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Experiment ID | Experiment name | DOI DOI of the related publication | Description | Link to raw data annotations See the raw data annotation results for this experiment |
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ERP009696 | Habitat-specific gene expression in stickleback immune tissues from four parametric lake-river population pairs | The three-spined stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to diverse freshwater habitats since the last glaciation. Among those freshwater habitats, adjacent lake and river populations harbour distinct parasite communities, a recurring ecological difference proposed to drive adaptive differentiation between lake and river stickleback ecotypes. To study the rapid adaptation of sticklebacks to lake and river habitats, we analysed gene expression profiles of 77 whole-transcriptome libraries of two immune-relevant tissues, the head kidney and the spleen, obtained from wild-caught sticklebacks of the two habitat types across multiple geographic locations. Differential expression analyses identified 189 genes showing statistically significant habitat-specific expression patterns among the three European locations. Among those genes, 15 genes are annotated with putative immune functions, and 50 have been experimentally associated with immune-responses in sticklebacks, reinforcing the hypothesis that parasites contribute to adaptive evolution of lake and river sticklebacks. Comparing expression profiles of European sticklebacks to populations in similar habitats in North America, five genes exhibited habitat-specific expression across continents. | Browse results | |
ERP119841 | Gene expression of immune tissues and ovaries from a marine population of threespine sticklebacks from Denmark | The threespine stickleback (Gasterosteus aculeatus) has repeatedly colonized and adapted to diverse freshwater habitats since the last glaciation. To study gene expression across different populations, we sequenced transcriptomes from wild-caught sticklebacks from a marine environment to compare with data from freshwater populations published with the project accessions PRJEB8677 and PRJEB26492. Genomic data from these individuals can be found under the project accession ERP001339. | Browse results | |
SRP012923 | Gasterosteus aculeatus RNA Sequencing | Gasterosteus aculeatus (Threespine stickleback) RNA sequencing from multiple tissues. | Browse results | |
SRP040543 | Maternal experience with predation risk influences genome-wide embryonic gene expression in threespined sticklebacks (Gasterosteus aculeatus) | Whole embryo mRNA profiles of 3dpf stickleback embryos of mothers exposed to simulated predation risk [E] and control mothers [C] were generated by barcoded, multiplexed high-throughput RNA-sequencing on Illumina Hiseq-2000. | Browse results | |
SRP043184 | Transcriptome analysis of threespine sticklebacks acclimated in different salinities | RNA sequencing was used to measure global gene expression in wild caught threespine sticklebacks. Native freshwater and marine fish were acclimated in water of different salinities before the gene expression in kidney was measured. The comparative transcriptomic analysis allowed the identification of salt-responsive genes. Overall design: We acclimated native freshwater (FW) and saltwater (SW) threespine sticklebacks to fresh (salinity: 0 g/L), brackish (salinity: 11 g/L), and sea water (salinity: 33 g/L) for 30 days, and then measured the global gene expression in fish kidneys. | Browse results | |
SRP061933 | Stickleback embryos use ABC transporters as a buffer against exposure to maternally derived cortisol | Purpose: Offspring from females that experience stressful conditions during reproduction often exhibit altered phenotypes and many of these effects are thought to arise due to increased exposure to maternal glucocorticoids. Here we used RNAseq to test whether the embryonic transcriptional response to increased levels of cortisol was similar to the transcriptional response to maternal stress in sticklebacks Methods: Eggs were treated by immersing eggs for 30 mins in water that contained 0, 5, or 10 ug/L, which represented baseline, predator induced, and super physiological levels of maternally derived cortisol. To isolated enough RNA for RNAseq, 10 embyros from each clutch/treatment were pooled prior to RNA extraction for a total of 18 pools (6 clutches x 3 treatments). Results: Analysis of genome-wide transcriptional profiles suggests that 17251 (genes which survived a cut-off of having cpm more than 1 in at least two samples; and had a significant likelihood ratio calculated in edgeR) genes out of the possible 22,456 genes in the stickleback genome were expressed in 72-hour embryos. However, we did not detect any differences in gene expression between embryos that were treated with cortisol compared to the control group. Overall design: mRNA profiles of egg clutches treated with 0, 5, or 10 ug/L are compared, which represented baseline, predator induced, and super physiological levels of maternally derived cortisol. | Browse results | |
SRP099849 | Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells [Stickleback] | Overall design: Examination of expression levels and chromatin accessibility in intestinal epithelaial cells in stickleback | Browse results | |
SRP101968 | Temporal Dynamics of Neurogenomic Plasticity in Response to Social Interactions in Male Threespined Sticklebacks [RNA-Seq] | Animals exhibit dramatic immediate behavioral plasticity in response to social interactions, and brief social interactions can shape the future social landscape. However, the molecular mechanisms contributing to behavioral plasticity are unclear. Here, we show that the genome dynamically responds to social interactions with multiple waves of transcription associated with distinct molecular functions in the brain of male threespined sticklebacks, a species famous for its behavioral repertoire and evolution. Some biological functions (e.g., hormone activity) peaked soon after a brief territorial challenge and then declined, while others (e.g., immune response) peaked hours afterwards. We identify transcription factors that are predicted to coordinate waves of transcription associated with different components of behavioral plasticity. Next, using H3K27Ac as a marker of chromatin accessibility, we show that a brief territorial intrusion was sufficient to cause rapid and dramatic changes in the epigenome. Finally, we integrate the time course brain gene expression data with a transcriptional regulatory network, and link gene expression to changes in chromatin accessibility. This study reveals rapid and dramatic epigenomic plasticity in response to a brief, highly consequential social interaction. Overall design: Adult males were collected from Putah Creek, a freshwater population, in spring 2013 and maintained in the lab on a 16:8 (L:D) photoperiod and at 18° C in separate 9-liter tanks. Males were provided with nesting material including algae, sand and gravel and were visually isolated from neighbors. All males were in the *territorial* phase of the nesting cycle, i.e. defending a territory. Males were randomly assigned to either the experimental or control group. Males in the experimental group were presented with a smaller, unrelated male intruder confined to a flask. Males in the control groups were presented with an empty flask. At the same time as a confined intruder was introduced to an experimental male's tank, an empty flask was introduced into a paired control male's tank. After 5 min the flask was removed, and after a predetermined period (see below) males were quickly netted and sacrificed by decapitation within seconds following an IACUC approved protocol (#15077) of the University of Illinois at Urbana-Champaign. For RNA Sequencing diencephalon and telencephalon tissue samples were collected 30, 60 or 120 minutes after the flask was introduced, with n=10 males per time point (5 experimental and 5 control). | Browse results | |
SRP286264 | Gasterosteus aculeatus Isoseq Transcriptome Reads | Long and short reads created for threespine stickleback tissues | Browse results |