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.
869
datasets available to search
ShareScore release 0.9.0
Dataset results
869 results for “Wnt.”
Stimulating Wnt signaling reveals context-dependent genetic effects on gene regulation in primary human neural progenitors
<p>Summary statistics for chromatin accessibility and gene expression quantitative trait loci (ca/eQTLs) from Matoba, N., Le, B.D., Valone, J.M. <em>et al.</em> Stimulating Wnt signaling reveals context-dependent genetic effects on gene regulation in primary human neural progenitors. <em>Nat Neurosci</em> (2024). https://doi.org/10.1038/s41593-024-01773-6</p>
Data for Altered Glia-Neuron Communication in Alzheimer's Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq
<p><strong>data.tar.gz contains all files from the data directory associated with the 230313_TS_CCCinHumanAD GitHub project and includes the following:</strong></p><ul><li><strong>CellRangerCounts/</strong><ul><li><strong>GSE157827/</strong><ul><li><strong>post_soupX/ : </strong>contains 21 directories for 21 samples, which each contain 3 files obtained from ambient RNA removal with soupX. Below is a representative example, but this repo contains 1 directory per sample:<ul><li><strong>SAMN16100290_S01_AD/</strong><ul><li><strong>barcodes.tsv</strong></li><li><strong>genes.tsv</strong></li><li><strong>matrix.mtx</strong></li></ul></li></ul></li><li><strong>pre_soupX/ : </strong>contains 21 directories for 21 samples, which each contain 2 files obtained from Cell Ranger after aligning fastq files to the reference genome. Below is a representative example, but this repo contains 1 directory per sample:<ul><li><strong>SAMN16100290_S01_AD/</strong><ul><li><strong>filtered_feature_ bc_matrix.h5</strong></li><li><strong>Raw_feature_bc_matrix.h5</strong></li></ul></li></ul></li></ul></li><li><strong>GSE174367/ : </strong>contains 19 directories for 19 samples, which contain 3 files each from Cell Ranger alignment of fastq files to the reference genome. Below is a representative example, but this repo contains 1 directory per sample:<ul><li><strong>SAMN19128610_S1_CTRL/</strong><ul><li><strong>barcodes.tsv</strong></li><li><strong>genes.tsv</strong></li><li><strong>Matrix.mtx</strong></li></ul></li></ul></li></ul></li><li><strong>ccc/</strong><ul><li><strong>nichenet_grn/</strong><ul><li><strong>gr_network_human_21122021.rds : </strong>accessed in October 2023, gene regulation network – gene regulatory information from MultiNicheNet</li><li><strong>ligand_tf_matrix_nsga2r_final.rds: </strong>accessed in October 2023, ligand tf matrix for signaling path determination from MultiNicheNet</li><li><strong>signaling_network_human_21122021.rds : </strong>accessed in October 2023, signaling network – protein-protein interaction information from MultiNicheNet</li><li><strong>weighted_networks_nsga2r_final.rds : </strong>accessed in October 2023, networks weighted by literature evidence from MultiNicheNet</li></ul></li><li><strong>nichenet_prior/</strong><ul><li><strong>ligand_target_matrix.rds : </strong>accessed in April 2023, ligand to target matrix from NicheNet</li><li><strong>lr_network.rds : </strong>accessed in April 2023, ligand-receptor matrix from NicheNet</li></ul></li><li><strong>nichenet_v2_prior/</strong><ul><li><strong>ligand_target_matrix_nsga2r_final.rds : </strong>accessed in June 2023, ligand to target matrix from MultiNicheNet used to predict target genes.</li><li><strong>lr_network_human_21122021.rds : </strong>accessed in June 2023, ligand-receptor matrix from MultiNicheNet used to predict ligand-receptor pairs.</li></ul></li><li><strong>geo_multinichenet_output.rds </strong>: MultiNicheNet output for Morabito et al., 2021 data</li><li><strong>geo_signaling_igraph_objects.rds </strong>: list of igraph objects for 17 overlapping LRTs and their signaling mediators in the Morabito et al., 2021 dataset. </li><li><strong>gse_multinichenet_output.rds</strong> : MultiNicheNet output for Lau et al., 2020 data</li><li><strong>gse_signaling_igraph_objects.rds</strong> : list of igraph objects for 17 overlapping LRTs and their signaling mediators in the Lau et al., 2020 dataset </li></ul></li><li><strong>seurat_preprocessing/</strong><ul><li><strong>geo_filtered_seurat.rds : </strong>merged and filtered seurat object of Morabito et al., 2021 data</li><li><strong>geo_integrated_seurat.rds :</strong> seurat object integrated using harmony of Morabito et al., 2021 data</li><li><strong>geo_clustered_seurat.rds : </strong>clustered seurat object of Morabito et al., 2021 data</li><li><strong>geo_processed_seurat.rds : </strong>processed seurat object with final cell type assignments at specified resolution of Morabito et al., 2021 data</li><li><strong>gse_filtered_seurat.rds : </strong>merged and filtered seurat object of Lau et al., 2020 data</li><li><strong>gse_integrated_seurat.rds : </strong>seurat object integrated using harmony of Lau et al., 2020 data</li><li><strong>gse_clustered_seurat.rds :</strong> clustered seurat object of Lau et al., 2020 data</li><li><strong>gse_processed_seurat.rds : </strong>processed seurat object with final cell type assignments at specified resolution of Lau et al., 2020 data </li></ul></li></ul>
Repository for: Combinatorial Wnt signaling landscape during brachiopod anteroposterior patterning
<p>This repository contains the data and analyses for the manuscript:</p> <p>Vellutini, B. C., Martín-Durán, J. M., Børve, A. & Hejnol, A. <strong>Combinatorial Wnt signaling landscape during brachiopod anteroposterior patterning.</strong> BMC Biol. 22, 1–23 (2024). <a href="https://doi.org/10.1186/s12915-024-01988-w" rel="nofollow">https://doi.org/10.1186/s12915-024-01988-w</a></p> <p>The source is maintained at <a href="https://github.com/bruvellu/terebratalia-wnts">https://github.com/bruvellu/terebratalia-wnts</a>.</p>
Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra
Open the record for dataset details and reuse information.
Data from: Aged-vascular niche hinders osteogenesis of mesenchymal stem cells through paracrine repression of Wnt-axis
<p>Raw data set for: Fleischhacker V, Milosic F, Bricelj M, Kührer K, Wahl-Figlash K, Heimel P, Diendorfer A, Nardini E, Fischer I, Stangl H, Pietschmann P, Hackl M, Foisner R, Grillari J, Hengstschläger M, and Osmanagic-Myers S. Aged-vascular niche hinders osteogenesis of mesenchymal stem cells through paracrine repression of Wnt-axis. Aging Cell. 2024 Jun;23(6):e14139. doi: 10.1111/acel.14139. Epub 2024 Apr 5.</p> <p><span>Age-induced decline in osteogenic potential of bone marrow mesenchymal stem cells (BMSCs) potentiates osteoporosis and increases risk for bone fractures. Despite e</span><span>pidemiology studies reporting concurrent development of vascular- and bone diseases in the elderly, the underlying mechanisms for the vascular-bone cross-talk in aging are largely unknown. </span><span>In this study, we show that accelerated endothelial aging deteriorates bone tissue through paracrine repression of Wnt-driven-axis in BMSCs. <span>Here, we utilize </span>physiologically aged mice<span> in conjunction with our transgenic endothelial progeria mouse model </span>(Hutchinson-Gilford progeria syndrome; HGPS) that<span> displays hallmarks of an aged bone marrow vascular niche</span>. We find bone defects associated with diminished BMSC osteogenic differentiation that implicate the existence of angiocrine factors with long-term inhibitory effects. microRNA-transcriptomics of HGPS-patient plasma combined with aged-vascular niche analyses in progeria mice reveal abundant secretion of Wnt-repressive microRNA-31-5p. Moreover, we show that inhibition of microRNA-31-5p as well as selective Wnt-activator CHIR99021 boost the osteogenic potential of BMSCs through de-repression and activation of the Wnt-signalling, respectively. Our results demonstrate that the vascular niche significantly contributes to osteogenesis defects in aging and pave ground for microRNA-based therapies of bone loss in elderly.</span></p> <h1> </h1>
Epigenetic deregulation of IFN and WNT pathways in AT2 cells impairs alveolar regeneration (in COPD)
<h2>Data-sets</h2><p>RNAseq_CountTable.tsv: Raw count table from RNA-seq experiments</p><p>WGBS_MethylationTable.tsv: Total read coverage and number of methylated sites at CpG positions (reference genome: hg19) </p><h2>Abstract</h2><p>Chronic lung diseases, including chronic obstructive pulmonary disease (COPD), affect over 500 million people and are a leading cause of death worldwide. A common feature of both chronic and acute lung diseases is altered respiratory barrier integrity and impaired lung regeneration. We hypothesized that alveolar type 2 (AT2) cells, as alveolar epithelial progenitors, will carry molecular alterations that compromise alveolar regeneration in COPD. Sorted AT2 cells from ex-smokers with and without COPD at different disease stages were subjected to RNA sequencing and whole-genome bisulfite sequencing to generate unbiased transcriptome and DNA methylation maps of alveolar progenitors in the lung. Our analysis revealed genome-wide epigenetic changes in AT2 cells during COPD that were associated with global gene expression changes. Integrative data analysis uncovered a strong anti-correlation between gene expression and promoter methylation, suggesting that dysregulation of COPD-associated pathways in AT2 cells may be regulated by DNA methylation. Interferon (IFN) signaling was the top-upregulated pathway associated with the concomitant loss of promoter DNA methylation. Epigenetic regulation of the IFN pathway was validated in both global and targeted DNA demethylation assays in A549 cells. Notably, targeted DNA demethylation of IRF9 triggered upregulation of IFN signaling, mimicking the effects observed in COPD AT2 cells in the profiling data. Our findings suggest that COPD-triggered epigenetic alterations in AT2 cells impair internal regeneration programs in human lung parenchyma.</p>
The Immp2l mutation causes ovarian aging through ROS-wnt/β-catenin-estrogen (cyp19a1) pathway: preventive effect of melatonin
<p>Mitochondria play important roles in ovarian follicle development. Mitochondrial dysfunction, including mitochondrial gene deficiency, impairs the ovarian development. Here, we explored the role and mechanism of mitochondrial inner membrane gene <i>Immp2l</i> in ovarian follicle growth and development. Our results revealed that the female Immp2l<sup>-/-</sup> mice were infertile, while the Immp2l<sup>+/- </sup>mice were normal. Body and ovarian weights were reduced in the female Immp2l<sup>-/- </sup>mice, ovarian follicle growth and development were stunted in the secondary follicle stage. Although a few ovarian follicles were ovulated, the oocytes were not fertilized due to mitochondrial dysfunction. Increased oxidative stress, decreased estrogen levels, and altered genes expression of Wnt/β-catenin and steroid hormone synthesis pathways were observed in 28-day-old Immp2l<sup>-/-</sup> mice. The Immp2l mutation accelerated ovarian aging process, as no ovarian follicles were detected in age of 5 months in Immp2l<sup>-/- </sup>mice. All the aforementioned changes in the Immp2l<sup>-/- </sup>mice were reversed by administration of antioxidant melatonin to the Immp2l<sup>-/-</sup> mice. Furthermore, our in vitro study using Immp2l knockdown granulosa cells confirmed that the Immp2l downregulation induced granulosa cell aging by enhancing ROS levels, suppressing <i>Wnt16</i>, increasing β-catenin and decreasing steroid hormone synthesis gene <i>cyp19a1</i> and estrogen levels, accompanied by an increase in the aging phenotype of granulosa cells. Melatonin treatment delayed granulosa cell aging progression. Taken together, Immp2l causes ovarian aging through the ROS-Wnt/β-catenin-estrogen (cyp19a1) pathway, which can be reversed by melatonin treatment.Mitochondria play important roles in ovarian follicle development. Mitochondrial dysfunction, including mitochondrial gene deficiency, impairs the ovarian development. Here, we explored the role and mechanism of mitochondrial inner membrane gene <i>Immp2l</i> in ovarian follicle growth and development. Our results revealed that the female Immp2l<sup>-/-</sup> mice were infertile, while the Immp2l<sup>+/- </sup>mice were normal. Body and ovarian weights were reduced in the female Immp2l<sup>-/- </sup>mice, ovarian follicle growth and development were stunted in the secondary follicle stage. Although a few ovarian follicles were ovulated, the oocytes were not fertilized due to mitochondrial dysfunction. Increased oxidative stress, decreased estrogen levels, and altered genes expression of Wnt/β-catenin and steroid hormone synthesis pathways were observed in 28-day-old Immp2l<sup>-/-</sup> mice. The Immp2l mutation accelerated ovarian aging process, as no ovarian follicles were detected in age of 5 months in Immp2l<sup>-/- </sup>mice. All the aforementioned changes in the Immp2l<sup>-/- </sup>mice were reversed by administration of antioxidant melatonin to the Immp2l<sup>-/-</sup> mice. Furthermore, our in vitro study using Immp2l knockdown granulosa cells confirmed that the Immp2l downregulation induced granulosa cell aging by enhancing ROS levels, suppressing <i>Wnt16</i>, increasing β-catenin and decreasing steroid hormone synthesis gene <i>cyp19a1</i> and estrogen levels, accompanied by an increase in the aging phenotype of granulosa cells. Melatonin treatment delayed granulosa cell aging progression. Taken together, Immp2l causes ovarian aging through the ROS-Wnt/β-catenin-estrogen (cyp19a1) pathway, which can be reversed by melatonin treatment.</p>
Red rice bran polyphenols suppress invasive properties of HepG2 cells, possibly through Wnt/β-catenin-mediated EMT reversal.
<p>Data collection in its raw form is performed in a specific sequence dictated by the manuscript.</p>
A Study of LGK974 in Patients With Malignancies Dependent on Wnt Ligands
ClinicalTrials.gov study NCT01351103. IPD Sharing: NO. Countries: 7. Publications: 1.
Study of WNT974 in Combination With LGX818 and Cetuximab in Patients With BRAF-mutant Metastatic Colorectal Cancer (mCRC) and Wnt Pathway Mutations
ClinicalTrials.gov study NCT02278133. IPD Sharing: Not stated. Countries: 10. Publications: 2.
Reduced Craniospinal Radiation Therapy and Chemotherapy in Treating Younger Patients With Newly Diagnosed WNT-Driven Medulloblastoma
ClinicalTrials.gov study NCT02724579. IPD Sharing: Not stated. Countries: 5. Publications: 0.
Study on the Probiotics Regulating miRNA in H. Pylori-induced Wnt/β-catenin Gastric Carcinogenesis.
ClinicalTrials.gov study NCT05544396. IPD Sharing: NO. Countries: 1. Publications: 3.
The Importance of Wnt-signaling After Cardiac Surgery
ClinicalTrials.gov study NCT04058496. IPD Sharing: Not stated. Countries: 1. Publications: 3.
The Immp2l mutation causes ovarian aging through ROS-wnt/β-catenin-estrogen (cyp19a1) pathway: preventive effect of melatonin
Open the record for dataset details and reuse information.
UBE3A Wnt signaling Cell Assay
<p>Describes the development of a Wnt signaling cell-based reporter assay for UBE3A.</p>
Data from: Wnt/PCP controls spreading of Wnt/β-catenin signals by cytonemes in vertebrates
Signaling filopodia, termed cytonemes, are dynamic actin-based membrane structures that regulate the exchange of signaling molecules and their receptors within tissues. However, how cytoneme formation is regulated remains unclear. Here, we show that Wnt/PCP autocrine signaling controls the emergence of cytonemes, and that cytonemes subsequently control paracrine Wnt/β-catenin signal activation. Upon binding of the Wnt family member Wnt8a, the receptor tyrosine kinase Ror2 gets activated. Ror2/PCP signaling leads to induction of cytonemes, which mediate transport of Wnt8a to neighboring cells. In the Wnt receiving cells, Wnt8a on cytonemes triggers Wnt/β-catenin-dependent gene transcription and proliferation. We show that cytoneme-based Wnt transport operates in diverse processes, including zebrafish development, the murine intestinal crypt, and human cancer organoids, demonstrating that Wnt transport by cytonemes and its control via the Ror2 pathway is highly conserved in vertebrates.
Study Assessing the Feasibility of a Surgery and Chemotherapy-Only in Children With Wnt Positive Medulloblastoma
ClinicalTrials.gov study NCT02212574. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: Wnt/PCP controls spreading of Wnt/β-catenin signals by cytonemes in vertebrates
Open the record for dataset details and reuse information.
Activation of Wnt signaling promotes olaparib resistant ovarian cancer.
GEO Series GSE117765. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Impact of BMP and WNT signaling modulation on mesendoderm progenitor cells specification from hPSCs in 3D culture conditions
GEO Series GSE184302. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
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.