Find research datasets worth reusing

opencc-by-sa-4.0Oct 2023View details →

seurat objects of FACS-sorted (CD31+/CD45-) endothelial cells - individual entities

Seurat objects of individual entities of FACS-sorted (CD31+/CD45-) endothelial cells -> part of the manuscript: Single-cell atlas of the human brain vasculature across development, adulthood and disease https://www.nature.com/articles/s41586-024-07493-y   -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------   -i) Fetal CNS sorted endothelial cells_seurat object.rds:       -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from fetal brain (Fetal CNS). -ii) Fetal periphery sorted endothelial cells_seurat object.rds:       -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from fetal peripheral organs (Fetal periphery). - iii) Adult control brain (temporal lobe) sorted endothelial cells_seurat object.rds:       -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from adult/control brains (temporal lobes). - iv) AVM sorted endothelial cells_seurat object.rds:       -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from brain arteriovenous malformations (AVM) (a brain vascular malformation). - v) LGG sorted endothelial cells_seurat object.rds:       -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from lower-grade gliomas (LGG) (a brain tumor). - vi) GBM sorted endothelial cells_seurat object.rds:       -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from high-grade gliomas (glioblastoma (GBM)) (a brain tumor). - vii) MET sorted endothelial cells_seurat object.rds:      -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from brain metastasis (MET) (a brain tumor). - viii) MEN sorted endothelial cells_seurat object.rds:       -> this seurat object is of FACS-sorted (CD31+/CD45-) endothelial cells isolated from brain meningioma (MEN) (a brain tumor).

opencc-by-sa-4.0Jun 2024View details →

seurat objects of FACS-sorted (CD31+/CD45-) endothelial cells - overall merges

Seurat objects of overall merges of FACS-sorted (CD31+/CD45-) endothelial cells -> part of the manuscript: Single-cell atlas of the human brain vasculature across development, adulthood and disease https://www.nature.com/articles/s41586-024-07493-y ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -i) Overall merge of all brain sorted endothelial cells_seurat object.rds:       -> this seurat object is the overall merge of FACS-sorted (CD31+/CD45-) endothelial cells isolated from fetal brain, adult/control brains (temporal lobes), brain tumors (lower-grade glioma, high-grade glioma (glioblastoma), brain metastasis, meningiomas) and brain vascular malformations (brain arteriovenous malformations).  -ii) Overall merge of all sorted brain and peripehry endothelial cells_seurat object.rds:       -> this seurat object is the overall merge of FACS-sorted (CD31+/CD45-) endothelial cells isolated from fetal brain, fetal peripheral organs, adult/control brains (temporal lobes), brain tumors (lower-grade glioma, high-grade glioma (glioblastoma), brain metastasis, meningiomas) and brain vascular malformations (brain arteriovenous malformations).  -iii) Overall merge of pathological sorted endothelial cells_seurat object.rds:       -> this seurat object is the overall merge of FACS-sorted (CD31+/CD45-) endothelial cells isolated from brain tumors (lower-grade glioma, high-grade glioma (glioblastoma), brain metastasis, meningiomas) and brain vascular malformations (brain arteriovenous malformations).  -iv) Overall merge of tumor sorted endothelial cells_seurat object.rds:       -> this seurat object is the overall merge of FACS-sorted (CD31+/CD45-) endothelial cells isolated from brain tumors (lower-grade glioma, high-grade glioma (glioblastoma), brain metastasis, meningiomas).

opencc-by-4.0Sep 2025View details →

Novel gene regulatory networks identified in response to nitro-conjugated linoleic acid in human endothelial cells

A distinct transcriptome regulated by NO2-CLA was revealed in primary human coronary artery endothelial cells (HCAECs) through RNA sequencing.

opencc-by-4.0Aug 2024View details →

Pan-cancer atlas of endothelial cells

Datasets used to generate a pan-cancer atlas of endothelial cells and additional datasets generated with sorted endothelial cells used for validation.

opencc-by-4.0Apr 2024View details →

Data supporting the analysis of lymphatic endothelial cell junctions and shape

Data in support of:  Dynamic cytoskeletal regulation of cell shape supports resilience of lymphatic endothelium Hans Schoofs1#, Nina Daubel1#, Sarah Schnabellehner1, Max Grönloh2, Sebastián Palacios Martínez3, Aleksi Halme4, Amanda M. Marks1, Marie Jeansson1, Sara Barcos5, Cord Brakebusch6, Rui Benedito7, Britta Engelhardt5, Dietmar Vestweber8, Konstantin Gängel1, Fabian Linsenmeier9, Sebastian Schürmann9, Pipsa Saharinen4,10, Jaap D. van Buul2,3,11, Oliver Friedrich9, Richard S. Smith12, Mateusz Majda13, and Taija Mäkinen1,4,10*   1Uppsala University, Department of Immunology, Genetics and Pathology, Dag Hammarskjölds väg 20, 751 85 Uppsala, Sweden. 2Department of Medical Biochemistry at the Amsterdam UMC, location AMC, The Netherlands. 3Department of Molecular Cytology, Leeuwenhoek Centre for Advanced Microscopy at Swammerdam Institute for Life Sciences at the University of Amsterdam, The Netherlands. 4Translational Cancer Medicine Program and Department of Biochemistry and Developmental Biology, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland. 5Theodor Kocher Institute, University of Bern, Bern, Switzerland. 6Biotech Research and Innovation Center, University of Copenhagen, Ole Maaløes Vej 5, 2200 Denmark. 7Centro Nacional de Investigaciones Cardiovasculares, Melchor Fernández Almagro 3, E-28029 Madrid, Spain. 8Max Planck Institute for Molecular Biomedicine, Münster, Germany. 9Institute of Medical Biotechnology, Department of Chemical and Biological Engineering, Friedrich-Alexander-University, Erlangen-Nürnberg, Paul-Gordan-Str.3, 91052 Erlangen, Germany. 10Wihuri Research Institute, Haartmaninkatu 8, 00290 Helsinki, Finland. 11Amsterdam UMC, Sanquin Research and Landsteiner Laboratory, The Netherlands. 12John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK. 13Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland. #These authors contributed equally. *Corresponding author: Taija Mäkinen, E-mail: <a href="mailto:taija.makinen@igp.uu.se">taija.makinen@igp.uu.se</a>, <a href="mailto:taija.makinen@helsinki.fi">taija.makinen@helsinki.fi</a>   DATASET A: Annotated cell-cell junction types in lymphatic capillaries of wild type mouse ear skin at different ages  __________________________________________________________________________________________________________ Contents <ul> <li>SOURCE DATA Fig1 FINAL. xlsx</li> <li>3w <ul> <li>animal 1</li> <li>animal 2</li> <li>animal 3</li> <li>animal 4</li> <li>animal 5</li> <li>sprouts</li> </ul> </li> <li>5w <ul> <li>animal 1</li> <li>animal 2</li> <li>animal 3</li> <li>animal 4</li> <li>animal 5</li> <li>diaphragm <ul> <li>Overview of diaphragm and high mag. of different capillary ends</li> </ul> </li> <li>trachea</li> </ul> </li> <li>25w <ul> <li>animal 1</li> <li>animal 2</li> <li>animal 3</li> <li>animal 4</li> <li>animal 5</li> <li>diaphragm</li> <li>trachea</li> </ul> </li> </ul> File legends C1 images: inverted LYVE1 signal (.tif) C2 images: inverted VE-cadherin signal (.tif) MAX images: RGB merge of LYVE1 (cyan) and VE-cadherin (red) (.tif) "NAME".roi: Regions of interest (ROI) of annotated junctions can be imported in ImageJ Methods Junctional classification:  Analysis of junction morphology was done on blunt-ended initial lymphatic capillaries in the segment between the intial tip and the first valve. Junction types were quantified in Z-stack projection by numbering of individual lobes of LYVE1 and VE-cadherin-stained LECs and subsequent categorizing of lobe-associated junctions based on VE-cadherin signal. Four categories were defined: 1) Button junction – a punctate VE-cadherin+ deposit at the neck of LYVE1+ lobe/overlap, with no detectable VE-cadherin at the borders of the overlap, 2) Curvilinear junction – unsegmented(continous) or segmented (discontinuous) distribution of VE-cadherin within one border of LYVE1+ lobe/cellular overlap, 3) Double junction – unsegmented(continous) or segmented (discontinuous) distribution of VE-cadherin within both borders of LYVE1+ lobe/cellular overlap, and 4) LYVE1- curvilineair junction – unsegmented(continous) linear VE-cadherin distribution at cell-cell contacts in the absence of LYVE1. Wild-type C57BL/6J mice were used for analysis of junction types, and 4-5 blunt ended vessels per mouse from five mice per age group and condition were analysed; in total 1785 junctions were annoted Imaging: Confocal images were obtained using a Leica Stellaris 5 confocal microscope equipped with 405 nm and white light lasers, 63x/1.3 HC PL APO CORR CS2 Glycerol immersion objective, and Leica LAS X software. Images were aquired at 1.51 digital zoom using a 2048x2048 resolution Tissue processing and staining:   Tissues were fixed in 4% paraformaldehyde for 2 h at RT and permeabilized in 0.3% Triton X-100 in PBS (PBST) for 10 min. After blocking in PBST with 2% bovine serum albumin, 1% FBS for 2 h, tissues were incubated with primary antibodies in blocking buffer overnight, followed by PBST washing and incubation with fluorescent dye-conjugated secondary antibodies for 2 h. All incubation steps were carried out at RT. Prior to mounting in Mowiol, samples were repeatedly washed in PBST and water. Antibodies used: Goat anti-mouse VE-cadherin (R&D Systems, AF1002; 1:200), Rat anti-mouse LYVE1 (R&D Systems, MAB2125; 1:200)   DATASET B: Finite element method (FEM) simulations of cellular stresses _______________________________________________________________ The FEM simulations were performed with MorphoMechanX using available models adapted from Sapala et al, eLife 7, e32794 (2018). A regular cylindrical grid 45 µm wide and 200 µm long was created and outlines from the cells of a lymphatic vessel were projected onto it and smoothed. These cells were then extruded inward to make 3D volumetric cells with a depth of 2 µm and triangulated using a threshold area of 4 µm.  The template was then used as the reference configuration for triangular 3 node membrane elements which were given a thickness of 0.1um. An isotropic St. Venant material model (linear, large deformation) was used with the Young's modulus set to 100 kPa to match a 10 kPa cell level Young's modulus estimated from the literature (ignoring the cell ends, the 2 x 0.1 µm membrane thickness occupied roughly 1/10th the cross-sectional area of the cell that were 2 µm deep). A uniform internal pressure was applied normal to the inside faces of the elements, which cancels out on the shared walls between cells. For simulations with a lower pressure inside the vessel, the inside faces were assigned a higher pressure. Stresses were visualized as the trace of the stress tensor.

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Data from: GATA2 controls lymphatic endothelial cell junctional integrity and lymphovenous valve morphogenesis through miR-126

Mutations in the transcription factor GATA2 cause lymphedema. GATA2 is necessary for the development of lymphatic valves (LVs) and lymphovenous valves (LVVs), and for the patterning of lymphatic vessels. Here, we report that GATA2 is not necessary for valvular endothelial cell (VEC) differentiation. Instead, GATA2 is required for VEC maintenance and morphogenesis. GATA2 is also necessary for the expression of cell junction molecules VE-Cadherin and Claudin5 in lymphatic vessels. We identified miR-126 as a target of GATA2, and miR-126-/- embryos recapitulate the phenotypes of mice lacking GATA2. Primary human lymphatic endothelial cells (HLECs) lacking GATA2 (GATA2ΔHLEC) have altered expression of Claudin5 and VE-Cadherin, and blocking miR-126 activity in HLECs phenocopies these changes in expression. Importantly, overexpression of miR-126 in GATA2ΔHLEC significantly rescues the cell junction defects. Thus, our work defines a new mechanism of GATA2 and uncovers miR-126 as a novel regulator of mammalian lymphatic vascular development.

opencc-zeroOct 2019View details →

openother-ncApr 2023View details →

Large-scale annotation dataset for cell/tissue segmentation in H&E-stained images : anti-ERG (endothelial cells)

LICENSE This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC-BY-NC-SA 4.0) For non-commercial use, please use the dataset under CC-BY-NC-SA. If you would like to use the dataset for commercial purposes, please contact us (ishum-prm@m.u-tokyo.ac.jp). A Tar.gz file contains the following files: - HE image file: {antigen}_{celltype}_{slideID}_{posx}_{posy}_HE.png - Mask image file: {antigen}_{celltype}_{slideID}_{posx}_{posy}_mask.png Each image file is 984x984 px. posX and posY are the leftmost position in WSI coordinate. Mask files store binary segmentation mask (background : 0, target : 1)   A csv file contains the following information: antigen : Antibodies for this antigen were used to create the segmentation mask. filename: filename of image or mask file. train_val_test : train, validation, or test sample in the paper.   Citation If you use this dataset for your research, please cite our paper. Daisuke Komura, Takumi Onoyama, Koki Shinbo, Hiroto Odaka, Minako Hayakawa, Mieko Ochi, Ranny Rahaningrum Herdiantoputri, Haruya Endo, Hiroto Katoh, Tohru Ikeda, Tetsuo Ushiku, Shumpei Ishikawa, Restaining-based annotation for cancer histology segmentation to overcome annotation-related limitations among pathologists, Patterns, Volume 4, Issue 2, 2023, 100688, https://doi.org/10.1016/j.patter.2023.100688.

dryad32/100

Evaluating the effects of pod-based electronic cigarettes on human endothelial cell function

Pod-based electronic (e-) cigarettes more efficiently deliver nicotine using a protonated formulation. The cardiovascular effects associated with these devices are poorly understood. We evaluated whether pod-based e-liquids and their individual components impair endothelial cell function. We isolated endothelial cells from people who are pod users (n=10), tobacco never users (n=7), and combustible cigarette users (n=6). After a structured use, pod users had lower acetylcholine-mediated endothelial nitric oxide synthase (eNOS) activation compared with never users and was similar to levels from combustible cigarette users (overall P=0.008, P=0.01 pod vs never; P=0.96 pod vs combustible cigarette). The effects of pod-based e-cigarettes and their constituents on vascular cell function were further studied in commercially available human aortic endothelial cells (HAECs) incubated with flavored JUUL e-liquids or propylene glycol (PG):vegetable glycerol (VG) at 30:70 ratio with or without 60 mg/mL nicotine salt for 90 min. A progressive increase in cell death with JUUL e-liquid exposure was observed across 0.0001-1% dilutions; PG:VG vehicle with and without nicotine salt-induced cell death. A23187-stimulated nitric oxide production was decreased with all JUUL e-liquid flavors, PG:VG and nicotine salt exposures. Aerosols generated by JUUL e-liquid heating similarly decreased stimulated nitric oxide production. Only mint-flavored e-liquids increased inflammation and menthol-flavored e-liquids enhanced oxidative stress in HAECs. In conclusion, pod e-liquids and their individual components appear to impair endothelial cell function. These findings indicate the potential harm of pod-based devices on endothelial cell function and thus may be relevant to cardiovascular injury in pod-type e-cigarette users.

opencc-zeroJan 2023View details →

opencc-by-4.0Jun 2023View details →

Endothelial single-cell Obesity Atlas

Ref to paper DOI: <a href="https://doi.org/10.1038/s42255-022-00674-x">10.1038/s42255-022-00674-x</a> <ul> <li>Single cell RNA-seq objects for 7 mouse organs, combined time points.</li> <li>Combined organs, 3 months time point object.</li> </ul> Format: .h5ad  Package used for transformation from/ to Seurat object: sceasy

opennotspecifiedJan 2023View details →

Fig. 8 in Structurally diverse polycyclic polyprenylated acylphloroglucinols with protective effect on human vein endothelial cells injured by high-glucose from Hypericum acmosepalum N. Robson

Fig. 8. Screening results of protective effect of compounds 1–4, and 7–16 at 50 μg/mL on HUVECs injured by high-glucose, using 0.1 mmol/L aspirin as the positive control. *P <0.01 compared with the control group; **P <0.01 compared with the model group, respectively.

opennotspecifiedJan 2023View details →

Fig. 9 in Structurally diverse polycyclic polyprenylated acylphloroglucinols with protective effect on human vein endothelial cells injured by high-glucose from Hypericum acmosepalum N. Robson

Fig. 9. The HUVECs morphologies of Control (A), Model (B), Positive Control (C), and sample groups at 1 (D), 5 (E), 50 (F) μg/mL of compound 13.

opencc-by-4.0Sep 2023View details →

Human dermal microvascular arterial and venous blood endothelial cells and their use in bioengineered dermo-epidermal skin substitutes in vitro and in vivo

The bio-engineering of vascular networks is pivotal to create complex tissues and organs in vitro for regenerative medicine applications. The vascular plexus is needed for a sufficient and fast blood supply after transplantation, and, thus, required for the survival and function of the engineered tissue or organ. Hence, human endothelial cells are an attractive source for bio-engineering purposes, for example human dermal microvascular endothelial cells (HDMECs). So far, a discrimination between arterial and venous blood endothelial cells after isolation of HDMECs from skin biopsies and if arterial and/or venous capillaries are formed in pre-vascularized bio-engineered substitutes was not investigated. In this study, we investigated employedby single cell sequencing for to investigate/compare human arterial and venous endothelial cell markers in human fetal and juvenile skin. Further, we analyzed if these markers are present after isolation of human skin derived endothelial cells under 2D culture conditions. In additionFinally, we investigated assessed if human endothelial cells form distinct arterial and venous capillaries in 3D collagen type I hydrogels, and if these capillaries retain their identity after transplantation. We determinedOur results showed that arterial and venous endothelial cell markers such as NRP1 and NR2F2 are expressed both in fetal and juvenile skin, and are retained after isolation in culture. We could show demonstrate that arterial and venous endothelial cells maintain their differentiation status and form arterial and venous capillaries in 3D in vitro culture systems and that the capillaries inosculate after transplantation. In summary, we could show that we could bio-engineer human arterial, venous, and lymphatic capillaries in a human skin substitute in view of regenerative medicine approaches for clinical applications.

closedIPD-NOFeb 2026View details →

Chemoradiation and Endothelial Progenitor Cells in Colorectal Cancer

ClinicalTrials.gov study NCT00325871. IPD Sharing: NO. Countries: 1. Publications: 1.

Autologous Bone Marrow Stromal Cell and Endothelial Progenitor Cell Transplantation in Ischemic Stroke

ClinicalTrials.gov study NCT01468064. IPD Sharing: Not stated. Countries: 1. Publications: 3.

Effects of Fenofibrate on Endothelial Progenitor Cells in Diabetes

ClinicalTrials.gov study NCT01927315. IPD Sharing: Not stated. Countries: 1. Publications: 1.

closedIPD-NOFeb 2026View details →

A Clinical Study of Recombinant Human Vascular Endothelial Inhibitor in Combination With PRaG for Advanced Refractory Non-small Cell Lung Cancer

ClinicalTrials.gov study NCT06047860. IPD Sharing: NO. Countries: 1. Publications: 0.

Adipose CELL Derived Regenerative Endothelial Angiogenic Medicine

ClinicalTrials.gov study NCT01211028. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Pterygium Head Body MMC1: Two Different Surgical Procedures and Their Effect on Endothelial Cell Count.

ClinicalTrials.gov study NCT02641132. IPD Sharing: Not stated. Countries: 1. Publications: 4.

Endothelial Cell Dysfunction in Pulmonary Hypertension

ClinicalTrials.gov study NCT00098072. IPD Sharing: UNDECIDED. Countries: 1. Publications: 3.

Study of Venous Endothelial Cells in Rheumatoid Arthritis

ClinicalTrials.gov study NCT02468986. IPD Sharing: Not stated. Countries: 1. Publications: 8.