Aphelocoma californica
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA292578 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2170810_1.fastq.gz | Fastqsanger.gz | |||
| SRR2170810_2.fastq.gz | Fastqsanger.gz | |||
| SRR2170820_1.fastq.gz | Fastqsanger.gz | |||
| SRR2170820_2.fastq.gz | Fastqsanger.gz | |||
| SRR2170840_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 62 |
Similar Datasets
Project description:Aphelocoma californica Genomic Resources
| PRJNA777134 | ENA
Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Here, we optimised the FAIRE and MNase assays for application upon heavily-fixed tissues as is typically found in historical formalin-preserved museum specimens. We demonstrate these assays in formalin-fixed mouse specimens and compare the chromatin signatures to specimen-matched fresh tissues. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are reproducible, tissue-specific and sex-specific in vertebrate specimens.
2024-03-15 | GSE261169 | GEO
Project description:Western scrub-jays (Aphelocoma californica) live double lives, storing food for the future while raiding the stores of other birds. One tactic scrub-jays employ to protect stores is "re-caching"-relocating caches out of sight of would-be thieves. Recent computational modelling work suggests that re-caching might be mediated not by complex cognition, but by a combination of memory failure and stress. The "Stress Model" asserts that re-caching is a manifestation of a general drive to cache, rather than a desire to protect existing stores. Here, we present evidence strongly contradicting the central assumption of these models: that stress drives caching, irrespective of social context. In Experiment (i), we replicate the finding that scrub-jays preferentially relocate food they were watched hiding. In Experiment (ii) we find no evidence that stress increases caching. In light of our results, we argue that the Stress Model cannot account for scrub-jay re-caching.
| S-EPMC3541402 | biostudies-literature
Project description:The manuscript by D. Licastro and colleagues “Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved sequence elements” presents an overview of experimental and computational approaches employed by the authors to perform a multi-facet characterization of ultraconserved elements (UCEs). The authors present an interesting analysis where they investigate the transcription of UCEs in mouse development at different stages by conductin an microarray experiment. Some of these results are further verified by RT-PCR.
2010-06-16 | GSE19371 | GEO
Project description:The manuscript by D. Licastro and colleagues “Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved sequence elements” presents an overview of experimental and computational approaches employed by the authors to perform a multi-facet characterization of ultraconserved elements (UCEs). The authors present an interesting analysis where they investigate the transcription of UCEs in mouse development at different stages by conductin an microarray experiment. Some of these results are further verified by RT-PCR. 12 Samples, 4 groups 3 samples per group.
2010-06-16 | E-GEOD-19371 | biostudies-arrayexpress
Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Here, we optimised the FAIRE and MNase assays for application upon heavily-fixed tissues as is typically found in historical formalin-preserved museum specimens. We demonstrate these assays in formalin-fixed mouse specimens and compare the chromatin signatures to specimen-matched fresh tissues. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are reproducible, tissue-specific and sex-specific in vertebrate specimens.
2024-03-01 | GSE256158 | GEO
Project description:Previous research has suggested that videos can be used to experimentally manipulate social stimuli. In the present study, we used the California scrub-jays' cache protection strategies to assess whether video playback can be used to simulate conspecifics in a social context. In both the lab and the field, scrub-jays are known to exhibit a range of behaviours to protect their caches from potential pilferage by a conspecific, for example by hiding food in locations out of the observer's view or by re-caching previously made caches once the observer has left. Here, we presented scrub-jays with videos of a conspecific observer as well as two non-social conditions during a caching period and assessed whether they would cache out of the observer's "view" (Experiment 1) or would re-cache their caches once the observer was no longer present (Experiment 2). In contrast to previous studies using live observers, the scrub-jays' caching and re-caching behaviour was not influenced by whether the observer was present or absent. These findings suggest that there might be limitations in using video playback of social agents to mimic real-life situations when investigating corvid decision making.
| S-EPMC5857174 | biostudies-literature
Project description:Sequence capture and phylogenetic utility of genomic ultraconserved elements obtained from pinned insect specimens more than 100 years-old
| PRJNA316103 | ENA
Project description:String-pulling is a widely used paradigm in animal cognition research to assess what animals understand about the functionality of strings as a means to obtain an out-of-reach reward. This study aimed to systematically investigate what rules Western scrub-jays (Aphelocoma californica) use to solve different patterned string tasks, i.e. tasks in which subjects have to choose between two or more strings of which only one is connected to the reward, or where one is more efficient. Arranging strings in a parallel configuration showed that the jays were generally capable of solving multiple-string tasks and acted in a goal-directed manner. The slanted and crossed configurations revealed a reliance on a "proximity rule", that is, a tendency to choose the string-end closest to the reward. When confronted with strings of different lengths attached to rewards at different distances the birds chose according to the reward distance, preferring the reward closest to them, and were sensitive to the movement of the reward, but did not consistently prefer the shorter and therefore more efficient string. Generally, the scrub-jays were successful in tasks where the reward was closest to the string-ends they needed to pull or when string length and reward distance correlated, but the birds had problems when the wrong string-end was closest to the reward or when the food items were in close proximity to each other. These results show that scrub-jays had a partial understanding of the physical principles underlying string-pulling but relied on simpler strategies such as the proximity rule to solve the tasks.
| S-EPMC5054065 | biostudies-literature
Project description:Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we applied an optimised MNase assay to fresh-frozen and archival eastern water dragon specimens, as old as 1905. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and that these chromatin profiles are sex-specific and environmental condition dependent.
2024-03-01 | GSE256157 | GEO