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.
3,818
datasets available to search
ShareScore release 0.9.0
Dataset results
3,818 results for “Differential Expression”
Supplemental Figure for Circulating MiRNA 887 is Differentially Expressed in ARDS and Modulates Endothelial Function
<p>Supplemental Figure 1. A) Among subjects who developed ARDS, there was no difference in plasma miR-887-3p levels between subjects who were (n = 9) or were not (n = 10) receiving mechanical ventilation when the sample was collected. B) Similarly, among subjects who did not develop ARDS, there was no difference in plasma-887-3p levels between subjects who were (n = 13) or were not (n = 9) receiving mechanical ventilation when the sample was collected. Standard deviation shown.</p>
Differentially expressed alternatively spliced genes associated with carcass and meat traits in Nelore cattle
<p>Quality control report from Qualimap 2.2.1. Basic statistics of the alignment (number of reads, coverage, GC-content, junction detection, etc.) were summarized. Quality control was performed with RNA-seq data from muscle tissue of Nelore Cattle. Transcript data were used to identify genes for which alternatively spliced transcripts were differentially expressed in ribeye muscle tissue between Nelore cattle that differed in their ribeye muscle area (REA) or intramuscular fat content (IF).</p>
Data Repository: Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes
<p>Data repository for the scMappR manuscript:</p> <p>Abstract from biorXiv (https://www.biorxiv.org/content/10.1101/2020.08.24.265298v1.full).</p> <p>RNA sequencing (RNA-seq) is widely used to identify differentially expressed genes (DEGs) and reveal biological mechanisms underlying complex biological processes. RNA-seq is often performed on heterogeneous samples and the resulting DEGs do not necessarily indicate the cell types where the differential expression occurred. While single-cell RNA-seq (scRNA-seq) methods solve this problem, technical and cost constraints currently limit its widespread use. Here we present single cell Mapper (scMappR), a method that assigns cell-type specificity scores to DEGs obtained from bulk RNA-seq by integrating cell-type expression data generated by scRNA-seq and existing deconvolution methods. After benchmarking scMappR using RNA-seq data obtained from sorted blood cells, we asked if scMappR could reveal known cell-type specific changes that occur during kidney regeneration. We found that scMappR appropriately assigned DEGs to cell-types involved in kidney regeneration, including a relatively small proportion of immune cells. While scMappR can work with any user supplied scRNA-seq data, we curated scRNA-seq expression matrices for ∼100 human and mouse tissues to facilitate its use with bulk RNA-seq data alone. Overall, scMappR is a user-friendly R package that complements traditional differential expression analysis available at CRAN.</p>
Data from: Differential gene expression according to race and host plant in the pea aphid
Host-race formation in phytophagous insects is thought to provide the opportunity for local adaptation and subsequent ecological speciation. Studying gene expression differences amongst host races may help to identify phenotypes under (or resulting from) divergent selection and their genetic, molecular and physiological bases. The pea aphid (Acyrthosiphon pisum) comprises host races specializing on numerous plants in the Fabaceae and provides a unique system for examining the early stages of diversification along a gradient of genetic and associated adaptive divergence. In this study, we examine transcriptome-wide gene expression both in response to environment and across pea aphid races selected to cover the range of genetic divergence reported in this species complex. We identify changes in expression in response to host plant, indicating the importance of gene expression in aphid–plant interactions. Races can be distinguished on the basis of gene expression, and higher numbers of differentially expressed genes are apparent between more divergent races; these expression differences between host races may result from genetic drift and reproductive isolation and possibly divergent selection. Expression differences related to plant adaptation include a subset of chemosensory and salivary genes. Genes showing expression changes in response to host plant do not make up a large portion of between-race expression differences, providing confirmation of previous studies' findings that genes involved in expression differences between diverging populations or species are not necessarily those showing initial plasticity in the face of environmental change.
Data from: Genomic identification, characterization and differential expression analysis of SBP-box gene family in Brassica napus
Background: SBP-box genes belong to one of the largest families of transcription factors. Though members of this family have been characterized to be important regulators of diverse biological processes, information of SBP-box genes in the third most important oilseed crop Brassica napus is largely undefined. Results: In the present study, by whole genome bioinformatics analysis and transcriptional profiling, 58 putative members of SBP-box gene family in oilseed rape (Brassica napus L.) were identified and their expression pattern in different tissues as well as possible interaction with miRNAs were analyzed. In addition, B. napus lines with contrasting branch angle were used for investigating the involvement of SBP-box genes in plant architecture regulation. Detailed gene information, including genomic organization, structural feature, conserved domain and phylogenetic relationship of the genes were systematically characterized. By phylogenetic analysis, BnaSBP proteins were classified into eight distinct groups representing the clear orthologous relationships to their family members in Arabidopsis and rice. Expression analysis in twelve tissues including vegetative and reproductive organs showed different expression patterns among the SBP-box genes and a number of the genes exhibit tissue specific expression, indicating their diverse functions involved in the developmental process. Forty-four SBP-box genes were ascertained to contain the putative miR156 binding site, with 30 and 14 of the genes targeted by miR156 at the coding and 3′UTR region, respectively. Relative expression level of miR156 is varied across tissues. Different expression pattern of some BnaSBP genes and the negative correlation of transcription levels between miR156 and its target BnaSBP gene were observed in lines with different branch angle. Conclusions: Taken together, this study represents the first systematic analysis of the SBP-box gene family in Brassica napus. The data presented here provides base foundation for understanding the crucial roles of BnaSBP genes in plant development and other biological processes.
Raw data for the article: Investigating the Differential Circulating microRNA Expression in Adolescent Females with Severe Idiopathic Scoliosis: A Proof-of-Concept Observational Clinical Study
<p>Adolescent Idiopathic Scoliosis (AIS) is the most common form of three-dimensional spinal disorder in adolescents between the ages of 10 and 18 years of age, most commonly diagnosed in young women when severe disease occurs. Patients with AIS are characterized by abnormal skeletal growth and reduced bone mineral density. The etiology of AIS is thought to be multifactorial, involving both environmental and genetic factors, but to date, it is still unknown. Therefore, it is crucial to further investigate the molecular pathogenesis of AIS and to identify biomarkers useful for predicting curve progression. In this perspective, the relative abundance of a panel of microRNAs (miRNAs) was analyzed in the plasma of 20 AIS patients and 10 healthy controls (HC). The data revealed a significant group of circulating miRNAs dysregulated in AIS patients compared to HC. Further bioinformatic analyses evidenced a more restricted expression of some miRNAs exclusively in severe AIS females. These include some members of the miR-30 family, which are considered promising regulators for treating bone diseases. We demonstrated circulating extracellular vesicles (EVs) from severe AIS females contained miR-30 family members and decreased the osteogenic differentiation of mesenchymal stem cells. Proteomic analysis of EVs highlighted the expression of proteins associated with orthopedic disease. This study provides preliminary evidence of a miRNAs signature potentially associated with severe female AIS and suggests the corresponding vesicular component may affect cellular mechanisms crucial in AIS, opening the scenario for in-depth studies on prognostic differences related to gender and grade.</p>
DIFFERENTIAL EXPRESS DIAGNOSIS OF ECHINOCOCCOSIS AND PECILOMYCOSIS OF THE LUNGS
Open the record for dataset details and reuse information.
Differential gene expression in aortae isolated from mice consuming normal water or that containing polystyrene beads
<p>Microplastics (MP) derived from the degradation of larger polymers or synthesized for commercial purposes are ubiquitous in the environment and have found their way into food supplies and water systems where human consumption is inevitable. We hypothesize that MP ingestion promotes CVD risk and atherosclerosis. To test this idea, we supplied ApoE-/- mice with normal chow and either normal water or that containing polystyrene (PS) beads (0.5 μm in diameter; dose of 1 μg/ml). After 20 weeks of exposure, we evaluated lesion formation and gene expression data in cardiovascular tissue. We observed that mice consuming the PS water had increased lesion size compared to those mice consuming normal water. but no changes in plasma lipids or cytokines. An RNAseq analysis of collected aortae identified 1622 differentially expressed genes between the groups, consisting of 414 that were up-regulated and 1208 that were down-regulated. </p>
Expression proteomics and histone analysis reveals extensive chromatin network changes and a role for histone tail trimming during cellular differentiation
Open the record for dataset details and reuse information.
Figure 3 in Differential gene expression pattern and plasma sex steroids during testicular development in Genyatremus luteus (Perciforme: Haemulidae) (Bloch, 1790)
Figure 3. Gene expression of er (A) andlhr (B) in the male gonad of Genyatremus luteus individuals at different maturation stages. Columns represent arithmetic mean and standard error of the mean. abc Different letters indicate statistically significant difference (p<0.05).
Data from: miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRs
<p>These datasets can be used to reproduce all analyses from the publication "miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRs" in conjunction with codes found at https://github.com/mccall-group/miRglmm_paper. </p> <p>"Monocyte_data_subset.rda", "monocyte_exact_subset_filtered2.rda" and "sims_N100_m2_s1_rtruncnorm.rda" can be used to reproduce the simulation analysis. </p> <p>"panel_B_SE.rda" and "ERCC_filtered.rda" can be used to reproduce the ERCC synthetic data analysis with known ground truth.</p> <p>"study89_data_subset.rda" and "study89_data_subset_filtered2.rda" can be used to reproduce the immune cell-type analysis. </p> <p>"bladder_testes_data_subset.rda" and "bladder_testes_data_subset_filtered2.rda" can be used to reproduce the bladder vs testes tissue analysis.</p>
Table S5 Differentially Expressed genes
Open the record for dataset details and reuse information.
Figure 5 in Identification and expression of Dmrt1 and Sox9 during the gonadal differentiation of Rana chensinensis
Figure 5. Expression of rcDmrt1 and rcSox9 in GMC/gonads of R. chensinensis tadpoles at stages 26–46. M, Male; F, female.
Data from: Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments.
Transcriptome Shotgun Sequencing (RNA-seq) has been readily embraced by geneticists and molecular ecologists alike. As with all high-throughput technologies, it is critical to understand which analytic strategies are best suited and which parameters may bias the interpretation of the data. Here we use a comprehensive simulation approach to explore how various features of the transcriptome (complexity, degree of polymorphism π, alternative splicing), technological processing (sequencing error ε, library normalization) and bioinformatic workflow (de novo vs. mapping assembly, reference genome quality) impact transcriptome quality and inference of differential gene expression (DE). We find that transcriptome assembly and gene expression profiling (edgeR vs. baySeq software) works well even in the absence of a reference genome, and is robust across a broad range of parameters. We advise against library normalization, and in most situations advocate mapping assemblies to an annotated genome of a divergent sister clade, which generally outperformed de novo assembly (Trans-Abyss, Trinity, SOAPdenovo-Trans). Transcriptome complexity (size, paralogs, alternative splicing isoforms) negatively affected the assembly and DE profiling, whereas the effects of sequencing error and polymorphism were almost negligible. Finally, we highlight the challenge of gene name assignment for de novo assemblies, the importance of mapping strategies, and raise awareness of challenges associated with the quality of reference genomes. Overall, our results have significant practical and methodological implications, and can provide guidance in the design and analysis of RNA-seq experiments, particularly for organisms where genomic background information is lacking.
Data from: Near absence of differential gene expression in the retina of rainbow trout after exposure to a magnetic pulse: implications for magnetoreception
The ability to perceive Earth's magnetic field, or magnetoreception, exists in numerous animals. Although the mechanism underlying magnetoreception has not been clearly established in any species, in salmonid fish it is hypothesized to occur by means of crystals of magnetite associated with nervous tissue such as the brain, olfactory organ, or retina. In this study, rainbow trout (Oncorhynchus mykiss) were exposed to a brief magnetic pulse known to disrupt magnetic orientation behavior in several animals. Changes in gene expression induced by the pulse were then examined in the retina. Analyses indicated that the pulse elicited differential expression of only a single gene, gamma-crystallin M3-like (crygm3). The near-absence of an effect of the magnetic pulse on gene expression in the retina stands in sharp contrast to a recent study in which 181 genes were differentially expressed in brain tissue of O. mykiss after exposure to the same pulse. Overall, our results suggest either that magnetite-based magnetoreceptors in trout are not located in the retina, or else that they are unaffected by magnetic pulses that can disrupt magnetic orientation behavior in animals.
Significant differentially expressed genes (DEG) for midgut tissue from bees maintained for four hours at 35°C or 45°C
<p><span><span>Honey bee colonies in the United States have suffered from increased die-off in the last few years with a complex set of interacting stresses playing a key role. With changing climate, an increase in the frequency of severe weather events, such as heat waves, is anticipated. Understanding how these changes may contribute to stress in honey bees is crucial. Individual honey bees appear to have a high capacity to endure thermal stress. One reason for this high-level endurance is likely their robust HSR which contributes to thermotolerance at the cellular level. However, less is known about other mechanisms of thermotolerance, especially those operating at the tissue level. To elucidate other determinants of this resilience in this species, we used <span>thermal stress coupled with RNAseq and identified broad transcriptional remodeling of a number of key signaling pathways in the honey bee, including those pathways known to be involved in digestive tract regeneration in the fruit fly such as the Hippo and JAK/STAT pathways. We also observe cell death and shedding of epithelial cells, which likely leads to induction of this regenerative transcriptional program. </span>We found that thermal stress affects many of these pathways in other tissues, suggesting a shared program of damage response. This study provides important foundational characterization of the tissue damage response program in this key pollinating species. In addition, our data suggest that a robust regeneration program may also be a critical contributor to thermotolerance at the tissue level, a possibility which warrants further exploration in this and other species. </span></span></p>
Confronting false discoveries in single-cell differential expression
<p>A repository containing 18 benchmarking datasets for single-cell method development.</p>
Fig. 6 in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 6. Relative expression of con (control) and tre (treat) genes by qRT-PCR (A) and RNA-Seq (B).
Fig. 2 in Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress
Fig. 2. Comparison of expression of differential unigenes identified between Treat and Control.
Differential Expression of CD200 in B-chronic Lymphoproliferative Disorders by Multicolour Flow Cytometry
ClinicalTrials.gov study NCT03712488. IPD Sharing: Not stated. Countries: 0. Publications: 5.
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.