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497 results for “stickleback”
Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [Stickleback]
GEO Series GSE94934. Gasterosteus aculeatus. 4 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Gene expression in stickleback (Apeltes quadracus) spine and fins
GEO Series GSE190498. Apeltes quadracus. 21 samples. Type: Expression profiling by high throughput sequencing.
Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish
GEO Series GSE254561. Gasterosteus aculeatus. 22 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish [ChIP-Seq]
GEO Series GSE254557. Gasterosteus aculeatus. 10 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
A Y-linked duplication of anti-Mullerian hormone is the sex determination gene in threespine stickleback
GEO Series GSE296766. Gasterosteus aculeatus. 36 samples. Type: Expression profiling by high throughput sequencing.
Epigenetic adaptation of stickleback to sea and freshwater conditions: RNA-seq
GEO Series GSE186925. Gasterosteus aculeatus. 17 samples. Type: Expression profiling by high throughput sequencing.
Resources for gasAcu1-4, a new stickleback reference genome
<p><em>gasAcu1-4</em> is a new version of the stickleback reference genome. It only minorly differs from the 2017 Hi-C guided assembly by Peichel, Sullivan, Liachko, and White (https://doi.org/10.1093/jhered/esx058) to improve the subtelomeric <em>Pitx1</em> locus and the mitochondrial genome. We here present basic resources for utilizing this version of the reference genome: the fasta sequence of the assembly and liftOver chains for converting coordinates between this reference version and the original (Broad S1) <em>gasAcu1 </em>assembly (https://www.nature.com/articles/nature10944).</p> <p>This assembly can be visualized and other data downloaded via the Table Browser of the UCSC Genome Browser by copying the following track hub URL into the "My Hubs" tab at https://genome.ucsc.edu/cgi-bin/hgHubConnect: https://sbwdev.stanford.edu/kingsleyAssemblyHub/hub.txt.</p>
Data from: Gene expression plasticity in response to salinity acclimation in threespine stickleback ecotypes from different salinity habitats
Phenotypic plasticity is thought to facilitate the colonization of novel environments and shape the direction of evolution in colonizing populations. However, the relative prevalence of various predicted patterns of changes in phenotypic plasticity following colonization remain unclear. Here we use a whole-transcriptome approach to characterize patterns of gene expression plasticity in the gills of a freshwater-adapted and a saltwater-adapted ecotype of threespine stickleback (Gasterosteus aculeatus) exposed to a range of salinities. The response of the gill transcriptome to environmental salinity had a large shared component common to both ecotypes (2,159 genes) with significant enrichment of genes involved in transmembrane ion transport and the restructuring of the gill epithelium. This transcriptional response to freshwater acclimation is induced at salinities below two parts per thousand. There was also differentiation in gene expression patterns between ecotypes (2,515 genes), particularly in processes important for changes in the gill structure and permeability. Only 508 genes that differed between ecotypes also responded to salinity and no specific processes were enriched among this gene set, and an even smaller number (87 genes) showed evidence of changes in the extent of the response to salinity acclimation between ecotypes. No pattern of relative expression dominated among these genes, suggesting that neither gains nor losses of plasticity dominated the changes in expression patterns between the ecotypes. These data demonstrate that multiple patterns of changes in gene expression plasticity can occur following colonization of novel habitats.
Data from: Evolution of stickleback in 50 years on earthquake-uplifted islands
How rapidly can animal populations in the wild evolve when faced with sudden environmental shifts? Uplift during the 1964 Great Alaska Earthquake abruptly created freshwater ponds on multiple islands in Prince William Sound and the Gulf of Alaska. In the short time since the earthquake, the phenotypes of resident freshwater threespine stickleback fish on at least three of these islands have changed dramatically from their oceanic ancestors. To test the hypothesis that these freshwater populations were derived from oceanic ancestors only 50 y ago, we generated over 130,000 single-nucleotide polymorphism genotypes from more than 1,000 individuals using restriction site-associated DNA sequencing (RAD-seq). Population genomic analyses of these data support the hypothesis of recent and repeated, independent colonization of freshwater habitats by oceanic ancestors. We find evidence of recurrent gene flow between oceanic and freshwater ecotypes where they co-occur. Our data implicate natural selection in phenotypic diversification and support the hypothesis that the metapopulation organization of this species helps maintain a large pool of genetic variation that can be redeployed rapidly when oceanic stickleback colonize freshwater environments. We find that the freshwater populations, despite population genetic analyses clearly supporting their young age, have diverged phenotypically from oceanic ancestors to nearly the same extent as populations that were likely founded thousands of years ago. Our results support the intriguing hypothesis that most stickleback evolution in fresh water occurs within the first few decades after invasion of a novel environment.
Data from: Temporal stability of genetic variability and differentiation in the three-spined stickleback (Gasterosteus aculeatus)
Temporal variation in allele frequencies, whether caused by deterministic or stochastic forces, can inform us about interesting demographic and evolutionary phenomena occurring in wild populations. In spite of the continued surge of interest in the genetics of three-spined stickleback (Gasterosteus aculeatus) populations, little attention has been paid towards the temporal stability of allele frequency distributions, and whether there are consistent differences in effective size (Ne) of local populations. We investigated temporal stability of genetic variability and differentiation in 15 microsatellite loci within and among eight collection sites of varying habitat type, surveyed twice over a six-year time period. In addition, Nes were estimated with the expectation that they would be lowest in isolated ponds, intermediate in larger lakes and largest in open marine sites. In spite of the marked differences in genetic variability and differentiation among the study sites, the temporal differences in allele frequencies, as well as measures of genetic diversity and differentiation, were negligible. Accordingly, the Ne estimates were temporally stable, but tended to be lower in ponds than in lake or marine habitats. Hence, we conclude that allele frequencies in putatively neutral markers in three-spined sticklebacks seem to be temporally stable – at least over periods of few generations – across a wide range of habitat types differing markedly in levels of genetic variability, effective population size and gene flow.
Secondary contact, introgressive hybridization and genome stabilization in sticklebacks
<p>Variant data in vcf format and SNPEFF annotation related files for the manuscript "Secondary contact, introgressive hybridization and genome stabilization in sticklebacks".</p>
Stickleback embryos use ABC transporters as a buffer against exposure to maternally derived cortisol
GEO Series GSE71649. Gasterosteus aculeatus. 18 samples. Type: Expression profiling by high throughput sequencing.
Resources for gasAcu1-4, a new stickleback reference genome
Open the record for dataset details and reuse information.
Data from: Gene expression plasticity in response to salinity acclimation in threespine stickleback ecotypes from different salinity habitats
Open the record for dataset details and reuse information.
Data from: Temporal stability of genetic variability and differentiation in the three-spined stickleback (Gasterosteus aculeatus)
Open the record for dataset details and reuse information.
Data from: Evolution of stickleback in 50 years on earthquake-uplifted islands
Open the record for dataset details and reuse information.
Marine and freshwater three-spined stickleback (Gasterosteus aculeatus) gene expression differences
GEO Series GSE34783. Gasterosteus aculeatus. 68 samples. Type: Expression profiling by array.
Fine-scale contemporary recombination variation and its fitness consequences in adaptively diverging stickleback fish [ATAC-Seq]
GEO Series GSE254559. Gasterosteus aculeatus. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
RAD methods paper - Threespine Stickleback Lateral Plate Mapping
GEO Series GSE5773. Gasterosteus aculeatus. 20 samples. Type: Other.
Brain transcriptomic response of the threespine stickleback Gasteroteus aculeatus to predator cues
GEO Series GSE21599. Gasterosteus aculeatus. 10 samples. Type: Expression profiling by array.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.