Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
54,099
datasets available to search
ShareScore release 0.9.0
Dataset results
54,099 results for “Expression”
Data from: A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations
Ranaviruses are responsible for a lethal, emerging infectious disease in amphibians and threaten their populations throughout the world. Despite this, little is known about how amphibian populations respond to ranaviral infection. In the United Kingdom, ranaviruses impact the common frog (Rana temporaria). Extensive public engagement in the study of ranaviruses in the UK has led to the formation of a unique system of field sites containing frog populations of known ranaviral disease history. Within this unique natural field system, we used RNA sequencing (RNA-Seq) to compare the gene expression profiles of R. temporaria populations with a history of ranaviral disease and those without. We have applied a RNA read filtering protocol that incorporates Bloom filters, previously used in clinical settings, to limit the potential for contamination that comes with the use of RNA-Seq in non-laboratory systems. We have identified a suite of 407 transcripts that are differentially expressed between populations of different ranaviral disease history. This suite contains genes with functions related to immunity, development, protein transport and olfactory reception amongst others. A large proportion of potential non-coding RNA transcripts present in our differentially expressed set provides first evidence of a possible role for long non-coding RNA (lncRNA) in amphibian response to viruses. Our read-filtering approach also removed significantly more bacterial reads from libraries generated from postitive disease history populations. Subsequent analysis revealed these bacterial read sets to represent distinct communities of bacterial species, which is suggestive of an interaction between ranavirus and the host microbiome in the wild.
Data from: Seasonally sympatric but allochronic: differential expression of hypothalamic genes in a songbird during gonadal development
Allochrony, the mismatch of reproductive schedules, is one mechanism that can mediate sympatric speciation and diversification. In songbirds, the transition into breeding condition and gonadal growth is regulated by the hypothalamic-pituitary-gonadal (HPG) axis at multiple levels. We investigated whether the difference in reproductive timing between two, seasonally sympatric subspecies of dark-eyed juncos (Junco hyemalis) was related to gene expression along the HPG axis. During the sympatric pre-breeding stage, we measured hypothalamic and testicular mRNA expression of candidate genes via qPCR in captive male juncos. For hypothalamic mRNA, we found our earlier breeding subspecies had increased expression of gonadotropin-releasing hormone (GnRH) and decreased expression of androgen receptor, estrogen receptor alpha, and mineralocorticoid receptor (MR). Subspecies did not differ in expression of hypothalamic gonadotropin-inhibitory hormone (GnIH) and glucocorticoid receptor (GR). While our earlier breeding subspecies had higher mRNA expression of testicular GR, subspecies did not differ in testicular luteinizing hormone receptor, follicle-stimulating hormone receptor, or MR mRNA expression levels. Our findings indicate increased GnRH production and decreased hypothalamic sensitivity to sex steroid negative feedback as factors promoting differences in the timing of gonadal recrudescence between recently diverged populations. Differential gene expression along the HPG axis may facilitate species diversification under seasonal sympatry.
Data from: Transcriptome profiles of sunflower reveal the potential role of microsatellites in gene expression divergence
The mechanisms by which natural populations generate adaptive genetic variation are not well understood. Some studies propose that microsatellites can function as drivers of adaptive variation. Here we tested a potentially adaptive role for transcribed microsatellites with natural populations of the common sunflower (Helianthus annuus L.) by assessing the enrichment of microsatellites in genes that show expression divergence across latitudes. Seeds collected from six populations at two distinct latitudes in Kansas and Oklahoma were planted and grown in a common garden. Morphological measurements from the common garden demonstrated that phenotypic variation among populations is largely explained by underlying genetic variation. An RNA–Seq experiment was conducted with 96 of the individuals grown in the common garden and differentially expressed (DE) transcripts between the two latitudes were identified. A total number of 825 DE transcripts were identified. DE transcripts and non-differentially expressed (NDE) transcripts were then scanned for microsatellites. The abundance of different motif lengths and types in both groups were estimated. Our results indicate that DE transcripts are significantly enriched with mononucleotide repeats and significantly depauperate in trinucleotide repeats. Further, the standardized mononucleotide repeat motif A and dinucleotide repeat motif AG were significantly enriched within DE transcripts while motif types, C, AT, ACC, and AAC in DE transcripts are significantly differentiated in microsatellite tract length between the two latitudes. The tract length differentiation at specific microsatellite motif types across latitudes and their enrichment within DE transcripts indicate a potential functional role for transcribed microsatellites in gene expression divergence in sunflower.
Manipulation of trait expression and pollination regime reveal the adaptive significance of spur length
<p class="Standardmedindrag">Understanding the mechanisms of adaptive population differentiation requires that both the functional and adaptive significance of divergent traits are characterized in contrasting environments. Here, we (a) determined the effects of floral spur length on pollen removal and receipt using plants with artificial spurs representing the species-wide variation in length, and (b) quantified pollinator-mediated selection on spur length and three traits contributing to floral display in two populations each of the short-spurred and the long-spurred ecotype of the orchid <i>Platanthera bifolia</i>. Both pollen receipt and removal reached a maximum at 28-29 mm long spurs in a short-spurred population visited by short-tongued moths. In contrast, pollen receipt increased linearly across the tested range (4-52 mm) and pollen removal was unrelated to spur length in a long-spurred population predominantly visited by a long-tongued moth. The experimentally documented effects on pollen transfer were not reflected in pollinator-mediated selection through female fitness or pollen removal indicating that the natural within-population variation in spur length was insufficient to result in detectable variation in pollen limitation. Our study illustrates how combining trait manipulation with analysis of causes and strength of phenotypic selection can illuminate the functional and adaptive significance of trait expression when trait variation is limited.</p>
Data from: Sperm competitive advantage of a rare mitochondrial haplogroup linked to differential expression of mitochondrial oxidative phosphorylation genes
Maternal inheritance of mitochondria creates a sex-specific selective sieve through which mitochondrial mutations harmful to males but not females accumulate and contribute to sexual differences in longevity and disease susceptibility. Because eggs and sperm are under disruptive selection, sperm are predicted to be particularly vulnerable to the genetic load generated by maternal inheritance, yet evidence for mitochondrial involvement in male fertility is limited and controversial. Here, we exploit the coexistence of two divergent mitochondrial haplogroups (A and B2) in a Neotropical arachnid to investigate the role of mitochondria in sperm competition. DNA profiling demonstrated that B2-carrying males sired more than three times as many offspring in sperm competition experiments than A males, and this B2 competitive advantage cannot be explained by female mitochondrial haplogroup or male nuclear genetic background. RNA-Seq of testicular tissues implicates differential expression of mitochondrial oxidative phosphorylation (OXPHOS) genes in the B2 competitive advantage, including a 22-fold upregulation of <i>atp8</i> in B2 males. Previous comparative genomic analyses have revealed functionally significant amino acid substitutions in differentially expressed genes, indicating that the mitochondrial haplogroups differ not only in expression but also in DNA sequence and protein functioning. However, mitochondrial haplogroup had no effect on sperm number or sperm viability, and, when females were mated to a single male, neither male haplogroup, female haplogroup nor the interaction between male/female haplogroup significantly affected female reproductive success. Our findings therefore suggest that mitochondrial effects on male reproduction may often go undetected in noncompetitive contexts and may prove more important in nature than is currently appreciated.
Data from: Expression of additive genetic variance for fitness in a population of partridge pea in two field sites
Despite the importance of adaptation in shaping biological diversity over many generations, little is known about populations' capacities to adapt at any particular time. Theory predicts that a population's rate of ongoing adaptation is the ratio of its additive genetic variance for fitness, VA (W), to its mean absolute fitness, W̅. We conducted a transplant study to quantify W̅ and standing VA (W) for a population of the annual legume Chamaecrista fasciculata in one field site from which we initially sampled it and another site where it does not currently occur naturally. We also examined genotype‐by‐environment interactions, G x E, as well as its components, differences between sites in VA (W) and in rank of breeding values for fitness. The mean fitness indicated population persistence in both sites, and there was substantial VA (W) for ongoing adaptation at both sites. Statistically significant G x E indicated that the adaptive process would differ between sites. We found a positive correlation between fitness of genotypes in the "home" and "away" environments, and G x E was more pronounced as the life cycle proceeds. This study exemplifies an approach to assessing whether there is sufficient VA (W) to support evolutionary rescue in populations that are declining.
The Influence of Lactobacillus Acidophilus on MUC1, GAL-3, IL-1β and IL-17 Gene Expression in BALB/c Mice Stomach
<p>Gene expression of MUC-1, GAL-3, IL-1 and IL-17 after treatment with low, moderate and high doses of Lactobacillus acidophilus ATCC 4356 in mice</p>
Distal and proximal hypoxia response elements cooperate to regulate organ-specific erythropoietin gene expression
<p>While it is well-established that distal hypoxia response elements (HREs) regulate hypoxia-inducible factor (HIF) target genes such as erythropoietin (Epo), an interplay between multiple distal and proximal (promoter) HREs has not been described so far. Hepatic Epo expression is regulated by a HRE located downstream of the <i>EPO</i> gene, but this 3' HRE is dispensable for renal <i>EPO</i> gene expression. We previously identified a 5' HRE and could show that both HREs direct exogenous reporter gene expression. Here, we show that whereas in hepatic cells the 3' but not the 5' HRE is required, in neuronal cells both the 5' and 3' HREs contribute to endogenous Epo induction. Moreover, two novel putative HREs were identified in the <i>EPO</i> promoter. In hepatoma cells HIF interacted mainly with the distal 3' HRE, but in neuronal cells HIF most strongly bound the promoter, to a lesser extent the 3' HRE, and not at all the 5' HRE. Interestingly, mutation of either of the two distal HREs abrogated HIF binding to the 3' and promoter HREs. These results suggest that a canonical functional HRE can recruit multiple, not necessarily HIF, transcription factors to mediate HIF binding to different distant HREs in an organ-specific manner.</p>
Data from: Changes in gene expression during female reproductive development in a colour polymorphic insect
<p>Pleiotropy (multiple phenotypic effects of single genes) and epistasis (gene interaction) have key roles in the development of complex phenotypes, especially in polymorphic taxa. The development of discrete and heritable phenotypic polymorphisms often emerges from major-effect genes that interact with other loci and have pleiotropic effects on multiple traits. We quantified gene expression changes during ontogenetic colour development in a polymorphic insect (damselfly: <i>Ischnura elegans</i>), with three heritable female morphs, one being a male mimic. This female colour polymorphism is maintained by male mating harassment and sexual conflict. Using transcriptome sequencing and <i>de novo</i> assembly, we demonstrate that all three morphs downregulate gene expression during early colour development. The morphs become increasingly differentiated during sexual maturation and when developing adult colouration. These different ontogenetic trajectories arise because the male-mimic shows accelerated (heterochronic) development, compared to the other female morphs. Many loci with regulatory functions in reproductive development are differentially regulated in the male-mimic, including upstream and downstream regulators of ecdysone signalling and transcription factors potentially influencing sexual differentiation. Our results suggest that long-term sexual conflict does not only maintain this polymorphism, but has also modulated the evolution of gene expression profiles during colour development of these sympatric female morphs.</p>
DB_Expressive_Arabic
<p>This is a free database of expressive speech for the Arabic language. The database contains 13 speakers uttering a set of 10 sentences in 4 expressive styles (neutral, sad, joyful, and angry). The utterances of the first speaker were annotated using Praat. The files are in the mp3, ogg and wav formats </p>
Mouse and Human Co-expression maps and supplementary material for: "A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels"
<p>Co-expression maps of the human and mouse species derived from microarray data for the first release of the GeneFriend tool.</p> <p>The two co-expression maps have been compared in order to discern similarities and differences between the two species. The results have been described in the manuscript titled: "A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels".</p> <p>The supplementary material of the manuscript have also been included in this repository.</p> <p> </p>
Dateset for article: Pupillary responses to infant facial expressions
<p>Pupil data related to study: <strong>Pupillary responses to infant facial expressions </strong></p> <p>Dataset contains "raw" eye-tracking data including timeseries of pupil diameter (.gazedata, SA pupil gazefiles anon.zip). The output of automated pupil analyses are included as Excel files (.xls, SA pupil xls.zip). These have been further restructured for statistical analyses into SPSS data files (.sav, SA pupil spss.zip). </p> <p>Matlab code and SPSS syntax for the analyses have been published and documented in GitHub repository: yrttiahoS/<strong>sa-pupil-analysis</strong></p>
Data on global expression of non-coding RNome in mice gastrocnemius muscle exposed to jararhagin, snake venom metalloproteinase
<p>This study describes the data on the global expression profile of small RNA (smRNAs) molecules in mice gastrocnemius muscle exposed to jararhagin, snake venom metalloproteinase. The data include smRNAs and microRNAs in mice gastrocnemius muscle challenged with Jararhagin (Jar; n=4) in the right paw or phosphate-buffered saline (PBS; control; n=4) in the left paw. smRNA-Seq libraries were generated after 24hs of exposure to PBS or jararhagin. </p>
R data set: The Cancer Genome Atlas Gene Expression data
<p>This compound data set comprises the following information from the The Cancer Genome Atlas:</p> <ul> <li>RNA-Seq counts for 60483 genes across 11093 samples</li> <li>HuEx 1.0 ST gene expression data for 18632 genes across 1211 samples</li> <li>clinical indicators for 11160 patients</li> </ul> <p>All gene expression data is annotated across ENSEMBL, ENTREZ and symbols. Samples are annotated by TCGA barcodes.</p> <p>To read the data set into R (requires 6 GB of RAM) use:</p> <p>tcga <- readRDS("tcga.rds")</p>
Analysis of gene expression in autoimmune and autoinflammatory diseases using GSEA
<p>This dataset contains the results of gene set enrichment analysis (GSEA) of gene expression in the studied diseases. The archive is organized in folders according the GEO accessions for the raw data (see table 1 of the main article). If multiple diseases were studied within one GEO data series, GSEA was performed for each disease separately. Healthy subject data included in each data series were used as reference. </p> <p>For example <strong><em>"GSE3365.IBD"</em></strong> folder contains GSEA for Crohn's disease (CD) and ulcerative colitis (US). The <em><strong>"results"</strong></em> folder in <em><strong>"GSE3365.IBD"</strong></em> contains two subfolders <strong><em>"GSE3365CDvcHC"</em></strong> and <em><strong>"GSE3365UCvcHC"</strong></em>, respectively. The results can be browsed with <em><strong>"index.html"</strong></em> files located in each subfolder. </p>
P. aeruginosa expression compendium for the PAO1 KEGG pathways case study in PathCORE.
<p>The normalized P. aeruginosa (PAO1) gene expression compendium uses datasets from ArrayExpress. Each gene expression vector is linearly normalized to the range between 0 and 1.</p> <p>The script used to download the PAO1 datasets and process all samples into a single expression compendium is available here: https://bitbucket.org/greenelab/eadage/src/d8a98586e0f448a5b7d497f5516cc4e241635361/data_collection/data_collection.sh</p>
Dataset for a Mouse and Rat heart trancriptomic and co-expression network analysis
<ul> <li>mouse_heart_data and rat_heart_expression contain GEO expression matrix for mouse and rat experiments.</li> <li>gse_gsm_mouse.txt and gse_gsm_rat.txt contain experiment IDs and series IDs from GEO.</li> <li>heart_quantNormData_mouse.tsv and heart_quantNormData_rat.tsv contain normalised expression matrices.</li> <li>heart_quantNormData_mouse_1sd.tsv and heart_quantNormData_rat_1sd.tsv contain the normalised expression matrices restricted to genes with a standard deviation higher than 1.</li> <li>fileForSCHypeThreshold0.5_heart.txt and fileForSCHypeThreshold0.75_heart.txt are the input for SCHype. schype_output_0.5th_heart.nodes.txt, schype_output_0.5th_heart.edges.txt, schype_output_0.75th_heart.nodes.txt and schype_output_0.75th_heart.edges.txt are the outputs.</li> <li>geneLists.zip contains gene lists used for ontology analysis (ENSEMBL gene id)</li> </ul>
Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
<pre>This repository contains data related to: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels Amanda J. Lea, Julie Peng, Julien F. Ayroles A preprint of this work can be found here: https://www.biorxiv.org/content/10.1101/2021.11.04.467311v2 Specifically, the filtered, normalized, and batch corrected gene expression data file (31Mar21_all_runs_voom_resid.txt) is provided along with the metadata. We also provide the output from matrix eQTL that was used as input for mashR. Scripts used to generate and analyze these data are provided here: https://github.com/AmandaJLea/LCLs_gene_exp</pre>
Joint profiling of cell morphology and gene expression during in vitro neurodevelopment
<p>Cell Painting processed data for "Joint profiling of cell morphology and gene expression during in vitro neurodevelopment".</p>
Coupled gene expression on single DNA molecules (raw single-molecule movies + description)
<p>Raw single-molecule movies and corresponding experimental details in description file</p>
ScienceDex guides
Understand access before you commit
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.