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441 results for “transcriptome comparison”
Comparison of spatial transcriptomics technologies used for tumor cryosections
<p>This repository contains data from a spatial transcriptomics (ST) analysis of brain tumor cryosections (medulloblastoma with extensive nodularity, MBEN). It is associated with the preprint by Rademacher, Huseynov, Bortolomeazzi et al. 2024, <em>bioRxiv</em>, <a href="https://doi.org/10.1101/2024.04.03.586404">https://doi.org/10.1101/2024.04.03.586404</a>, that has a full description of the work. In the study four imaging-based ST methods – RNAscope HiPlex, Molecular Cartography, MERFISH/Merscope, and Xenium – as well as sequencing-based ST (Visium) and single cell RNA sequencing of dissociated nuclei (snRNA-seq) were compared. The files provided here are described in readme.txt and include the transcript count matrices acquired on the Visium platform as well as Seurat objects of the data and analysis results for the comparison of the different technologies. The data for snRNA-seq, RNAscope HiPlex and Molecular Cartography included in the Seurat objects are based on the primary data acquired in a previous study (Ghasemi et al. 2024, Nat Commun, <a href="https://doi.org/10.1038/s41467-023-44117-x">https://doi.org/10.1038/s41467-023-44117-x</a>). </p>
Supplementary data for: Comparison of transcriptomic profiles between HFPO-DA and prototypical PPARa, PPARg, and cytotoxic agents in mouse, rat, and pooled human hepatocytes
<p>Like many per- or polyfluorinated alkyl substances (PFAS), toxicity studies with HFPO-DA (ammonium,2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)-propanoate), a short-chain PFAS used in the manufacture of some types of fluorinated polymers, indicate that the liver is the primary target of toxicity in rodents following oral exposure. Although the current weight of evidence supports the PPARa mode of action (MOA) for liver effects in HFPO-DA-exposed mice, alternate MOAs have also been hypothesized including PPARg or cytotoxicity. To further evaluate the MOA for HFPO-DA in rodent liver, transcriptomic analyses were conducted on samples from primary mouse, rat and pooled human hepatocytes treated for 12, 24 or 72 hours with various concentrations of HFPO-DA, or agonists of PPARa (GW7647), PPARg (rosiglitazone), or cytotoxic agents (i.e., acetaminophen or d-galactosamine). Concordance analyses of enriched pathways across chemicals within each species demonstrated greatest concordance between HFPO-DA and PPARa agonist GW7647-treated hepatocytes compared to the other chemicals evaluated. These findings were supported by benchmark concentration modeling and predicted upstream regulator results. In addition, transcriptomic analyses across species demonstrated a greater transcriptomic response in rodent hepatocytes treated with HFPO-DA or agonists of PPARa or PPARg, indicating rodent hepatocytes are more sensitive to HFPO-DA or PPARa/g agonist treatment. These results are consistent with previously published transcriptomic analyses and further support that liver effects in HFPO-DA-exposed rodents are mediated through rodent-specific PPARa signaling mechanisms as part of the MOA for PPARa activator-induced rodent hepatocarcinogenesis. Thus, effects observed in mouse liver are not appropriate endpoints for toxicity value development for HFPO-DA in human health risk assessment.</p>
Supplementary data for: Comparison of phenotypic and transcriptomic profiles between HFPO-DA and prototypical PPARα, PPARγ, and cytotoxic agents in wild-type and Ppara-null mouse livers
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Supplementary data for: Comparison of transcriptomic profiles between HFPO-DA and prototypical PPARa, PPARg, and cytotoxic agents in wild-type and PPARa knockout mouse hepatocytes
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Supplementary data for: Comparison of transcriptomic profiles between HFPO-DA and prototypical PPARa, PPARg, and cytotoxic agents in mouse, rat, and pooled human hepatocytes
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Data from: Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii
<p>Different host species often differ considerably in susceptibility to a given pathogen, but the causes of such differences are rarely known. The natural hosts of the tick-transmitted bacterium <i>Borrelia afzelii</i>, which is one of causative agents of Lyme borreliosis in humans, include a variety of small mammals like voles and mice. Previous studies have shown that <i>B. afzelii-</i>infected bank voles (<i>Myodes glareolus</i>) have about ten times higher bacterial load than infected yellow-necked mice (<i>Apodemus flavicollis</i>), indicating that these two species differ in resistance. In this study, we compared the immune response to <i>B. afzelii </i>infection in these host species by using RNA-sequencing to quantify gene expression in spleen. Gene set enrichment analysis (GSEA) showed that several immune pathways were down-regulated in infected animals in both bank voles and yellow-necked mice. Moreover, IFNα response was up-regulated in <i>B. afzelii</i>-infected yellow-necked mice, while IL6 signaling and the complement pathway were down-regulated in infected bank voles; differences in regulation of these three pathways between bank voles and yellow-necked mice could thus contribute to the difference in resistance to <i>B. afzelii</i> between the species. This study provides knowledge of gene expression induced by a zoonotic pathogen in its natural host, and possible species-specific regulation of immune responses associated with resistance.</p>
Comparison of Fixed Single Cell RNA-seq Methods to Enable Transcriptome Profiling of Neutrophils in Clinical Samples
<p>Monitoring neutrophil gene expression is a powerful tool for understanding disease mechanisms, developing new diagnostics, therapies and optimizing clinical trials. Neutrophils are sensitive to the processing, storage and transportation steps that are involved in clinical sample analysis. This study is the first to evaluate the capabilities of technologies from 10X Genomics, PARSE Biosciences, and HIVE (Honeycomb Biotechnologies) to generate high-quality RNA data from human blood-derived neutrophils. Our comparative analysis shows that all methods produced high quality data, importantly capturing the transcriptomes of neutrophils. 10X FLEX cell populations in particular showed a close concordance with the flow cytometry data. Here, we establish a reliable single-cell RNA sequencing workflow for neutrophils in clinical trials: we offer guidelines on sample collection to preserve RNA quality and demonstrate how each method performs in capturing sensitive cell populations in clinical practice.</p> <p><strong>This dataset includes the FACS, 10X 3', Parse, 10X Flex, and Hive data and analysis.</strong></p>
Genomic, transcriptomic and proteomic comparison of MRSA CC398 isolates collected from human and wild animal samples (Genome assembly and annotation dataset)
<p>This dataset includes the assembled contigs (.fasta and .gbk files), the nucleotide sequences of the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) (.ffn files) and the respective amino acid sequences of the translated CDS sequences (.faa files) for the following methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) strains: MRSA CC398 isolates recovered from humans, namely C5621 and C9017, and from a wild boar, namely OR418.</p> <p>All raw sequence reads used in this study were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB35102).</p>
Comparison of Fixed Single Cell RNA-seq Methods to Enable Transcriptome Profiling of Neutrophils in Clinical Samples - Time course data
<p>Monitoring neutrophil gene expression is a powerful tool for understanding disease mechanisms, developing new diagnostics, therapies and optimizing clinical trials. Neutrophils are sensitive to the processing, storage and transportation steps that are involved in clinical sample analysis. This study is the first to evaluate the capabilities of technologies from 10X Genomics, PARSE Biosciences, and HIVE (Honeycomb Biotechnologies) to generate high-quality RNA data from human blood-derived neutrophils. Our comparative analysis shows that all methods produced high quality data, importantly capturing the transcriptomes of neutrophils. 10X FLEX cell populations in particular showed a close concordance with the flow cytometry data. Here, we establish a reliable single-cell RNA sequencing workflow for neutrophils in clinical trials: we offer guidelines on sample collection to preserve RNA quality and demonstrate how each method performs in capturing sensitive cell populations in clinical practice.</p> <p><strong>This dataset includes only the 10X Flex time course data and analysis.</strong></p>
Data from: Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii
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Transcriptome-wide comparisons and virulence gene polymorphisms of host-associated genotypes of the cnidarian parasite Ceratonova shasta in salmonids
<p><i>Ceratonova shasta</i> is an important myxozoan pathogen affecting the health of salmonid fishes in the Pacific Northwest of North America. <i>C. shasta</i> exists as a complex of host-specific genotypes, some with low to moderate virulence, and one that causes a profound, lethal infection in susceptible hosts. High throughput sequencing methods are powerful tools for discovering the genetic basis of these host/virulence differences, but deep sequencing of myxozoans has been challenging due to extremely fast molecular evolution of this group, yielding strongly divergent sequences that are difficult to identify, and unavoidable host contamination. We designed and optimized different bioinformatic pipelines to address these challenges. We obtained a unique set of comprehensive, host-free myxozoan RNA-seq data from <i>C. shasta </i>genotypes of varying virulence from different salmonid hosts. Analyses of transcriptome-wide genetic distances and maximum likelihood multigene phylogenies elucidated the evolutionary relationship between lineages and demonstrated the limited resolution of the established Internal Transcribed Spacer marker for <i>C. shasta</i> genotype identification, as this marker fails to differentiate between biologically distinct genotype II lineages from coho salmon and rainbow trout. We further analyzed the datasets based on polymorphisms in two gene groups related to virulence: cell migration and proteolytic enzymes including their inhibitors. The developed SNP-calling pipeline identified polymorphisms between genotypes and demonstrated that variations in both motility and protease genes were associated with different levels of virulence of <i>C. shasta</i> in its salmonid hosts. The prospective use of proteolytic enzymes as promising candidates for targeted interventions against myxozoans in aquaculture is discussed. We developed host-free transcriptomes of a myxozoan model organism from strains that exhibited different degrees of virulence, as a unique source of data that will foster functional gene analyses and serve as a base for the development of potential therapeutics for efficient control of these parasites.</p>
Technology comparison (image-based spatial transcriptomics)- annotated datasets
<p>This repository contains all the AnnData datasets, regionally annotated, used in the comparison of image-based spatial transcriptomics technologies (Marco Salas et al. 2024)</p>
Data from: Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: performance and a comparison with AFLP-derived distances
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Data from: Microsatellites for the marsh Fritillary butterfly: de novo transcriptome sequencing, and a comparison with amplified fragment length polymorphism (AFLP) markers
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Data from: A comparison between transcriptome sequencing and 16S metagenomics for detection of bacterial pathogens in wildlife
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Transcriptome-wide comparisons and virulence gene polymorphisms of host-associated genotypes of the cnidarian parasite Ceratonova shasta in salmonids
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Expression and comparison of unigene in the transcriptome in Siniperca chuatsi
<p>Muscle from 3-month old individuals of different sizes was used for transcriptome analysis. After screening, 39005 unigenes were annotated into four databases, including Nr (38833, 52.9%), Swissprot (337479, 46.0%), COG (10926, 14.8%) and KEGG (19791, 26.9%). Finally, the results was annotated by Nr database which defined the maximum number of unigenes.</p>
Petal size in rapeseed: novel QTL and candidate genes detected through genome-wide association study and transcriptome comparison
<p>Petal size determines the value of ornamental plants, and thus their economic worth. However, the molecular mechanisms controlling petal size remain unclear in most non-model species. To identify quantitative trait loci and candidate genes regulating petal size in rapeseed (<i>Brassica napus</i>), we performed a genome-wide association study (GWAS) using data from 588 accessions over three consecutive years. We detected 17 significant single nucleotide polymorphisms (SNPs) associated with petal size, with the most significant SNPs located on chromosomes A05 and C06. A combination of GWAS and transcriptomic sequencing based on two accessions with extreme differences in petal size identified 11 differentially expressed genes (DEGs) that may control petal size variation in rapeseed. In particular, <i>BnaA05</i><i>.</i><i>RAP2.2</i> homologous to <i>RAP2.2</i> in rapeseed may be a critical gene negatively influencing petal size through the ethylene signaling pathway. In addition, a comparison of petal epidermal cells indicated that petal size differences between the two extreme accessions were determined mainly by cell number differences. Finally, we propose a preliminary model for the control of petal size in rapeseed. Our results provide insights into the genetic mechanisms regulating petal size, and also lay the foundation for a better understanding of petal development in plants.</p>
Petal size in rapeseed: novel QTL and candidate genes detected through genome-wide association study and transcriptome comparison
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Data from: Understanding the loss of maternal care in avian brood parasites using preoptic area transcriptome comparisons in brood parasitic and non-parasitic blackbirds
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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.