Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1171139 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30970800_1.fastq.gz | Fastqsanger.gz | |||
| SRR30970800_2.fastq.gz | Fastqsanger.gz | |||
| SRR30970801_1.fastq.gz | Fastqsanger.gz | |||
| SRR30970801_2.fastq.gz | Fastqsanger.gz | |||
| SRR30970802_1.fastq.gz | Fastqsanger.gz |
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Project description:Species characterisation and pathogen detection in bulk mosquito pools using metabarcoding
| PRJNA343688 | ENA
Project description:The Flavivirus genus contains some of the most prevalent vector-borne viruses such as dengue, Zika and yellow fever viruses that cause devastating diseases in humans. However, the insect-specific clade of flaviviruses is restricted to mosquito hosts; albeit they have retained the general features of the genus such as genome structure and replication. The interaction between insect-specific flaviviruses (ISFs) and their mosquito hosts are largely unknown. Pathogenic flaviviruses are known to modulate host-derived microRNAs (miRNAs), a class of non-coding RNAs that are important in controlling gene expression. Alteration in miRNAs may represent changes in host gene expression and provide understanding of virus-host interactions. The role of miRNAs in ISF-mosquito interactions is largely unknown. A recently discovered Australian ISF, Palm Creek virus (PCV), has the ability to suppress medically relevant flaviviruses. Here, we investigated the potential involvement of miRNAs in PCV infection using the model mosquito Aedes aegypti. By combining small RNA sequencing and bioinformatics analysis, differentially expressed miRNAs were determined. Our results indicated that PCV infection hardly affects host miRNAs. Out of 101 reported miRNAs of Ae. aegypti, only aae-miR-2940-5p had significant altered expression over the course of infection. However, further analysis of aae-miR-2940-5p revealed that this miRNA does not have any direct impact on PCV replication in vitro. Thus, the results overall suggest that PCV infection has a limited effect on the mosquito miRNA profile and therefore, they may not play a significant role the PCV- Ae. aegypti interaction.
2017-07-08 | GSE100917 | GEO
Project description:Anopheles gambiae mosquitoes of the M form N'gousso laboratory colony were antibiotic treated and subsequently orally infected with the Db11-GFP fluorescent strain of Serratia marcescens. Bacteria-fed mosquitoes were separated 2 days post infection based on the presence in the mosquito gut of a dye contained in the sugar solution. Mosquitoes were dissected 5 days post infection and the level of S. marcescens infection was determined through microscopic observation of mosquito guts under a fluorescence microscope. Highly infected mosquitoes, with an extensive presence of fluorescent S. marcescens throughout their gut and non-infected mosquitoes, with no sign of fluorescence traced in their gut, were further used for SNP genotyping. Genomic DNA from pools of 15 highly infected and 15 non-infected mosquitoes, in equimolar amounts, was hybridized in a customized Affymetrix 400k SNP genotyping arrays, interrogating genetic variation at ~400,000 variable positions in the An. gambiae genome, as determined by a previous sequencing effort of M/S An. gambiae molecular forms. Allele calls in both array hybridizations were used to determine the minor allele frequency difference for each individual SNP between the two phenotypic pools, which were subsequently used to determine loci associated with the outcome of S. marcescens infection.
2013-11-30 | E-MEXP-3951 | biostudies-arrayexpress
Project description:<p>The results from a small number of melanoma GWAS have been published. Initial studies identified several pigmentation- and nevus-associated loci that mediate an effect on melanoma risk, however, these studies were somewhat limited in that sample number (hence power) was low, they used first-generation low density SNP arrays, or used pools of DNA samples. Subsequently, additional melanoma GWAS have been completed, including a "Phase 2" study by the International Melanoma Genetics Consortium (<a href="http://www.genomel.org">GenoMEL</a>), a full GWAS of the Australian sample resource previously used in a pooled-DNA GWAS, and study conducted through the MD Anderson Cancer Center and the Brigham and Women's Hospital. The groups who performed these studies have recently shared data and replicated a number of new melanoma susceptibility loci.</p> <p>Aside from the identification of novel loci, there are two additional notable outcomes of these studies. Firstly, an examination of the observed versus expected test statistics (Q-Q plot) from the Australian study, even after removing data from SNPs within known replicated susceptibility loci, reveals that there remains an excess of positive results. Similarly, the latest GenoMEL study finds almost three times as many SNPs reaching p-values between 10<sup>-4</sup> and 10<sup>-5</sup> as would be expected by chance. In the light of other studies of complex traits [1], <i>these data suggest that studies based on additional melanoma samples from the same population are likely to identify an even larger "polygenic tail" and should prove invaluable in identifying and characterizing the underlying loci.</i> </p> <p>A second observation, is that the effect size for replicated associations differs very little between GWAS. Given the strong effect of ultraviolet radiation (UVR) on risk of melanoma this might be expected to affect penetrance, particularly in the Australian and English samples, which are ethnically similar, but have very different sun exposures. <i>We hypothesize that those SNPs whose effects are strongly mediated by UVR exposure may have smaller marginal effects on risk and are therefore harder to detect initially, suggesting a whole category of genetic effects that are unexplored.</i>Indeed, most melanoma GWAS performed to date used samples from both European and Australian populations in discovery and or replication, and thus, <i>existing studies have been poorly powered to detect associations with a wide difference in effect </i>between these low- and high-UVR populations.</p> <p>Here, we wish to pursue this hypothesis further and plan to genotype additional cases drawn from the English and Australian populations. This will serve two complementary objectives: firstly, it will greatly increase our collective power to detect additional new melanoma risk alleles; secondly, it will highlight associations that are stronger specifically within the context of either low-UVR or high-UVR exposure environments. We posit that these data will be invaluable, not just for identifying novel melanoma-associated loci, but also for addressing gene-environment interactions.</p> <p>We have available a collection of valuable resources to help fulfill our aims. These include a considerable number of well-characterized and ungenotyped Australian and UK melanoma cases, as well as existing genotype data from sets of Australian and UK cases and population-based controls.</p> <p>We propose the following <b>Specific Aims: </b> <ol><li>To extend our current collective melanoma GWAS by genotyping a large number of additional UK and Australian cases.</li> <li>To jointly analyze these data and identify new melanoma risk loci.</li> <li>To determine whether pre-existing and new melanoma risk alleles show different degrees of association between the English and Australian populations, and assess whether these differences might be due to differences in sunlight exposure. </li></ol></p>
| phs000519 | dbGaP
Project description:Immune thrombocytopenia (ITP) is an autoimmnue bleeding disorder characterized by low platelet count. To identify susceptibility loci for disease progression of ITP, we performed this genome-wide association study using DNA pools of 200 ITP cases and 200 controsl in Han Chinese. Performing GWAS on pools of DNA samples is an effective strategy to reduce the costs of studies and pooling DNA has been shown to be an efficient method to select candidate susceptibility loci for follow-up by individual genotyping.
2016-01-12 | GSE76744 | GEO
Project description:mosquito metagenome Targeted Locus (Loci)
| PRJNA342829 | ENA