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.
25,372
datasets available to search
ShareScore release 0.7.1
Dataset results
25,372 results for “Transcriptomics”
Optimized Analytical Workflow for Single-Nucleus Transcriptomics in Main Metabolic Tissues
<p><span>Single-nucleus RNA sequencing (snRNA-seq) has emerged as a powerful approach for studying cellular heterogeneity in metabolic tissues. However, snRNA-seq analysis remains challenging due to low gene expression and data complexity. Here, we introduce an optimized analytical workflow for snRNA-seq data from 67 samples across four main metabolic tissues white adipose tissue, hypothalamus, muscle and liver. We emphasized the importance of key steps including ambient RNA removal, doublet identification, normalization and data integration to ensure accurate downstream analysis. </span><span>This workflow </span><span>offers a valuable resource for researchers in metabolism, facilitating deeper insights into cellular diversity and metabolic function through rigorous snRNA-seq analysis.</span></p>
Karyorelict ciliate transcriptome assemblies from project Karyocode
<p>Transcriptome assemblies of karyorelict ciliates, as described in the publication "Karyorelict ciliates use an ambiguous genetic code with context-dependent stop/sense codons" (https://doi.org/10.24072/pcjournal.141).</p> <p>Files are named with internal short names for each read library. The corresponding INSDC accessions of the read libraries are documented in the following spreadsheet:</p> <p>"Dataset accessions for comparative analysis of ciliate genetic codes", <a href="https://doi.org/10.17617/3.XWMBKT" target="_blank" rel="noopener">https://doi.org/10.17617/3.XWMBKT</a>, Edmond, V1; Table_S1.xlsx [fileName]</p> <p>Files with the suffix ".polyA_min7.fasta" contain the subset of assembled transcripts with a poly-A tail of at least 7 nt; this was done to filter out likely bacterial contaminants.</p>
Regulatory T cell therapy is associated with distinct immune regulatory lymphocytic infiltrates in kidney transplants: Spatial transcriptomic dataset and images
<p>The outputs of the NanoString GeoMx DSP platform were concatenated into three xlsx files, each illustrating a separate experiment along with their sample annotations. This technique analyzes protein or RNA abundance within regions of interest (ROIs) or specific cell segments selected based on histological features and immunofluorescence. In this repository, the concatenated GeoMx output files are presented, along with PowerPoint presentations for each biopsy that show immunofluorescence images of the selected ROIs and/or cell segments.</p> <ul> <li><strong>Protein_Full ROI:</strong> This experiment measured the abundance of 41 proteins in discrete regions of interest (ROIs) within transplant kidney biopsies.</li> <li><strong>Protein_Rare cell:</strong> This experiment measured the abundance of 40 proteins in specific cell segments, such as CD4+FoxP3- cells vs. CD4+FoxP3+ cells, within transplant kidney biopsies.</li> <li><strong>RNA:</strong> This experiment measured the abundance of 90 genes in discrete ROIs within transplant kidney biopsies.</li> </ul>
Transcriptomic Analysis Data for MSTN Mutations and Mechanisms of Muscle Hypertrophy in a New Guinea Pig Breed
<p>This dataset contains raw RNA-seq data from six guinea pig muscle samples, split into two groups:</p> <ul> <li><strong>Native guinea pigs (B1 to B3):</strong> Control group with no selective breeding.</li> <li><strong>Kuri breed guinea pigs (B4 to B6):</strong> Synthetic hybrid group selectively bred for increased muscle mass.<br>Each sample has paired-end FASTQ files (e.g., B1_1.fq.gz and B1_2.fq.gz).</li> </ul>
Supplementary material for paper "A fresh look at the celery collenchyma and parenchyma cell walls through a combination of biochemical, histochemical, and transcriptomic analyses"
Open the record for dataset details and reuse information.
Chromosome Numbers and Reproductive Life Cycles in Green Plants: A phylo-transcriptomic perspective
<p>The supplemental dataset for "Chromosome Numbers and Reproductive Life Cycles in Green Plants: A phylo-transcriptomic perspective."</p>
Optimized Analytical Workflow for Single-Nucleus Transcriptomics in Main Metabolic Tissues
<p>Single-nucleus RNA sequencing (snRNA-seq) has emerged as a powerful approach for studying cellular heterogeneity in metabolic tissues. However, snRNA-seq analysis remains challenging due to low gene expression and data complexity. Here, we introduce an optimized analytical workflow for snRNA-seq data from 67 samples across four main metabolic tissues white adipose tissue, hypothalamus, muscle and liver. We emphasized the importance of key steps including ambient RNA removal, doublet identification, normalization and data integration to ensure accurate downstream analysis. This workflow offers a valuable resource for researchers in metabolism, facilitating deeper insights into cellular diversity and metabolic function through rigorous snRNA-seq analysis.</p>
De novo transcriptome assembly Aegilops cylindrica
<p>De novo transcriptome assembly of Aegilops cylindrica was created using trinity v. 2.15.1. The assembly contains 285000 transcripts encoding for 174040 genes.</p>
De novo transcriptome assembly of the rockrose Helianthemum marifolium
<p>Illumina paired-end RNA sequences from leaves of 16 individuals of Helianthemum marifolium (four individuals from each of the four recognised taxonomic subspecies) were cleaned and assembled de novo using Trinity and Oases. EvidentialGene provides the curated assembled transcriptome containing 122002 transcripts, which are contained in the file Helianthemum_marifolium_transcriptome.fa.</p> <p>The predicted peptide sequences obtained with TransDecoder are in the file Helianthemum_marifolium_fa_transdecoder.pep.</p> <p>Gene ontology annotations from Trinotate are in the file Helianthemum_marifolium_trinotate_annotation.xls.</p>
Mitigating autocorrelation during spatially resolved transcriptomics data analysis
<p>Here we include the marmoset brain and mouse gut STARmap data introduced in the corresponding manuscript, "Mitigating autocorrelation during spatially resolved transcriptomics data analysis". We also include the mouse brain STARmap PLUS data that was used to demonstrate cross-species spatial integration and was previously published in Shi, He, Zhou et al. 2022.</p>
Supplementary data: The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia in a xenotransplantation model of Alzheimer's disease
<p>Supplementary data for: The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia in a xenotransplantation model of Alzheimer’s disease. </p> <p>Supplementary_Table1_QC: Excel sheet containing QC metrics for the RNA-seq data and the other containing QC metrics for the ATAC-seq data. </p> <p>Supplementary_Table2_DEGs: Excel sheet containing DeSeq2 differential expression analysis results for the following comparisons: APOE2 vs APOE3, APOE4 vs APOE3, APOE4 vs APOE2, APOE-KO vs APOE3. </p> <p>Supplementary_Table3_MAGMA_geneset_analysis_res: CSV file containing MAGMA gene set analysis results using the differentially expressed genes (FDR < 0.05) for the comparisons outlined in Supplementary_Table2_DEGs and three independent AD GWAS. </p> <p>Supplementary_Table4_DARs: Excel sheet containing DeSeq2 differential accessibility analysis results for the following comparisons: APOE2 vs APOE3, APOE4 vs APOE3, APOE4 vs APOE2, APOE-KO vs APOE3. </p> <p>Supplementary_Table5_sLDSC_res.csv: CSV file containing s-LDSC results using the consensus set of ATAC-seq peaks with three brain disorder GWAS (Alzheimer's disease, autism spectrum disorder, and amyotrophic lateral sclerosis). </p> <p>Supplementary_Table6_WGCNA_clusterProfiler_pathway_enrichment.csv: CSV file containing pathway enrichment results using two WGCNA-identified modules that were significantly upregulated in APOE2-expressing microglia. </p> <p>Supplementary_Table7_homer_motifEnrichment_res.xlsx: Excel sheet containing Homer motif enrichment analysis results using top 100 peaks with increased and decreased chromatin accessibility for APOE2 vs APOE3, APOE4 vs APOE3, and APOE4 vs APOE2.</p>
The Transcriptome Architecture of Polyomaviruses
<p>Processed data and code sufficient to reproduce findings from <strong>The Transcriptome Architecture of Polyomaviruses</strong>.</p>
Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes
<p><span><span><span>Cave-dwelling animals evolve distinct troglomorphic traits, such as loss of eyes, skin pigmentation, and augmentation of senses following long-term adaptation to the perpetual darkness. However, the molecular genetic mechanisms underlying these phenotypic variations remain unclear. In this study, we conducted comparative histology and comparative transcriptomics study of the skin of eight <i>Sinocyclocheilus</i> species (Cypriniformes: Cyprinidae) that included surface and cave-dwelling species. We analyzed four surface and four cavefish species by using next-generation sequencing, and a total of 802,798,907 clean reads were generated and assembled into 505,495,009 transcripts, which contributed to 1,037,334 unigenes. Bioinformatics comparisons of four different surface-cave fish groups revealed between 10,629 and 6442 significantly differentially expressed unigenes. Further, tens of differentially expressed genes (DEGs) potentially related to skin pigmentation were identified. Most of these DEGs (including <i>GNAQ</i>, <i>PKA</i>, <i>NRAS</i>, and <i>p38</i>) are downregulated in cavefish species. They are involved in key signaling pathways of pigment synthesis, such as the melanogenesis, Wnt, and MAPK pathways. This trend of downregulation was confirmed through qPCR experiments. This study will deepen our understanding of the formation of troglomorphic traits in cavefishes.</span></span></span></p>
Liver and Blood Expression Prediction Generated for Opportunities and challenges for transcriptome-wide association studies
<p>db files are in sqlite format and contain weights to calculate genetic predictors of gene expression</p> <p>Blood, Liver indicate the tissue where the RNA was extracted from</p> <p>Crohns and LDL indicate that prediction models were generated using SNPs available in the GWAS summary results used in the paper (Wainberg et al <a href="https://doi.org/10.1038/s41588-019-0385-z">https://doi.org/10.1038/s41588-019-0385-z</a>)</p> <p>*txt.gz filex contain covariances between SNPs needed to run the summary version of PrediXcan or other TWAS methods</p> <p>Information about the RNAseq data can be found here https://pubmed.ncbi.nlm.nih.gov/27540175/</p> <p>Sample size n=522</p>
Blood Cell Transcriptomics and Proteomics of Axial Spondyloarthritis patients undergoing adalimumab treatment
<p>This study aims at identifying molecular biomarkers differentiating good responders and non-responders to treatment with TNF inhibitors (TNFi), among patients with axial spondyloarthritis (axSpA). Publication: <em>Biomolecules</em> <strong>2024</strong>, <em>14</em>(3), 382; <a href="https://doi.org/10.3390/biom14030382">https://doi.org/10.3390/biom14030382</a></p>
Projection of high-dimensional genome-wide expression on SOM transcriptome landscapes: supplementary datasets
<p>This is a supplementary dataset with raw data, scripts, and complete analysis results for the paper "Supervised projection of high-dimensional genome-wide expression on SOM transcriptome landscapes". </p> <p>The archive contains three folders:</p> <p>1. "Simdata" folder contains data, scripts, and results of performance evaluation of extension SOM and supervised SOM with simulated data. </p> <p>2. "IBD" - folder contains data, scripts, and results of analysis of Inflammatory bowel disease datasets.</p> <p>3. "BC" - folder contains data, scripts, and results of analysis of breast cancer datasets.</p>
Supplementary Data for: Unique Transcriptomic Changes Underlie Hormonal Interactions During Mammary Histomorphogenesis in Female Pigs
<p>Successful lactation and the risk for developing breast cancer depend on growth and differentiation of the mammary gland (MG) epithelium that is regulated by ovarian steroids (17beta-estradiol [E] and progesterone [P]) and pituitary-derived prolactin (PRL). Given that the MG of pigs share histomorphogenic features present in the normal human breast, we sought to define the transcriptional responses within the MG of pigs following exposure to all combinations of these hormones. Hormone-ablated female pigs were administered combinations of E, medroxyprogesterone 17-acetate (source of P), and either haloperidol (to induce PRL) or 2-bromo-a-ergocryptine. We subsequently monitored phenotypic changes in the MG including mitosis, receptors for E and P (ESR1 and PGR), level of phosphorylated STAT5 (pSTAT5), and the frequency of terminal ductal lobular unit (TDLU) subtypes; these changes were then associated with all transcriptomic changes. Estrogen altered the expression of ~20% of all genes that mostly associated with mitosis, whereas PRL stimulated elements of fatty acid metabolism and an inflammatory response. Several outcomes, including increased pSTAT5, highlighted the ability of E to enhance PRL action. Regression of transcriptomic changes against several MG phenotypes revealed 1,669 genes correlated with proliferation, among which 29 were E-inducible. Additional gene expression signatures were associated with TDLU formation and the frequency of ESR1 or PGR. These data provide a link between the hormone-regulated genome and phenome of the MG in a species having a complex histoarchitecture like that in the human breast, and highlight an underexplored synergy between the actions of E and PRL during MG development.</p>
Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery
<p>This contains data described in detail in our paper, "Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery", where we develop a novel algorithm called RPath that prioritizes drugs for a given disease by reasoning over causal paths in a knowledge graph (KG), guided by both drug-perturbed as well as disease-specific transcriptomic signatures.</p>
Single-Cell Transcriptomic Atlas of Human Cardiac Arteries
<p>This dataset contains the processed single-cell RNA sequencing data and code in article "Single-Cell Transcriptomic Atlas of Different Human Cardiac Arteries Identifies Cell Types Associated With Vascular Physiology". Please refer to the article for the detailed sample information, sequencing and data processing methods.</p> <p>cardiac_arteries_processed_data.zip: Processed single-cell RNA sequencing data from Cellranger output.</p> <p>merged_all_samples: The output of Cellranger aggr, merging processed data of all samples.</p> <p>Abbreviations in samples: AO, aorta; CA, coronary artery; PA, pulmonary artery.</p> <p>notebook.zip: Jupyter notebooks containing code for data analysis.</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>
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.