprinopsis cinerea

Project description: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.

2022-01-16 | GSE185550 | GEO

Analysis of botrytis cinerea mycelium proteins

Project description:Comparison of Botrytis cinerea wild-type B.05.10 and T4 strains using label-free nUPLC-MSE and 2-DE approaches. B. cinerea strain mycelium were grown in synthetic minimal medium-modified Czapeck-Dox. Protein extracts were obtained from pulverized mycelium using TCA-phenol method. Acquired spectra were internally calibrated with peptides from trypsin 180 autolysis (M+H+=842.509,M+H+=2211.104) with an m/z precision of ±20 ppm. A combined search (PMF and MS/MS) was performed with GPS ExplorerTM software v3.5 (Applied Biosystems) over non-redundant NCBI databases using the MASCOT search engine. The database search utilized the following parameters: taxonomy restrictions to Fungi (06.17.2011), one missed cleavage sites, 100 ppm mass tolerance in MS and 0.5 Da for MS/MS data, cysteine carbamidomethylation as a fixed modification, and methionine oxidation as a variable modification. The confidence in the peptide mass fingerprinting matches (p<0.05) was based on the MOWSE score.

2013-05-02 | PXD000165 | Pride

Coprinopsis cinerea transcriptome in response to hyphal damage, nematode predation or bacterial co-cultivation

Project description:We have recently shown that the coprophilous model mushroom Coprinopsis cinerea transcribes a broad array of genes encoding defense proteins in the vegetative mycelium and fruiting bodies that target bacterial competitors and animal predators challenging the respective tissues of this fungus. In addition, we have demonstrated in previous work that two nematotoxic defense proteins from Coprinopsis, CGL1 and CGL2, were induced in vegetative mycelium challenged with the predatory nematode Aphelenchus avenae; however, the specificity and broadness of this response remained unclear. In order to resolve these issues, we sequenced the poly(A)-positive transcriptome of vegetative mycelium of C. cinerea confronted with nematode predation, hyphal mechanical damage or bacterial co-culture.

2015-09-01 | E-MTAB-2763 | biostudies-arrayexpress

RNA-seq analysis of Coprinopsis cinerea mycelium challenged with gram negative and gram positive bacteria

Project description:RNA-seq analysis of Coprinopsis cinerea mycelium challenged with gram negative and gram positive bacteria

| PRJEB27226 | ENA

Gene expression analysis of monokaryotic and dikaryotic mycelia from Coprinopsis cinerea

Project description:Sexual reproduction is an ancient trait that evolved shortly after the appearance of the first eukaryotic cell. In order to identify the set of genes differentially expressed in monokaryotic and dikaryotic mycelia, the poly(A)-positive transcriptomes of C. cinerea Okayama7 and C. cinerea A43mutB43mut were sequenced.

2014-06-01 | E-MTAB-1993 | biostudies-arrayexpress

Ectomycorrhizal fungi decompose humus-rich litter material using oxidative mechanisms adapted from saprotrophic ancestors

Project description: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. Nevertheless, here we demonstrate that ectomycorrhizal fungi representing at least four origins of symbiosis have retained significant capacity to degrade humus-rich litter amended with glucose. Spectroscopy showed that this decomposition involves an oxidative mechanism and that the extent of oxidation varies with the phylogeny and ecology of the species. RNA-Seq analyses revealed that the genome-wide set of expressed transcripts during litter decomposition has diverged over evolutionary time. Each species expressed a unique set of enzymes that are involved in oxidative lignocellulose degradation by saprotrophic fungi. A comparison of closely related species within the Boletales showed that ectomycorrhizal fungi oxidized litter material as efficiently as brown-rot saprotrophs. The ectomycorrhizal species within this clade exhibited more similar decomposing mechanisms than expected from the species phylogeny in concordance with adaptive evolution occurring as a result of similar selection pressures. Our data shows that ectomycorrhizal fungi are potential organic matter decomposers, yet not saprotrophs. We suggest that the primary function of this decomposing activity is to mobilize nutrients embedded in organic matter complexes and that the activity is driven by host carbon supply. Comparative transcriptomics of ectomycorrhizal (ECM) versus brown-rot (BR) fungi while degrading soil-organic matter

2015-09-24 | E-GEOD-64897 | biostudies-arrayexpress

Pre-assembled Cas9 ribonucleoprotein-mediated gene deletion identifies the carbon catabolite repressor and its target genes in Coprinopsis cinerea

Project description:Cre1 is an important transcription factor that regulates carbon catabolite repression (CCR) and is widely conserved across fungi. This gene has been extensively studied in several Ascomycota species, whereas its role in gene expression regulation in the Basidiomycota remains poorly understood. Here, we identified and investigated the role of cre1 in Coprinopsis cinerea, a basidiomycete model mushroom that can efficiently degrade lignocellulosic plant wastes. We used a rapid and efficient gene deletion approach based on PCR-amplified split-marker DNA cassettes together with in-vitro assembled Cas9-guide RNA ribonucleoproteins (Cas9-RNPs) to generate C. cinerea cre1 gene deletion strains. Gene expression profiling of two independent C. cinerea cre1 mutants showed significant deregulation of carbohydrate metabolism, plant cell wall degrading enzymes (PCWDEs), plasma membrane transporter-related and several transcription factor encoding genes, among others. Our results support the notion that, similarly to reports in the ascomycetes, Cre1 of C. cinerea orchestrates CCR through a combined regulation of diverse genes, including PCWDEs, transcription factors that positively regulate PCWDEs and membrane transporters which could import simple sugars that can induce the expression of PWCDEs. Somewhat paradoxically, though in accordance with other Agaricomycetes, genes related to lignin degradation were mostly downregulated in cre1 mutants, indicating they fall under different regulation than other PCWDEs. The gene deletion approach and the data presented in this paper expand our knowledge of CCR in the Basidiomycota and provide functional hypotheses on genes related to plant biomass degradation.

2022-11-01 | GSE205749 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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