IdCisGlob
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB51331 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR12765108_1.fastq.gz | Fastqsanger.gz | |||
| ERR12765108_2.fastq.gz | Fastqsanger.gz | |||
| ERR9127945.fastq.gz | Fastqsanger.gz | |||
| ERR9127946.fastq.gz | Fastqsanger.gz | |||
| ERR9123839_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 6 |
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Project description:Cistogaster globosa genome assembly, idCisGlob1, alternate haplotype
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Project description:The human gut is inhabited by a complex ecosystem of microorganisms, encompassing bacteria, viruses, protozoa, and fungi. Recent research has illuminated the significance of the gut fungal microbiota (mycobiota) in shaping host immunity and influencing the onset and progression of various human diseases. While most investigations into gut microbiota have centered on bacteria, accumulating evidence has underscored the role of mycobiota in the development of inflammatory bowel diseases (IBD), including both ulcerative colitis (UC) and Crohn's disease (CD). In this study, we present the isolation of the live Malassezia globosa strains from the intestinal mucosa of UC patients for the first time. We provide a comprehensive analysis of the characteristics and virulence of this fungus. Malassezia, primarily known to inhabit human skin, prompted us to compare the genomes, transcriptomes, and virulence of M. globosa gut isolates with those of M. globosa strains isolated from the skin. This comparative analysis aimed to discern potential niche-specific adaptations of the fungus. Our findings reveal a striking disparity in the pathogenicity of M. globosa isolated from the gut compared to its skin counterpart. In a mouse model, gut-isolated M. globosa exhibited a more pronounced exacerbation of DSS-induced colitis and elevated production of inflammatory cytokines. Additionally, transcriptome analysis indicated that gut isolates of M. globosa display heightened sensitivity to normoxia compared to their skin-isolated counterparts, suggesting adaptation to the hypoxic conditions prevalent in the intestinal mucosal environment
2024-02-01 | GSE254809 | GEO
Project description:purose:The large-scale reproduction of Phaeocystis globosa has caused serious damage to the marine ecosystem in the coastal waters of China. The outbreak of algae blooms depends on the competitive advantage of their heteromorphic life history: colonial formation is beneficial to resist zooplankton predation, and the single isolated cells can absorb nutrients rapidly. To better understand the different types of cells characteristics of P. globosa that facilitate rapid expansion, single isolated cells (GX-S) and colonial cells (GX-C) are separated by filtration. methods:For RNA exaction, the biomass was resuspended in 2 mL RNA extraction buffer (1:1 mix of aqua-phenol and buffer L [0.5% SDS, 10 mM EDTA, 0.2 M sodium acetate (pH 5), and 1:100 β-mercaptoethanol)] and then incubated with DNase I (Takara, Japan) for 30 min at 37 °C to remove genomic DNA. RNA quality analysis, library construction, sequencing, data filtering and mapping were performed by the Novogene Bioinformatics Technology Co., Ltd. (Beijing, China). mRNA profiles of 10 days GX-C and GX-S were generated by deep sequencing, in triplicate. results:Three biological replicates from GX-S and GX-C were ensured statistical comparability and reliability of data. Raw data ranged from 25, 608,632 to 35,516,726 reads per sample. After producing more than 24 million clean reads, removing low-quality sequences and adapter sequences. Additionally, 4386 genes were differentially expressed at statistically significant levels, which included 2268 up-regulated genes and 2118 down-regulated genes. Genes with significant differential expression were involved in several pathways, including starch and sucrose, phagosome, inositol phosphate metabolism, fatty acid degradation. conclusions: In summary, we can find that colonial cells have stronger carbon fixation capacity. It is not used to synthesize fatty acids as reserves of energy, but to secrete EPS. The reduction of fatty acid makes P. globosa become “low-quality food” and the formation of colony from EPS reduces the chance of being ingestion by zooplankton.
2020-09-22 | GSE140985 | GEO
Project description:Gordius_albopunctatus, genomic and transcriptomic data
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Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.
2017-12-18 | PXD006238 | Pride
Project description:purpose:The large-scale reproduction of Phaeocystis globosa has caused serious damage to the marine ecosystem in the coastal waters of China. The outbreak of algae blooms depends on the competitive advantage of their heteromorphic life history: colonial formation is beneficial to resist zooplankton predation, and the single isolated cells can absorb nutrients rapidly. methods:For RNA exaction, the biomass was resuspended in 2 mL RNA extraction buffer (1:1 mix of aqua-phenol and buffer L [0.5% SDS, 10 mM EDTA, 0.2 M sodium acetate (pH 5), and 1:100 β-mercaptoethanol)] and then incubated with DNase I (Takara, Japan) for 30 min at 37 °C to remove genomic DNA. RNA quality analysis, library construction, sequencing, data filtering and mapping were performed by the Novogene Bioinformatics Technology Co., Ltd. (Beijing, China). results:Three biological replicates from GX-C and ST-C were ensured statistical comparability and reliability of data. Raw data ranged from 25, 608,632 to 35,516,726 reads per sample. After producing more than 24 million clean reads, removing low-quality sequences and adapter sequences. Additionally, 4386 genes were differentially expressed at statistically significant levels, which included 2268 up-regulated genes and 2118 down-regulated genes. Genes with significant differential expression were involved in several pathways, including starch and sucrose, phagosome, inositol phosphate metabolism, fatty acid degradation. conclusions: In summary, we can find that colonial cells have stronger carbon fixation capacity. It is not used to synthesize fatty acids as reserves of energy, but to secrete EPS. The reduction of fatty acid makes P. globosa become “low-quality food” and the formation of colony from EPS reduces the chance of being ingestion by zooplankton.
2020-03-01 | GSE141662 | GEO
Project description:Virophages are small dsDNA viruses dependent on a nucleocytoplasmic large-DNA virus infection of a cellular host for replication. Putative virophages infecting algal hosts are classified together with Polinton-like viruses, transposable elements widely found in algal genomes, yet the lack of isolated strains raises questions about their existence as independent entities. We isolated and characterized a virophage (PgVV-14T) co-infecting Phaeocystis globosa with the Phaeocystis globosa virus-14T (PgV-14T).
2023-02-11 | PXD036892 | Pride