Rodent metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA254995 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Here we aim to demonstrate a novel approach enabling standardised and rapid characterisation of transplanted xenografts in the rodent brain. The approach employs bulk tissue dissection, inclusive of the grafted human cells and surrounding host (rodent) tissue, and utilises differences in the RNA sequences between the species to discriminate the xenograft from host gene expression. To demonstrate and validate this technique, we assessed grafts of undifferentiated human stem cells, immature neural progenitors and mature neurons following transplantation into the rodent brain. Mixed species RNAseq was conducted on the bulk dissected tissue, and a high stringency analysis pipeline developed to discriminate the human reads. Xenograft-specific RNAseq allowed accurate profiling the complete transcriptome of the transplant with high sensitivity and accuracy. The profile allowed the identification of novel gene expression and an unbiased characterisation of graft composition, providing a valuable tool for the analysis of xenografts. This characterisation will be especially crucial for the characterisation of grafts in pre-clinical and batch testing of therapeutic cell preparations prior to translation to the clinic.
2019-08-31 | GSE126804 | GEO
Project description:Understanding biological diversity and distribution patterns at multiple spatial scales is a central issue in ecology. Here, we investigated the biogeographical patterns of functional genes in soil microbes from 24 arctic heath sites using GeoChip-based metagenomics and principal coordinates of neighbour matrices (PCNM)-based analysis. Functional gene richness varied considerably among sites, while the proportions of each major functional gene category were evenly distributed. Functional gene composition varied significantly at most medium and broad spatial scales, and the PCNM analyses indicated that 14-20% of the variation in total and major functional gene categories could be attributed primarily to relatively broad-scale spatial effects that were consistent with broad-scale variation in soil pH and total nitrogen. The combination of variance partitioning and multi-scales analysis indicated that spatial distance effects contributed 12% to variation in functional gene composition，whereas environmental factors contributed only 3%. This relatively strong influence of spatial as compared to environmental variation in determining functional gene distributions contrasts sharply with typical microbial phylotype/species-based biogeographical patterns in the Arctic and elsewhere. Our results suggest that the distributions of soil functional genes cannot be predicted from phylogenetic distributions because spatial factors associated with historical contingencies are relatively important determinants of their biogeography.
2014-12-10 | GSE63927 | GEO
Project description:RNA viromes of rodent lungs in Mainland Southeast Asia Metagenome
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Project description:It has been reported that Cryptosporidium parvum, a species of a protozoan frequently isolated from humans and animals, is able to induce digestive adenocarcinoma in a rodent model. Consistently, some epidemiological studies have reported an association with cryptosporidiosis in patients with colorectal adenocarcinoma. However, the correlation between cryptosporidiosis and human digestive cancer remains unclear at this time, and it is not known whether this intracellular parasite, considered an opportunistic agent, is able to induce gastrointestinal malignancies in humans. In order to add new arguments for a probable association between cryptosporidiosis and digestive human cancer, the main aim of this study is to determine prevalence and to identify species of Cryptosporidium among a French digestive cancer population.
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Project description:To test the conservation and evolution of long non-coding RNAs across multiple rodent species by transcriptome sequencing and histone modification mapping. Part of experiment series: E-MTAB-867 RNA-Seq, E-MTAB-959 ChIP-Seq.
2012-04-01 | E-MTAB-959 | biostudies-arrayexpress
Project description:Patterns in functional diversity of organisms at large spatial scales can provide insight into possible responses to future climate change, but it remains a challenge to link large-scale patterns at the organismal level to their underlying physiological mechanisms. The climate variability hypothesis predicts that temperate ectotherms will be less vulnerable to climate warming than tropical ectotherms, due to their superior acclimatization capacity.We investigate thermal acclimation of three species of Takydromus lizards distributed along a broad latitudinal gradient in China, by studying metabolic modifications at the level of the whole organism,organ, mitochondria, metabolome, and proteome.
2021-12-12 | PXD029083 | Pride
Project description:Orthohantaviruses are rodent-borne emerging viruses known to cause severe diseases in humans but no apparent pathology in their small mammal reservoirs. However, the mechanisms leading to tolerance or pathogenicity in humans and persistence in rodent reservoirs are poorly understood, as is the manner in which they spread within and between organisms. Here, we used a range of cellular and molecular approaches to investigate the interactions of three different orthohantaviruses – Puumala virus (PUUV), responsible for a mild form of hemorrhagic fever in humans, Tula virus (TULV) with low pathogenicity, and nonpathogenic Prospect Hill virus (PHV) – with human and rodent host cell lines. We showed that the three orthohantaviruses were able to infect Vero E6 and HuH7 cells but only the former secreted infectious particles. In cells derived from the PUUV reservoir (Myodes glareolus), PUUV achieved complete viral cycling, while TULV did not enter the cells and PHV infected them but did not produce infectious particles, reflecting some differences in host specificity. A search for mature virions by electron microscopy revealed that TULV assembly occurred in part at the plasma membrane, whereas PHV particles were trapped in autophagic vacuoles in cells of the heterologous rodent host. The interaction of orthohantaviruses with cellular factors was investigated by studying the colocalization of viral nucleocapsids with markers of cell compartments, identifying interactors of viral proteins by mass spectrometry analysis, and measuring the regulation of gene expression by transcriptomic analysis in infected cells. Overall, our study highlighted the complexity of the host-virus relationship, demonstrated that orthohantaviruses were restricted at different levels of the viral cycle, and provided different levels of analysis to further investigate how these viruses differ in their interactions with cells to evade innate immunity and how this depends on the tissue and host species.
2022-10-04 | PXD032365 | Pride
Project description:Sequence data and draft assemblies and annotation for a set of rodent malaria species.
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Project description:Rodent malaria parasite RNA hybridized on Illumina Mouse WG-6 v2.0 Expression BeadChip To investigate whether parasite RNA interfere with mouse beadchip analaysis. Malaria parasite resides in red blood cell, therefore RNA isolated from whole infected blood contains host RNA as well as parasite RNA
2020-04-30 | GSE145634 | GEO