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ABSTRACT: Raw data of hazel (Corylus spp.)

PROVIDER: PRJNA591492 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR10541222_1.fastq.gz	Fastqsanger.gz
	SRR10541222_2.fastq.gz	Fastqsanger.gz
	SRR10541223_1.fastq.gz	Fastqsanger.gz
	SRR10541223_2.fastq.gz	Fastqsanger.gz
	SRR10541224_1.fastq.gz	Fastqsanger.gz

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Comparative proteomics of common allergenic tree pollens of birch, alder and hazelComparative proteomics of common allergenic tree pollens of birch, alder and hazel

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.

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Laser capture microdissection and microarray analysis of ectomycorrhizas formed by the ascomycete Tuber melanosporum reveal functional heterogeneity between mantle and Hartig net compartments

Project description:The aim of this analysis was to better understand the complex symbiotic stage of Tuber melanosporum by combining the use of laser capture microdissection and microarray gene expression analysis. We isolated the fungal/soil (i.e. the mantle) and the fungal/plant (i.e. the Hartig net) interfaces from transverse sections of T. melanosporum/Corylus avellana ectomycorrhizas and identified the transcriptional landscape associated with each compartment. We compared these data to the transcriptome of ectomycorrhizal root tips, free-living mycelium and fruiting bodies of Tuber melanosporum (Series GSE17529). The T. melanosporum custom-exon expression array (4 x 72K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) contained five independent, nonidentical, 60-mer probes per gene model coding sequence. Included in the oligoarray were 12,232 annotated gene models, 3,913 random 60-mer control probes and labelling controls. Sequences used for the oligonucleotide design were from an early draft of the gene catalog containing several TE families. For 1,876 gene models, technical duplicates were included on the array. We performed 6 hybridizations (NimbleGen) with samples derived from microdissected mantles (3 biological replicates) and Hartig nets ((3 biological replicates each) from T. melanosporum/Corylus avellana ectomycorrhizal root tips . All samples were labeled with Cy3.

2013-03-01 | E-GEOD-36870 | biostudies-arrayexpress

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