Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10154440.fastq.gz | Fastqsanger.gz | |||
| SRR10154440_1.fastq.gz | Fastqsanger.gz | |||
| SRR10154440_2.fastq.gz | Fastqsanger.gz | |||
| SRR10154441.fastq.gz | Fastqsanger.gz | |||
| SRR10154441_1.fastq.gz | Fastqsanger.gz |
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Project description:Genomics of Divergence-with-Gene-Flow in an Island Bird
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Project description:Understanding the environmental factors that shape microbial communities is crucial, especially in extreme environments, like Antarctica. Two main forces were reported to influence Antarctic soil microbes: birds and plants. Both birds and plants are currently undergoing unprecedented changes in their distribution and abundance due to global warming. However, we need to clearly understand the relationship between plants, birds and soil microorganisms. We therefore collected rhizosphere and bulk soils from six different sampling sites subjected to different levels of bird influence and colonized by Colobanthus quitensis and Deschampsia antarctica in the Admiralty Bay, King George Island, Maritime Antarctic. Microarray and qPCR assays targeting 16S rRNA genes of specific taxa were used to assess microbial community structure, composition and abundance and analyzed with a range of soil physico-chemical parameters. The results indicated significant rhizosphere effects in four out of the six sites, including areas with different levels of bird influence. Acidobacteria were significantly more abundant in soils with little bird influence (low nitrogen) and in bulk soil. In contrast, Actinobacteria were significantly more abundant in the rhizosphere of both plant species. At two of the sampling sites under strong bird influence (penguin colonies), Firmicutes were significantly more abundant in D. antarctica rhizosphere but not in C. quitensis rhizosphere. The Firmicutes were also positively and significantly correlated to the nitrogen concentrations in the soil. We conclude that the microbial communities in Antarctic soils are driven both by bird and plants, and that the effect is taxa-specific.
2012-06-01 | GSE33847 | GEO
Project description:This clinical trial studies the effectiveness of a web-based cancer education tool called Helping Oncology Patients Explore Genomics (HOPE-Genomics) in improving patient knowledge of personal genomic testing results and cancer and genomics in general. HOPE-Genomics is a web-based education tool that teaches cancer/leukemia patients, and patients who may be at high-risk for developing cancer, about genomic testing and provide patients with information about their own genomic test results. The HOPE-Genomics tool may improve patient’s genomic knowledge and quality of patient-centered care. In addition, it may also improve education and care quality for future patients.
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Project description:The great tit is a widely studied passerine bird species in ecology that, in the past decades, has provided important insights into speciation, phenology, behavior and microevolution. After completion of the great tit genome sequence, a customized high density 650k SNP array was developed enabling more detailed genomic studies in this species.
2018-02-19 | GSE105131 | GEO
Project description:Influenza A virus (IAV) pandemics result from interspecies transmission events within the avian reservoir and further into mammals including humans. Investigating the molecular basis for virus–host interactions enabling this process is vital to understand zoonotic IAV spread. Receptor incompatibility has been suggested to limit zoonotic IAV transmission from the wild bird reservoir as well as between different bird species. Using glycoproteomics, we have studied the repertoires of expressed glycan structures with focus on putative receptors for IAV in mallards, chickens and tufted ducks; three bird species with different roles in the zoonotic ecology of IAV. The methodology used could not only pinpoint specific glycan structures to the specific glycosylation sites of identified glycoproteins but could also be used to successfully discriminate α2,3- from α2,6-linked terminal sialic acids by careful analysis of oxonium ions released from glycopeptides during MS/MS (MS2), and MS/MS/MS (MS3). Our analysis clearly demonstrated that all three bird species can produce complex α2,3 and α2,6-linked Neu5Ac N-glycans including α2,3-linked sialyl Lewis structures, as well as both N- and O- glycans terminated with both α2,3 and α2,6-linked Neu5Ac. Furthermore, we reveal many similarities in the repertoires of expressed receptors both between the bird species investigated and to previously published data from pigs and humans. Our findings of sialylated glycan structures previously anticipated to be mammalian specific in all three bird species have major implications for our understanding of the role of receptor incompatibility in interspecies transmission of IAV.
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Project description:We sorted for GFP+ cells using the enhancer trap J0571 with the UAS promoter driving the expression of different BIRD genes. Different genetic backgrounds are use and listed below.
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