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6,383 results for “isolates”
Genetic and transcriptomic characteristics of RhlR-dependent quorum sensing in cystic fibrosis isolates of Pseudomonas aeruginosa: isolate E104
GEO Series GSE198534. Pseudomonas aeruginosa. 6 samples. Type: Expression profiling by high throughput sequencing.
RNA sequencing of isolated mouse CD8 T cells treated with IL2, IL7 or IL15
GEO Series GSE259434. Mus musculus. 15 samples. Type: Expression profiling by high throughput sequencing.
Transcriptional analysis of CD45+ leukocytes isolated from syngeneic MC38 tumors from mice fed high-fat or control diet
GEO Series GSE157990. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
Bulk RNA-seq of eyes isolated from wildtype and Stra6 knockout mice maintained on either a vitamin A sufficient or deficient diet
GEO Series GSE219252. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
Isolating Independent Effects of Diet/Energy Balance and Body Weight on Behavior and Metabolic Health
GEO Series GSE104709. Mus musculus. 21 samples. Type: Expression profiling by high throughput sequencing.
microRNA expression profile of human thymus populations corresponding to 8 sequential T-cell developmental stages isolated from 3 independent pediatric thymus samples.
GEO Series GSE299842. Homo sapiens. 23 samples. Type: Non-coding RNA profiling by array.
Sex differences in Non-Alcoholic Steatohepatitis (NASH) in mice evoked by a fructose-palmitate-cholesterol (FPC)-enriched diet [bulk_isolated_cells]
GEO Series GSE256502. Mus musculus. 31 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq of DRG neurons isolated from alum vs. alum+KLH immunized mice
GEO Series GSE108428. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Genome assembly of Malassezia pachydermatis isolated from a canine otitis clinical sample
<p>We report the raw signal data output obtained from a <em>Malassezia pachydermatis</em> isolate of a canine clinical sample (otitis). Multiple barcoded samples run was performed with the MinION device, Oxford Nanopore Technologies, and the barcode02 was assigned to this sample. The raw signal data, fast5 files (showed in the Fats5.zip directory), were basecalled and demultiplexed in order to achieve the fastq file format which includes only the sequences targeted with barcode02 (M13_UAB2019.fastq).</p>
Figure 5 in Temporal patterns of the calanoid copepod community in Veliko Jezero, an isolated marine lake (South Adriatic Sea): links to a larger-scale climate changes
Figure 5. Dendogram of sample units identified by cluster analysis.
Figure 1 in Temporal patterns of the calanoid copepod community in Veliko Jezero, an isolated marine lake (South Adriatic Sea): links to a larger-scale climate changes
Figure 1. Study area with the sampling station.
ImageStream Data of Isolating Coccospheres within Sediment
<p><strong>ImageStream data for the development of ISX+PL, a method to isolate and analyse coccospheres within sediment. </strong></p> <p>Data includes raw image files of:</p> <ul> <li>Positive control sample of coccospheres and coccoliths (Coccolithophore_control), and negative control sample of marine sediment with CaCO<sub>3</sub> removed (Sediment_control) for characterising morphological properties of these populations.</li> <li>Field sample in which the developed protocol and template were applied (Fieldsample) and the defined coccosphere population (Coccosphere)</li> <li>Validation of ISX diameter measurements with Scanning Electron Microscopy (SEM_validation). </li> </ul>
Table S1. Unique set of pncA alleles among MDR+PZA-R isolates reported by Mansjö et al
<p>The unique set of pncA alleles among MDR PZA-R isolates reported by Mansjö & colleagues https://pubmed.ncbi.nlm.nih.gov/28559517/</p>
The effects of social isolation among elderly people in nursing homes in Austria during the Covid-19 pandemic
<p>This dataset contains data from a study in which we examined the extent to which isolation affected degenerative cognitive performance, depression and the subjective quality of life of people with dementia. 49 participants (58-94 of age) living in nursing homes were tested before and after the social isolation from the COVID-19 pandemic in cognitive performance, depressed mood, anxiety and subjective life quality.</p>
Figure 1 from: Al-Rafyai HM, Alwash MS, Al-Khafaji NS (2021) Quinolone resistance (qnrA) gene in isolates of Escherichia coli collected from the Al-Hillah River in Babylon Province, Iraq. Pharmacia 68(1): 1-7. https://doi.org/10.3897/pharmacia.68.e57819
Figure 1 Geographic locations of the three sampling sites (S1–S3) along the Al Hillah River.
Data from: Hydrocarbon divergence and reproductive isolation in Timema stick insects
Background: Individuals commonly prefer certain trait values over others when choosing their mates. If such preferences diverge between populations, they can generate behavioral reproductive isolation and thereby contribute to speciation. Reproductive isolation in insects often involves chemical communication, and cuticular hydrocarbons, in particular, serve as mate recognition signals in many species. We combined data on female cuticular hydrocarbons, interspecific mating propensity, and phylogenetics to evaluate the role of cuticular hydrocarbons in diversification of Timema walking-sticks. Results: Hydrocarbon profiles differed substantially among the nine analyzed species, as well as between partially reproductively-isolated T. cristinae populations adapted to different host plants. In no-choice trials, mating was more likely between species with similar than divergent hydrocarbon profiles, even after correcting for genetic divergences. The macroevolution of hydrocarbon profiles, along a Timema speciesphylogeny, fits best with a punctuated model of phenotypic change concentrated around speciation events, consistent with change driven by selection during the evolution of reproductive isolation. Conclusion: Altogether, our data indicate that cuticular hydrocarbon profiles vary among Timema species and populations, and that most evolutionary change in hydrocarbon profiles occurs in association with speciation events. Similarities in hydrocarbon profiles between species are correlated with interspecific mating propensities, suggesting a role for cuticular hydrocarbon profiles in mate choice and speciation in the genus Timema.
Data from: Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish
Habitat loss and fragmentation often result in small, isolated populations vulnerable to environmental disturbance and loss of genetic diversity. Low genetic diversity can increase extinction risk of small populations by elevating inbreeding and inbreeding depression, and reducing adaptive potential. Due to their linear nature and extensive use by humans, freshwater ecosystems are especially vulnerable to habitat loss and fragmentation. Although the effects of fragmentation on genetic structure have been extensively studied in migratory fish, they are less understood in low-mobility species. We estimated impacts of instream barriers on genetic structure and diversity of the low-mobility river blackfish (Gadopsis marmoratus) within five streams separated by weirs or dams constructed 45–120 years ago. We found evidence of small-scale (<13 km) genetic structure within reaches unimpeded by barriers, as expected for a fish with low mobility. Genetic diversity was lower above barriers in small streams only, regardless of barrier age. In particular, one isolated population showed evidence of a recent bottleneck and inbreeding. Differentiation above and below the barrier was greatest (FST =0.13) in this stream, but in other streams did not differ from background levels. Spatially explicit simulations suggest that short-term barrier effects would not be detected with our dataset unless effective population sizes were very small (<100). Our study highlights that, in structured populations, the ability to detect short-term genetic effects from barriers is reduced and requires more genetic markers compared to panmictic populations. We also demonstrate the importance of accounting for natural population genetic structure in fragmentation studies.
Data from: Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus
The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity—both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography.
Data from: Variable post-zygotic isolation in Drosophila melanogaster/D. simulans hybrids
The study of hybrid inviability reveals cryptic divergence between the genetic interactions that maintain stable phenotypes in the pure species. We characterized the effects of natural variation on the penetrance of hybrid inviability phenotypes in crosses between Drosophila melanogaster and two species of the D. simulans subcomplex, D. simulans and D. sechellia. Using a panel of wild-caught lines, we studied the levels of genetic variance present in D. simulans and D. sechellia affecting prezygotic and post-zygotic isolation in hybridizations with D. melanogaster females. We observed extensive variability in the viability of hybrid individuals, dependent on the genotype of the parents, suggesting that intraspecific natural variation manifests directly in hybrid phenotypes. Furthermore, we found that genetic background significantly affects the penetrance of a well-studied determinant of hybrid inviability: the interaction between Hmrmel–Lhrsim. Our results suggest that hybrid inviability – and reproductive isolation generally – can be modified by polymorphisms at multiple loci segregating within the parental species. Just as the penetrance of most mutant phenotypes can be modified by the genetic background within the pure species, the penetrance of hybrid inviability phenotypes is highly influenced by the parental genotypes.
Data from: Climatic suitability, isolation by distance and river resistance explain genetic variation in a Brazilian whiptail lizard
Spatial patterns of genetic variation can help understand how environmental factors either permit or restrict gene flow and create opportunities for regional adaptations. Organisms from harsh environments such as the Brazilian semiarid Caatinga biome may reveal how severe climate conditions may affect patterns of genetic variation. Herein we combine information from mitochondrial DNA with physical and environmental features to study the association between different aspects of the Caatinga landscape and spatial genetic variation in the whiptail lizard Ameivula ocellifera. We investigated which of the climatic, environmental, geographical and/or historical components best predict: (1) the spatial distribution of genetic diversity, and (2) the genetic differentiation among populations. We found that genetic variation in A. ocellifera has been influenced mainly by temperature variability, which modulates connectivity among populations. Past climate conditions were important for shaping current genetic diversity, suggesting a time lag in genetic responses. Population structure in A. ocellifera was best explained by both isolation by distance and isolation by resistance (main rivers). Our findings indicate that both physical and climatic features are important for explaining the observed patterns of genetic variation across the xeric Caatinga biome.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.