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8 results for “ultra-conserved element”
Phylogeny of euophryine jumping spiders from ultra-conserved elements, with evidence on the intersexual coevolution of genitalia (Araneae: Salticidae: Euophryini)
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Clarifying the phylogenetic placement of the Eupoinae Maddison, 2015 with ultra-conserved element data (Araneae, Salticidae)
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Data from: Ultra-Conserved Element phylogenomics of new world Ponera (Hymenoptera: Formicidae) illuminates the origin and phylogeographic history of the endemic exotic ant Ponera exotica
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data sets for "Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea)"
<p>data sets used in :</p> <p>Cruaud A, Delvare G, Nidelet S, Sauné L, Ratnasingham S, Chartois M, Blaimer BB, Gates M, Brady SG, Faure S, van Noort S, Rossi J-P, and Rasplus J-Y. in press. Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea). Cladistics.</p> <p>1) morphological matrix (matrix_morphology_chalcididae_cladistics2020.nex) : Further details on characters and character states as well as illustrations can be found in the manuscript.</p> <p>2) concatenated UCE data set (merge_UCEs_chalcididae_cladistics2020.phy)</p> <p>3) all phylogenetic trees (morphology, UCEs, subset of UCEs; see paper for further details)</p> <p>4) a mesquite file with mapping of morphological characters on alternative UCE trees and the MJ consensus tree of the morphological analysis (mesquite_trees_and_morphological_transformations_chalcididae_cladistics2020.nex)</p>
Data from: Post K-Pg diversification of the mammalian order Eulipotyphla as suggested by phylogenomic analyses of ultra-conserved elements
The origin of the mammalian order Eulipotyphla has been debated intensively with arguments around whether they began diversifying before or after the Cretaceous-Palaeogene (K-Pg) boundary at 66 Ma. Here, we used an in-solution nucleotide capture method and next generation DNA sequencing to determine the sequence of hundreds of ultra-conserved elements (UCEs), and conducted phylogenomic and molecular dating analyses for the four extant eulipotyphlan lineages—Erinaceidae, Solenodontidae, Soricidae, and Talpidae. Concatenated maximum-likelihood analyses with single or partitioned models and a coalescent species-tree analysis showed that divergences among the four major eulipotyphlan lineages occurred within a short period of evolutionary time, but did not resolve the interrelationships among them. Alternative suboptimal phylogenetic hypotheses received consistently the same amount of support from different UCE loci, and were not significantly different from the maximum likelihood tree topology, suggesting the prevalence of stochastic lineage sorting. Molecular dating analyses that incorporated among-lineage evolutionary rate differences supported a scenario where the four eulipotyphlan families diversified between 57.8 and 63.2 Ma. Given short branch lengths with low support values, traces of rampant genome-wide stochastic lineage sorting, and post K-Pg diversification, we concluded that the crown eulipotyphlan lineages arose through a rapid diversification after the K-Pg boundary when novel niches were created by the mass extinction of species.
Effect of deleting ultra-conserved elements PAX6_Tarzan, PBX3_Claudia on gene expression in K562 cells
GEO Series GSE247234. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Data from: Post K-Pg diversification of the mammalian order Eulipotyphla as suggested by phylogenomic analyses of ultra-conserved elements
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An Evolutionary Cancer Epigenetic approach revealed DNA hypermethylation of Ultra-Conserved Non-coding Elements in squamous cell carcinoma of different mammalian species
GEO Series GSE157436. Felis catus; Bos taurus; Homo sapiens; Canis lupus familiaris; Equus caballus; Meles meles; Hystrix cristata. 120 samples. Type: Methylation profiling by high throughput sequencing.
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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.