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5 results for “mixed-species transcriptomes”
Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses
<p>Recent high-throughput sequencing endeavors have yielded multi-gene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of <i>Mesodinium</i> and to generate the most taxonomically-rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multi-protein dataset, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. <i>Mesodinium</i> always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of <i>Mesodinium</i> – <i>M. rubrum</i>, <i>M. major</i>, and <i>M. chamaeleon</i> - being more closely related to each other than to the heterotrophic member, <i>M. pulex</i>. The well-supported position of <i>Mesodinium</i> as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination - particularly for <i>Mesodinium</i> species where expression from stolen prey nuclei appears to dominate – requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.</p>
Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses
<p>Recent high-throughput sequencing endeavors have yielded multi-gene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of <i>Mesodinium</i> and to generate the most taxonomically-rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multi-protein dataset, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. <i>Mesodinium</i> always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of <i>Mesodinium</i> – <i>M. rubrum</i>, <i>M. major</i>, and <i>M. chamaeleon</i> - being more closely related to each other than to the heterotrophic member, <i>M. pulex</i>. The well-supported position of <i>Mesodinium</i> as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination - particularly for <i>Mesodinium</i> species where expression from stolen prey nuclei appears to dominate – requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.</p>
Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses
Open the record for dataset details and reuse information.
Data from: A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses
Open the record for dataset details and reuse information.
Transcriptomic analyses of Staphylococcus epidermidis in mixed-species biofilms with Candida albicans
GEO Series GSE35438. Staphylococcus epidermidis; Candida albicans; Staphylococcus epidermidis RP62A. 4 samples. Type: Expression profiling by array.
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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.