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410 results for “eukaryotic”
Data from: ITS1: a DNA barcode better than ITS2 in eukaryotes?
A DNA barcode is a short piece of DNA sequence used for species determination and discovery. The internal transcribed spacer (ITS/ITS2) region has been proposed as the standard DNA barcode for fungi and seed plants, and has been widely used in DNA barcoding analyses for other biological groups, e.g. algae, protists, and animals. The ITS region consists of both ITS1 and ITS2 regions. Here, a large scale meta-analysis was carried out to compare ITS1 and ITS2 from three aspects: PCR amplification, DNA sequencing and species discrimination, in terms of the presence of DNA barcoding gaps, species discrimination efficiency, sequence length distribution, GC content distribution and primer universality. In total, 85,345 sequence pairs in ten major groups of eukaryotes, including ascomycetes, basidiomycetes, liverworts, mosses, ferns, gymnosperms, monocotyledons, eudicotyledons, insects, and fishes, covering 611 families, 3,694 genera, and 19,060 species, were analyzed. Using similarity-based methods, we calculated species discrimination efficiencies for ITS1 and ITS2 in all major groups, families, and genera. Using Fisher's exact test, we found that ITS1 has significantly higher efficiencies than ITS2 in 17 of the 47 families and 20 of the 49 genera, which are sample-rich. By in silico PCR amplification evaluation, primer universality of the extensively applied ITS1 primers was found superior to that of ITS2 primers. Additionally, shorter length of amplification product and lower GC content were discovered to be two other advantages of ITS1 for sequencing. In summary, ITS1 represents a better DNA barcode than ITS2 for eukaryotic species.
CLassifier of Essentiality AcRoss EukaRyotes (CLEARER)
<p># CLassifier of Essentiality AcRoss EukaRyotes (CLEARER)<br> ---------------------------------------------------------------------------------<br> #CLAERER is a machine learning approach for essential gene #prediction across eukaryotes</p> <p>Please read the README.</p> <p><strong>Abstract</strong></p> <p>Identifying essential genes on a genome scale is resource intensive and has been performed for only a few eukaryotes. For less studied organisms essentiality might be predicted by gene homology. However, this approach cannot be applied to non-conserved genes. Additionally, divergent essentiality information is obtained from studying single cells or whole, multi-cellular organisms, and particularly when derived from human cell line screens and human population studies. We employed machine learning across six model eukaryotes and 60,381 genes, using 41,635 features derived from sequence, gene functions and network topology. Within a leave-one-organism-out cross-validation, the classifiers showed a high generalizability with an average accuracy close to 80% in the left-out species. As a case study, we applied the method to <em>Tribolium castaneum</em> and <em>Bombyx mori</em> and validated predictions experimentally yielding similar performance. Finally, using the classifier based on the studied model organisms enabled linking the essentiality information of human cell line screens and population studies.</p>
Data presented in "Short tandem repeats bind transcription factors to tune eukaryotic gene expression"
<p>Here you can find the data supporting the conclusions in "Short tandem repeats bind transcription factors to tune eukaryotic gene expression." The accompanying code repository can be found at https://doi.org/10.5281/zenodo.8161422.</p>
Genome-wide mapping of 5-hydroxymethyluracil in eukaryote parasite Leishmania
GEO Series GSE83384. Leishmania donovani; Leishmania major. 24 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing.
Transcriptome maps of general eukaryotic RNA degradation factors
GEO Series GSE128312. Saccharomyces cerevisiae. 30 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals
GEO Series GSE57450. Saccharomyces cerevisiae. 9 samples. Type: Non-coding RNA profiling by high throughput sequencing; Expression profiling by genome tiling array.
Evolutionary and functional analysis of DNA methyltransferases in micro-eukaryotes: Insights from the model diatom Phaeodactylum tricornutum
GEO Series GSE186857. Phaeodactylum tricornutum. 9 samples. Type: Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Cannabinoid Modulation of Eukaryotic Initiation Factors (eIF2α and eIF2B1) and Behavioral Cross-Sensitization to Cocaine in Adolescent Rats
GEO Series GSE102946. Rattus norvegicus. 6 samples. Type: Expression profiling by high throughput sequencing.
Non-canonical DNA structures at eukaryotic centromeres can resolve the CENP-B paradox
GEO Series GSE102111. Chlorocebus aethiops; Homo sapiens. 7 samples. Type: Other; Genome binding/occupancy profiling by high throughput sequencing.
High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq
GEO Series GSE152621. Homo sapiens; Saccharomyces cerevisiae; Schizosaccharomyces pombe; Drosophila melanogaster. 29 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Data from: Short term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes
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Data from: ITS1: a DNA barcode better than ITS2 in eukaryotes?
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Data from: Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis
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Data from: Gene similarity networks provide new tools for understanding eukaryote origins and evolution
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Highly parallel identification of sequence preferences for eukaryotic C2H2 zinc finger domains using a bacterial 1-hybrid assay
GEO Series GSE52521. synthetic construct. 403 samples. Type: Other.
Inhibition of the Eukaryotic Initiation Factor-2-α Kinase PERK Decreases Risk of Autoimmune Diabetes in Mice
GEO Series GSE245004. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
PAT-seq: a simple approach to digital gene expression, the measure of poly(A)-tail length and its position in eukaryotic transcriptomes
GEO Series GSE53461. Saccharomyces cerevisiae. 13 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Methylation of human eukaryotic elongation factor alpha (eEF1A) by a member of a novel protein lysine methyltransferase family modulates mRNA translation
GEO Series GSE97140. Homo sapiens. 11 samples. Type: Expression profiling by high throughput sequencing; Other.
Eukaryotic enteric virus infections modulate the host tissue transcriptome
GEO Series GSE168293. Mus musculus. 127 samples. Type: Expression profiling by high throughput sequencing.
Defining the Essential Function of Yeast Hsf1 Reveals a Compact Transcriptional Program for Maintaining Eukaryotic Proteostasis
GEO Series GSE108736. Saccharomyces cerevisiae; Mus musculus. 38 samples. Type: Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.