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54,099 results for “Expression”
Novel sex-specific genes and diverse interspecific expression in the antennal transcriptomes of ithomiine butterflies"
<p>The following repository contains both the genomic and functional annotations for 4 Ithomiini species. Data that was used in GBE paper "Novel sex-specific genes and diverse interspecific expression in the antennal transcriptomes of ithomiine butterflies".</p>
Effects of a plant-based diet from first feeding on the intestinal expression of nutrient sensors in rainbow trout
<p>Raw data corresponding to results included in the above mentioned publication </p>
Single-cell analysis reveals host S phase drives large T antigen expression during BK polyomavirus infection
Open the record for dataset details and reuse information.
Supplementary Material for the paper "Assessing the Understanding of Expressions: A Qualitative Study of Notional-Machine-Based Exam Questions"
<p>Supplementary Material for the paper "Assessing the Understanding of Expressions: A Qualitative Study of Notional-Machine-Based Exam Questions":</p> <ul> <li>exam_questions.pdf: Complete statement of the 12 exam questions.</li> <li>mistakes.xlsx: Excel sheet with the full comprehensive list detailing all the mistakes and codes that resulted from our analysis.</li> </ul> <p> </p> <p> </p>
Emotions expressed by the police, their state supporters, and experienced by officers
<p>Rak Joanna, Emotions expressed by the police, their state supporters, and experienced by officers.</p> <p>This dataset was elaborated for the research project <em>Civil Disorder in Pandemic-ridden European Union</em>. The latter was financially supported by the National Science Centre, Poland [grant number 2021/43/B/HS5/00290].</p>
Emotions expressed by the police, their state supporters, and experienced by officers
<p>Rak Joanna, <span>Emotions expressed by the police, their state supporters, and experienced by officers.</span></p> <p>This dataset dwas elaborated for the research project <em>Civil Disorder in Pandemic-ridden European Union</em>. The latter was financially supported by the National Science Centre, Poland [grant number 2021/43/B/HS5/00290].</p>
A fMRI dataset in response to large number of short natural dynamic facial expression videos
<p><span>Facial expression is among the most natural methods for human beings to convey their emotional information in daily life. Although </span>the neural mechanism of facial expression has been extensively studied employing lab-controlled images and a <span>small number of</span> lab-controlled video stimuli, how the human brain processes <span>natural</span> facial expressions still needs to be investigated. <span>T</span>o our knowledge<span>,</span> this type of data <span>specifically</span> <span>on </span><span>large number of </span><span>natural</span> <span>facial expression videos</span> is currently missing. <span>W</span>e describe <span>here </span>the <span>natural </span>Facial Expressions Dataset (NFED), a fMRI dataset <span>including </span>responses to 1,320 short (<span>3-second</span>) <span>natural</span> facial expression video clips. <span>These video clips is </span><span>annotated</span> <span>with three types of labels: emotion, gender, and ethnicity</span><span>, along with accompanying metadata</span>. We validate that the dataset has good quality within and across participants and, notably, can capture temporal and spatial stimuli features. NFED provides researchers with fMRI data for understanding of the visual processing of large number of <span>natural </span> <span>facial expression videos.</span></p>
A fMRI dataset in response to large-scale short natural dynamic facial expression videos
<p>Facial expression is among the most natural methods for human beings to convey their emotional information in daily life. Although the neural mechanism of facial expression has been extensively studied employing lab-controlled images and a small number of lab-controlled video stimuli, how the human brain processes natural facial expressions still needs to be investigated. To our knowledge, this type of data specifically on large<span>-scale</span> natural facial expression videos is currently missing. We describe here the natural Facial Expressions Dataset (NFED), a fMRI dataset including responses to 1,320 short (3-second) natural facial expression video clips. These video clips is annotated with three types of labels: emotion, gender, and ethnicity, along with accompanying metadata. We validate that the dataset has good quality within and across participants and, notably, can capture temporal and spatial stimuli features. NFED provides researchers with fMRI data for understanding of the visual processing of large number of natural facial expression videos.</p>
Meta-analysis of scRNA-seq Co-expression in Human Neural Organoids Reveals High Variability in Recapitulating Primary Tissue
<p>Contains all code and data for Werner and Gillis, Meta-analysis of scRNA-seq Co-expression in Human Neural Organoids Reveals High Variability in Recapitulating Primary Tissue, 2024. </p> <p>Additionally, the code and data for this paper can be found at https://github.com/JonathanMWerner/meta_organoid_analysis with an easy to view github markdown file containing all the code used to generate all figure panel plots at https://github.com/JonathanMWerner/meta_organoid_analysis/blob/main/figure_plots_with_data_code.md.</p> <p>Due to file size limits on github, there are several data files not available on github, but are available here on zenodo in the data_for_plots.zip file, see below:</p> <pre>umap_embeddings_Fig2A.Rdata<br>cross_dataset_aggregated_exp_metaMarker_all_fetal_SuppFig1B_Fig2E.Rdata<br>organoid_egad_results_ranked_6_26_24_Fig3D.Rdata<br>fetal_egad_results_ranked_6_26_24_Fig3D.Rdata<br>org_eigenvec_matrices_SuppFig3CD.Rdata</pre> <p><br>The R package developed for this paper is available at https://github.com/JonathanMWerner/preservedCoexp</p>
Lung ECs scRNA-seq: Gene Expression and Metadata
<p>Normalized gene expression and cell metadata derived from a Seurat object.</p>
A comprehensive dataset of Infant Facial expressions of Pain Intensity
<p><span>Facial expression plays an import role in daily life routine whether people dealing each other or diagnosing internal feelings of one another. Facial expression of pain is very much import to recognize and properly handle. There is a large number of database representing facial expression of pain, including adult’s pain databases and infant’s pain databases. Most of the databases are focusing on adults pain expressions while some deals in infant’s pain expressions. This paper represent a new infants’ pains’ facial expression database called “Infant Facial Expression of Pain Intensity” (IFEPI). This database mainly focuses on four-pain levels i.e. No pain, Mild Pain, Moderate Pain and Severe Pain. The database consist of large collection of 25000 spontaneous images collected from 120 infants of two different hospitals of Khyber Pakhtunkhwa, Pakistan, works under Health department of Pakistan Government and UNICEF. The paper represent the process from setting environment to images/frame collections to the preprocessing and refinement of the images. This database is the largest database available on pain, also there is no database, available in our knowledge, of infant which deals with four level of pain intensity. To check the validation of the proposed database we use 4 state of the art machine learning models including logistic regression, SVM, KNN and Random Forest and 2 state of the art deep learning models including LeNet and AlexNet. As the database is the largest database available, the deep learning models i.e LeNet achieves training accuracy and testing accuracy of 98.2% and 86.3% respectively while AlexNet secure training and testing accuracy of 99.1% and 89.1% respectively</span></p>
Chapter 4 Effects of orange peel extract on the oxidative potential and laccase gene expression in Trametes versicolor
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Fig. 4 in Direct somatic embryogenesis of drought resistance pistachio (Pistacia vera L.) and expression analysis of somatic embryogenesis-related genes
Fig. 4. Somatic embryos induction of P. vera L. Sarakhs variety from immature zygotic embryos under dark condition after 60 days. Somatic embryos exhibited by arrows (a) Somatic embryos in globular stage, (b) Somatic embryos in heart stage, (c) Cotyledonary somatic embryos. Bar 2 mm.
Fig. 6 in Direct somatic embryogenesis of drought resistance pistachio (Pistacia vera L.) and expression analysis of somatic embryogenesis-related genes
Fig. 6. Secondary somatic embryos produced from primay somatic embryos of P. vera L. Sarakhs variety. Bar 2 mm.
Fig. 8 in Direct somatic embryogenesis of drought resistance pistachio (Pistacia vera L.) and expression analysis of somatic embryogenesis-related genes
Fig. 8. Relative expression of selected embryogenesis-related genes on embryonic and non-embryonic samples of two genotypes (a: Sarakhs variety and b: Ghazvini cultivar) of P.vera L in three technical replication.ACT was used as a reference gene for data normalization.Mean value and standard deviation (SD) were presented for three biological replicates.The significance differences (p <.01) and non-significant differences showed with two stars and "ns", respectively.
Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs
<div> <div> <h2>Abstract</h2> <a href="https://github.com/christabel-bucao/fish-variability-across-organs/#abstract"></a></div> <p>Phenotypic variation among individuals plays a key role in evolution, since variation provides the material on which natural selection can act. One important link between genetic and phenotypic variation is gene expression. As for other phenotypes, the range of accessible expression variation is limited and biased by different evolutionary and developmental constraints. Gene expression variability broadly refers to the tendency of a gene to vary in expression (i.e., between individuals or cells) due to stochastic fluctuations or differences in genetic, epigenetic, or environmental factors, separately from the differences between e.g. organs. Variability due to biomolecular stochasticity (transcriptional ‘noise’) and cell-to-cell heterogeneity has been well-studied in isogenic populations of unicellular organisms such as bacteria and yeasts. However, for more complex organisms with multiple cells, tissues, and organs sharing the same genetic background, the interplay between inter-individual expression variability, gene and organ function, and gene regulation remains an open question. In this study, we used highly multiplexed 3’-end Bulk RNA Barcoding and sequencing (BRB-seq) to generate transcriptome profiles spanning at least nine organs in outbred individuals of three ray-finned fish species: zebrafish, Northern pike, and spotted gar. For each condition, we measured expression variation per gene independent of mean expression level. We observed that lowly variable genes are enriched in cellular housekeeping functions whereas highly variable genes are enriched in stimulus-response functions. Furthermore, genes with highly variable expression between individuals evolve under weaker purifying selection at the coding sequence level, indicating that intra-species gene expression variability predicts inter-species protein sequence divergence. Genes that are broadly expressed across organs tend to be both highly expressed and lowly variable between individuals, whereas organ-biased genes are typically highly variable within their top organ of expression. For genes with organ-biased expression profiles, we inferred differences in selective pressure on gene regulation depending on their top organ. We found that genes with peak expression in the brain have low inter-individual expression variability across non-nervous organs, suggesting stabilizing selection on regulatory evolution of brain-biased genes. Conversely, liver-biased genes have highly variable expression across organs, implying weaker regulatory constraints. These patterns show that gene regulatory mechanisms evolved differently based on constraints on the primary organ.</p> <h2>Directory Structure</h2> </div> <ul> <li> <p><code>config/</code>: Contains YAML file indicating package versions for conda environment</p> </li> <li> <p><code>data/</code>: Contains input data</p> <ul> <li><code>counts/</code>: Contains counts and UMI-deduplicated counts. Currently under embargo and will be made available upon acceptance for publication.</li> <li><code>gene_metadata/</code>: Contains gene biotype information from Ensembl</li> <li><code>sample_metadata/</code>: Contains sample metadata files for each species</li> <li><code>selectome/</code>: Contains selection statistics from the <a href="https://selectome.org/" rel="nofollow">Selectome</a> database<br><br></li> </ul> </li> <li> <p><code>results/</code>: Contains output files sorted by subfolders labeled after each step of the analysis pipeline. Only R notebook HTML files are available on the Git repository, please check Zenodo for R data files.</p> <ul> <li><code>run_pipeline.Rdata</code>: Contains all parameters used for each step of the analysis pipeline<br><br></li> </ul> </li> <li> <p><code>workflow/</code>: Contains scripts used for the analysis pipeline</p> <ul> <li><code>analysis/</code>: Contains all steps of the analysis pipeline, available as .Rmd files</li> <li><code>functions/</code>: Contains all functions used for analysis/</li> <li><code>renv/</code>: Used for package management in R</li> <li><code>run_pipeline.R</code>: Runs all the steps under analysis/</li> <li><code>run_go_figure.sh</code>: Runs <a href="https://gitlab.com/evogenlab/GO-Figure" rel="nofollow">GO-Figure!</a> 1.0.0 (downloaded separately)</li> <li><code>demultiplex_brbseq_fastq.sh</code>: Used for demultiplexing BRB-seq fastq files using <a href="https://github.com/DeplanckeLab/BRB-seqTools">BRB-seqTools</a> 1.6.1 (downloaded separately) for uploading to NCBI SRA</li> <li><code>rename_fastq_files.sh</code>: Used for renaming demultiplexed fastq files by mapping each barcode to their corresponding sample name</li> <li><code>renv.lock</code>: Lockfile for managing R package versions. Run <code>renv::restore()</code> to set up the R environment based on packages specified in the lockfile. All package versions used are also specified in the output HTML files under results/.</li> </ul> </li> </ul> <div> <h2>Species Codes</h2> </div> <ul> <li><strong>LOC</strong>: <em>Lepisosteus oculatus</em> (spotted gar)</li> <li><strong>ELU</strong>: <em>Esox lucius</em> (Northern pike)</li> <li><strong>DRE</strong>: <em>Danio rerio</em> (zebrafish)</li> </ul>
Data from: Multiple large inversions and breakpoint rewiring of gene expression in the evolution of the fire ant social supergene
Supergenes consist of co-adapted loci that segregate together and are associated with adaptive traits. In the fire ant Solenopsis invicta, two 'social' supergene variants regulate differences in colony queen number and other traits. Suppressed recombination in this system is maintained, in part, by a >9 Mb inversion, but the supergene is larger. Has the supergene in S. invicta undergone multiple large inversions? The initial gene content of the inverted allele of a supergene would be the same as that of the wild-type allele. So, how did the inversion increase in frequency? To address these questions, we cloned one extreme breakpoint in the fire ant supergene. In doing so, we found a second large (>800 Kb) rearrangement. Furthermore, we determined the temporal order of the two big inversions based on the translocation pattern of a third small fragment. Because the S. invicta supergene lacks evolutionary strata, our finding of multiple inversions may support an introgression model of the supergene. Finally, we showed that one of the inversions swapped the promoter of a breakpoint-adjacent gene, which might have conferred a selective advantage relative to the non-inverted allele. Our findings provide a rare example of gene alterations arising directly from an inversion event.
Data from: Gene expression correlates of facultative predation in the blow fly Chrysomya rufifacies (Diptera: Calliphoridae)
Effects of intraguild predation (IGP) on omnivores and detritivores are relatively understudied when compared to work on predator guilds. Functional genetic work in IGP is even more limited, but its application can help answer a range of questions related to ultimate and proximate causes of this behavior. Here we integrate behavioral assays and transcriptomic analysis of facultative predation in a blow fly (Diptera: Calliphoridae) to evaluate the prevalence, effect, and correlated gene expression of facultative predation by the invasive species Chrysomya rufifacies. Field work observing donated human cadavers indicated facultative predation by C. rufifacies on the native blow fly Cochliomyia macellaria was rare under undisturbed conditions, owing in part to spatial segregation between species. Laboratory assays under conditions of starvation showed predation had a direct fitness benefit (i.e., survival) to the predator. As a genome is not available for C. rufifacies, a de novo transcriptome was developed and annotated using sequence similarity to Drosophila melanogaster. Under a variety of assembly parameters, several genes were identified as being differentially expressed between predators and non-predators of this species, including genes involved in cell-to-cell signaling, osmotic regulation, starvation responses, and dopamine regulation. Results of this work were integrated to develop a model of the processes and genetic regulation controlling facultative predation.
Data from: Field performance of Bt eggplants (Solanum melongena L.) in the Philippines: Cry1Ac expression and control of the eggplant fruit and shoot borer (Leucinodes orbonalis Guenée)
Plants expressing Cry proteins from the bacterium, Bacillus thuringiensis (Bt), have become a major tactic for controlling insect pests in maize and cotton globally. However, there are few Bt vegetable crops. Eggplant (Solanum melongena) is a popular vegetable grown throughout Asia that is heavily treated with insecticides to control the eggplant fruit and shoot borer, Leucinodes orbonalis (EFSB). Herein we provide the first publicly available data on field performance in Asia of eggplant engineered to produce the Cry1Ac protein. Replicated field trials with five Bt eggplant open-pollinated (OP) lines from transformation event EE-1 and their non-Bt comparators were conducted over three cropping seasons in the Philippines from 2010–2012. Field trials documented levels of Cry1Ac protein expressed in plants and evaluated their efficacy against the primary target pest, EFSB. Cry1Ac concentrations ranged from 0.75–24.7 ppm dry weight with the highest in the terminal leaves (or shoots) and the lowest in the roots. Cry1Ac levels significantly increased from the vegetative to the reproductive stage. Bt eggplant lines demonstrated excellent control of EFSB. Pairwise analysis of means detected highly significant differences between Bt eggplant lines and their non-Bt comparators for all field efficacy parameters tested. Bt eggplant lines demonstrated high levels of control of EFSB shoot damage (98.6–100%) and fruit damage (98.1–99.7%) and reduced EFSB larval infestation (95.8–99.3%) under the most severe pest pressure during trial 2. Moths that emerged from larvae collected from Bt plants in the field and reared in their Bt eggplant hosts did not produce viable eggs or offspring. These results demonstrate that Bt eggplant lines containing Cry1Ac event EE-1 provide outstanding control of EFSB and can dramatically reduce the need for conventional insecticides.
Data from: Adult plasticity in African Cichlids: rapid changes in opsin expression in response to environmental light differences
Phenotypic plasticity allows organisms to adapt quickly to local environmental conditions and could facilitate adaptive radiations. Cichlids have recently undergone an adaptive radiation in Lake Malawi where they inhabit diverse light environments and tune their visual sensitivity through differences in cone opsin expression. While cichlid opsin expression is known to be plastic over development, whether adults remain plastic is unknown. Adult plasticity in visual tuning could play a role in cichlid radiations by enabling survival in changing environments and facilitating invasion into novel environments. Here we examine the existence of and temporal changes in adult visual plasticity of two closely related species. In complementary experiments, wild adult Metriaclima mbenji from Lake Malawi were moved to the lab under UV-deficient fluorescent lighting; while lab raised M. benetos were placed under UV-rich lighting designed to mimic light conditions in the wild. Surprisingly, adult cichlids in both experiments showed significant changes in the expression of the UV-sensitive single cone opsin, SWS1, in only three days. Modeling quantum catches in the light environments revealed a possible link between the light available to the SWS1 visual pigment and SWS1 expression. We conclude that adult cichlids can undergo rapid and significant changes in opsin expression in response to environmental light shifts that are relevant to their habitat and evolutionary history in Lake Malawi. This could have contributed to the rapid divergence characteristic of these fantastic fishes.
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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.