Ontology highlight
ABSTRACT:
PROVIDER: PRJNA396959 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5891391_1.fastq.gz | Fastqsanger.gz | |||
| SRR5891391_2.fastq.gz | Fastqsanger.gz | |||
| SRR5891392_1.fastq.gz | Fastqsanger.gz | |||
| SRR5891392_2.fastq.gz | Fastqsanger.gz | |||
| SRR5891393_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
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Project description:Gene expression profiles before and after spore formation of Lentinula edodes (L54)grown at sawdust. Keywords: time-course SAGE were used to generate tags from RNA of fruit bodies of L. edodes. RNA were extracted from the fruit bodies before and after spore observed. Gene expression profiles of both stages were compared to screen out genes may relate to spore formation.
2006-02-08 | E-GEOD-4202 | biostudies-arrayexpress
Project description:Gene expression profiles before and after spore formation of Lentinula edodes (L54) grown at sawdust. SAGE were used to generate tags from RNA of fruit bodies of L. edodes. RNA were extracted from the fruit bodies before and after spore observed. Gene expression profiles of both stages were compared to screen out genes may relate to spore formation. To facilitate comparison of LongSAGE and SAGE data in GEO, LongSAGE tags (15bp) were trimmed to become 10bp and uploaded in previous submission (GSM87320, GSM87321). The current submission are actual LongSAGE experimental data without any extrapolation from SAGE data.
2010-11-24 | E-GEOD-25463 | biostudies-arrayexpress
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
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Project description:Bioactivities of fungal peptides are of interest for basic research and therapeutic drug development. Some of these peptides are derived from “KEX2-processed repeat proteins” (KEPs), a recently defined class of precursor proteins that contain multiple peptide cores flanked by KEX2 protease cleavage sites. Genome mining has revealed that KEPs are widespread in the fungal kingdom. Their functions are largely unknown. Here, we present the first in-depth structural and functional analysis of KEPs in a basidiomycete. We bioinformatically identified KEP-encoding genes in the genome of the model agaricomycete Coprinopsis cinerea and established a detection protocol for the derived peptides by overexpressing the C. cinerea KEPs in the yeast Pichia pastoris. Using this protocol, which includes peptide extraction and mass spectrometry with data analysis using the search engine Mascot, we confirmed the presence of several KEP-derived peptides in C. cinerea as well as in the edible mushrooms Lentinula edodes, Pleurotus ostreatus and Pleurotus eryngii. Processing by the dipeptidyl aminopeptidase STE13 is likely involved in the biosynthesis of some of these peptides. While CRISPR-mediated knockouts of the C. cinerea kep genes did not result in any detectable phenotype, knockout of kex genes caused defects in mycelial growth and fruiting body formation. These results suggest that KEP-derived peptides may play a role in the interaction of C. cinerea with the biotic environment and that the KEP-processing KEX proteases target a variety of substrates in agaricomycetes, including some important for mycelial growth and differentiation. In the past, fungal RiPPs and KEP-derived peptides were mostly studied using forward genetics, where the peptides were first isolated and characterized and only then the corresponding precursor genes were identified (e.g., ustiloxins, phomopsins, candidalysin, Rep1, omphalotin). In this paper, we established a protocol for the identification of KEP-derived peptides in fungal samples by a combination of reverse genetics and peptidomics. The protocol was developed using the model agaricomycete Coprinopsis cinerea, but is also applicable to other fungi. In a first step, we bioinformatically screened the predicted proteome of C. cinerea for KEP-encoding genes. Second, we expressed six different KEP genes from C. cinerea in the yeast Pichia pastoris to (1) establish a protocol for extraction and detection of KEP-derived peptides by mass spectrometry in P. pastoris culture supernatants known for their low complexity in terms of proteins and peptides (Higgins 1995); (2) obtain an indication that the detected KEPs were indeed processed to peptides, and (3) use the structures of the detected peptides as a guide for which peptides to expect in C. cinerea in terms of peptide length and peptide modifications. In a third step, we applied the established peptide extraction and detection method to detect KEP-derived peptides in culture supernatants and tissue samples of the agaricomycetes C. cinerea, Lentinula edodes, Pleurotus ostreatus and Pleurotus eryngii.
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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.
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