Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1131278 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective fashion. Here, we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67X coverage, Sample GSM1551550). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Aedes aegypti and Culex quinquefasciatus, each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that virtually all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, accurate, and can be applied to many species.
2017-03-24 | GSE95797 | GEO
Project description:Genome Assemblies of 19 Tick Species in China
| PRJEB89832 | ENA
Project description:Ixodes species ticks are competent vectors of tick-borne viruses including tick-borne encephalitis and Powassan encephalitis. Tick saliva has been shown to facilitate and enhance viral infection. This likely occurs by saliva-mediated modulation of host responses into patterns favorable for viral infection and dissemination. Because of the rapid kinetics of tick-borne viral transmission, this modulation must occur as early as tick attachment and initiation of feeding. In this study, the gene expression profile of cutaneous bite-site lesions created by uninfected ticks were analyzed at 1, 3, 6, and 12 hours after Ixodes scapularis nymphal tick attachment to discover host pathways or responses potentially important in tick-borne viral establishment.
2012-12-21 | GSE39100 | GEO
Project description:Ixodes species ticks are competent vectors of tick-borne viruses including tick-borne encephalitis and Powassan encephalitis. Tick saliva has been shown to facilitate and enhance viral infection. This likely occurs by saliva-mediated modulation of host responses into patterns favorable for viral infection and dissemination. Because of the rapid kinetics of tick-borne viral transmission, this modulation must occur as early as tick attachment and initiation of feeding. In this study, the gene expression profile of cutaneous bite-site lesions created by uninfected ticks were analyzed at 1, 3, 6, and 12 hours after Ixodes scapularis nymphal tick attachment to discover host pathways or responses potentially important in tick-borne viral establishment. Four milimeter ear biopsies from BALB/cJ mice infested with Ixodes scapularis nymphs were assayed using Affymetrix genechip 430A 2.0 arrays at 1, 3, 6, and 12 hours after infestation during a primary exposure. 3 mice were measured at each time point. Controls were 3 similarly housed but tick-free mice.
2012-12-21 | E-GEOD-39100 | biostudies-arrayexpress
Project description:Parasitism is a major ecological niche for a variety of nematodes. Multiple nematode lineages have specialized as pathogens, including deadly parasites of insects that are used in biological control. We have sequenced and analyzed the draft genomes and transcriptomes of the entomopathogenic nematode Steinernema carpocapsae and four congeners (S. scapterisci, S. monticolum, S. feltiae, S. glaseri) distantly related to Caenorhabditis elegans. We used these genomes to establish phylogenetic relationships, explore gene conservation across species, identify genes uniquely expanded in insect parasites, and to identify conserved non-coding regulatory motifs that influence similar biological processes. Protein domain analysis of these genomes reveals a striking expansion of numerous putative parasitism genes including certain protease and protease inhibitor families as well as fatty acid- and retinol-binding proteins. We identify rapid evolution and expansion of the important developmental Hox gene cluster and identify novel conserved non-coding regulatory motifs associated with orthologous genes in Steinernema and Caenorhabditis. The deep conservation of the network of non-coding DNA motifs between these two genera for a subset of orthologous genes involved in neurogenesis and embryonic development suggests that a kernel of protein-DNA relationships is conserved through nematode evolution. We analyzed the gene expression of a total of 24 RNA-seq samples from 3 nematode species( S. carpocapsae, S. feltiae, and C. elegans) for comparative analysis. We collected the RNA at four developmental time points (mixed embryo, L1, infective juvenile/dauer, young adult) for each species in replicates.
2015-06-05 | E-GEOD-68588 | biostudies-arrayexpress