Ontology highlight
ABSTRACT:
PROVIDER: PRJNA679451 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13091100_1.fastq.gz | Fastqsanger.gz | |||
| SRR13091100_2.fastq.gz | Fastqsanger.gz | |||
| SRR13091101_1.fastq.gz | Fastqsanger.gz | |||
| SRR13091101_2.fastq.gz | Fastqsanger.gz | |||
| SRR13091102_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 132 |
Similar Datasets
Project description:It is known that, in addition to known allergens, other proteins in pollen can aid the development of an immune response in allergenic individuals. The contribution of the “unknown” protein allergens becomes especially prominent in phylogenetically related species where, despite of high homology of the lead allergens, the degree of allergenic potential can greatly vary. The aim of this study was to identify other potentially allergenic proteins in pollen of three common and very related allergenic tree species: birch (Betula pendula), hazel (Corylus avellana) and alder (Alnus glutinosa). For that purpose, we carried out a comprehensive, comparative proteomic screening of the pollen from the three species. In order to maximize protein recovery and coverage, different protein extraction and isolation strategies during sample preparation were employed. As a result, we report 2500 - 3000 identified proteins per each of the pollen species. Identified proteins were further used for a number of annotation steps, providing insight into differential distribution of peptidases, peptidase inhibitors and other potential allergenic proteins across the three species. Moreover, we carried out functional enrichment analysis that, interestingly, corroborated high species similarity in spite of their relatively distinct protein profiles. We provide to our knowledge first insight into proteomes of three very important allergenic pollen types, which is particularly vital for pollen of hazel and alder where not even transcriptomics data is available. Datasets provided in this study can be readily used as protein databases, and as such serve as an excellent starting point for further allergenic studies.
2021-04-21 | PXD021133 | Pride
Project description:LC-MS/MS data used in a work titled "Assessing Specialized Metabolite Diversity of Alnus species by Digitized LC_MS/MS Data Analysis Workflow". Negative ion mode DDA data from 15 extracts of 4 Alnus species (barks, twigs, leaves, and fruits)
2019-08-12 | MSV000084202 | MassIVE
Project description:The actinobacteria Frankia alni is able to induce the formation of nodules on the root of a large spectrum of actinorhizal plants, where it converts dinitrogen to ammonia in exchange for plant photosynthates. In the present study, transcriptional analyses were performed on nitrogen-replete free-living cells and on Alnus glutinosa nodule bacteria, using whole genome microarrays. Distribution of nodule-induced genes on the genome was found to be mostly over regions with high synteny between three Frankia genomes, while nodule-repressed genes, which were mostly hypothetical and not conserved, were spread around the genome. Genes known to be related to symbiosis were highly induced: nif (nitrogenase), hup2 (hydrogenase uptake), suf (sulfur-iron cluster) and shc (hopanoids synthesis). The expression of genes involved in ammonium assimilation and transport was strongly modified suggesting that bacteria ammonium assimilation was limited. Genes involved in particular in transcriptional regulation, signalling processes, protein drug export, protein secretion, lipopolysaccharide and peptidoglycan biosynthesis that may play a role in symbiosis were also identified. We showed that this nodule transcriptome of Frankia was highly similar among phylogenetically distant plant families. To address gene expression changes of Frankia alni ACN in the symbiotic state, we compared transcript levels between young nodules formed on 4 species of trees (Alnus glutinosa, Alnus nepalensis, Myrica gale and Myrica rubra) and free-living cells grown in nitrogen-replete minimal medium. For A. glutinosa nodule and free-living cells, two sets of experiments (A and B) were performed in two different laboratories. Three biological replicates were preformed for each condition.
2010-09-12 | E-GEOD-18190 | biostudies-arrayexpress
Project description:Corylus americana Genome sequencing and assembly
| PRJNA437041 | ENA
Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
2022-06-27 | E-MTAB-11830 | biostudies-arrayexpress
Project description:The naked mole-rat (NMR; Heterocephalus glaber) has recently gained considerable attention in the scientific community for its unique potential to unveil novel insights in the fields of medicine, biochemistry, and evolution. NMRs exhibit unique adaptations that include protracted fertility, cancer resistance, eusociality, and anoxia. This suite of adaptations is not found in other rodent species, suggesting that interrogating conserved and accelerated regions in the NMR genome will find regions of the NMR genome fundamental to their unique adaptations. However, the current NMR genome assembly has limits that make studying structural variations, heterozygosity, and non-coding adaptations challenging. We present a complete diploid naked-mole rat genome assembly by integrating long-read and 10X-linked read genome sequencing of a male NMR and its parents, and Hi-C sequencing in the NMR hypothalamus (N=2). Reads were identified as maternal, paternal or ambiguous (TrioCanu). We then polished genomes with Flye, Racon and Medaka. Assemblies were then scaffolded using the following tools in order: Scaff10X, Salsa2, 3d-DNA, Minimap2-alignment between assemblies, and the Juicebox Assembly Tools. We then subjected the assemblies to another round of polishing, including short-read polishing with Freebayes. We assembled the NMR mitochondrial genome with mitoVGP. Y chromosome contigs were identified by aligning male and female 10X linked reads to the paternal genome and finding male-biased contigs not present in the maternal genome. Contigs were assembled with publicly available male NMR Fibroblast Hi-C-seq data (SRR820318). Both assemblies have their sex chromosome haplotypes merged so that both assemblies have a high-quality X and Y chromosome. Finally, assemblies were evaluated with Quast, BUSCO, and Merqury, which all reported the base-pair quality and contiguity of both assemblies as high-quality. The assembly will next be annotated by Ensembl using public RNA-seq data from multiple tissues (SRP061363). Together, this assembly will provide a high-quality resource to the NMR and comparative genomics communities.
2022-06-27 | E-MTAB-11831 | biostudies-arrayexpress