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Dataset results
339 results for “In vitro models”
An in vitro model of intestinal infection reveals a developmentally regulated transcriptome of Toxoplasma sporozoites and a NF-κB-like signature in infected host cells
GEO Series GSE94473. Rattus norvegicus. 24 samples. Type: Expression profiling by high throughput sequencing.
Integrated Gut/Liver-on-a-Chip platform as in vitro human model of non-alcoholic fatty liver disease
GEO Series GSE152091. Homo sapiens. 23 samples. Type: Expression profiling by high throughput sequencing.
Efficient derivation of transgene-free porcine induced pluripotent stem cells enables in vitro modeling of species-specific developmental timing
GEO Series GSE227985. Sus scrofa. 36 samples. Type: Expression profiling by high throughput sequencing.
Immortalized human choroid plexus endothelial cells enable an advanced endothelial-epithelial two-cell type in vitro model of the choroid plexus
GEO Series GSE198846. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
SDR42E1 modulates vitamin D absorption and cancer pathogenesis: insights from an in vitro model
GEO Series GSE275021. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Data from: Evaluation of the innate immunostimulatory potential of originator and non-originator copies of insulin glargine in an in vitro human immune model
Background: The manufacture of insulin analogs requires sophisticated production procedures which can lead to differences in the structure, purity, and/or other physiochemical properties of resultant products that can affect their biologic activity. Here, we sought to compare originator and non-originator copies of insulin glargine for innate immune activity and mechanisms leading to differences in these response profiles in an in vitro model of human immunity. Methods: An endothelial/dendritic cell-based innate immune model was used to study antigen-presenting cell activation, cytokine secretion, and insulin receptor signalling pathways induced by originator and non-originator insulin glargine products. Mechanistic studies included signalling pathway blockade with specific inhibitors, analysis of the products in a Toll-like receptor reporter cell line assay, and insulin removal from the products by immunopurification. Findings: All insulin glargine products elicited at least a minor innate immune response comparable to human insulin, but some lots of a non-originator copy product induced the elevated secretion of the cytokines, IL-8 and IL-6. In studies aimed at addressing the mechanisms leading to differential cytokine production by these products, we found (1) the inflammatory response was not mediated by bacterial contaminants, (2) the innate response was driven by the insulin receptor through the MAPK pathway, and (3) the removal of insulin significantly reduced their capacity to induce innate activity. No evidence of product aggregates was detected, though the presence of some high molecular weight proteins argues for the presence of insulin dimers or others contaminants in these products. Conclusion: The data presented here suggests some non-originator insulin glargine product lots drive heightened in vitro human innate activity and provides preliminary evidence that changes in their biochemical composition (dimers, impurities) might be responsible for their greater immunostimulatory potential.
scRNA-seq data of: A novel in vitro tubular model to recapitulate features of distal airways: the bronchioid
<p>We provide a .Rds file of an annotated Seurat Object of scRNA-seq data of two bronchioid models derived from distinct donors after 21days of culture using 10x genomics 3' v3 chemistry. Raw data was processed using CellRanger v7.1.0. Cells were filtered based on detected UMIs (>2000) and fraction of mitochondrial counts (<10%).<br>Metadata annotations contain:<br>- Patient -> patient information for every cell (patient1 or patient2)<br>- nCount_RNA -> UMI counts per cell<br>- nFeature_RNA -> genes detected per cell<br>- percent.mt -> mitochondrial count fraction per cell<br>- seurat_clusters -> unsupervised clustering results using Louvain algorithm with resolution = 0.5<br>- Manual.Annotation -> Cell types annotated based on marker gene expression<br>- Celltypist.prediction -> Cell types predicted with CellTypist Python package<br>- Celltypist.prediction.ari -> Cell types predicted with CellTypist Python package, with harmonized names for comparison with manual annotation</p>
Data from: Progression of neuronal damage in an in vitro model of the ischemic penumbra
Improvement of neuronal recovery in the ischemic penumbra around a brain infarct has a large potential to advance clinical recovery of patients with acute ischemic stroke. However, pathophysiological mechanisms leading to either recovery or secondary damage in the penumbra are not completely understood. We studied neuronal dynamics in a model system of the penumbra consisting of networks of cultured cortical neurons exposed to controlled levels and durations of hypoxia. Short periods of hypoxia (pO2≈20mmHg) reduced spontaneous activity, due to impeded synaptic function. After ≈6 hours, activity and connectivity partially recovered, even during continuing hypoxia. If the oxygen supply was restored within 12 hours, changes in network connectivity were completely reversible. For longer periods of hypoxia (12–30 h), activity levels initially increased, but eventually decreased and connectivity changes became partially irreversible. After ≈30 hours, all functional connections disappeared and no activity remained. Since this complete silence seemed unrelated to hypoxic depths, but always followed an extended period of low activity, we speculate that irreversible damage (at least partly) results from insufficient neuronal activation. This opens avenues for therapies to improve recovery by neuronal activation.
Exploring the effects of experimental parameters and data modeling approaches on in vitro transcriptomic point-of-departure estimates
Open the record for dataset details and reuse information.
Tissue-engineered oral epithelial barrier for dental material testing: towards establishing in vitro biomimetic models - Underlying data
<p>Underlying CT data of "<strong>Tissue-engineered oral epithelial barrier for dental material testing: towards establishing <em>in vitro </em>biomimetic models</strong>"<br><a href="https://doi.org/10.1089/ten.tec.2024.0154">https://doi.org/10.1089/ten.tec.2024.0154</a></p> <p>Foteini Machla a, Paraskevi Kyriaki Monou b, c, Chrysanthi Bekiari d, Dimitrios Andreadis e Evangelia Kofidou d, , Emmanouel Panteris f, Orestis L. Katsamenis g, h, Maria Kokoti a, Petros Koidis a, Imad About i, Dimitrios Fatourosb, c, Athina Bakopoulou a</p> <p>a Department of Prosthodontics, Tissue Engineering Core Unit, School of Dentistry, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>b Department of Pharmaceutical Technology, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>c Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Thessaloniki 57001, Greece</p> <p>d Laboratory of Anatomy and Histology, Veterinary School, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>e Department of Oral Medicine/Pathology, School of Dentistry, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>f Department of Botany, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>g μ-VIS X-ray Imaging Centre, Faculty of Engineering and the Environment, University of Southampton, Southampton SO17 1BJ, United Kingdom</p> <p>h Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom UK</p> <p>i Centre National de la Recherche Scientifique, Institute of Movement Sciences, Aix Marseille University, Marseille 13385, France</p> <p> </p> <p><strong>Measurement of ΤΕΟΕ thickness</strong></p> <p>X-ray computed micro-tomography (μCT) as employed to examine the microstructure of the paraffin-embedded tissue engineered oral epithelium (TEOE), enabling comprehensive 3D assessment of thickness using volumetric analysis (cf. supplementary for imaging parameters) (11). Imaging was conducted using an isotropic voxel-edge of 6.0 μm. Local Thickness was carried out in 3D using the “Volume Thickness Map” tool within Dragonfly software (cf. supplementary), allowing for the visualization and quantification of the spatial distribution and variability of tissue thickness.</p> <p>Imaging was conducted at the University of Southampton’s μ-VIS X-ray Imaging Centre ( https://muvis.org ) / 3D X-ray Histology facility, utilizing a customised μCT scanner optimisedfor intricate histological analyses(1), based on Nikon’s XTH225ST system (Nikon Metrology, UK). Operating parameters were set at 80 kVp / 86 μA (6.88 W), with a source-to-object distance of 37.5 mm and a source-to-detector distance of 937.4 mm, resulting in a magnification factor of 25x and an isotropic voxel-edge of 6.0 μm. Imaging acquisition involved the collection of 4001 projections using a 2850 x 2850 dexels detector, by averaging 4 frames per projection, with an exposure time of 500 ms per projection.</p> <p>Visualisation and analysis of the reconstructed dataset was done using Dragonfly software (Comet Technologies Canada Inc.; software accessible at http://www.theobjects.com/dragonfly). Assessment of Local Thickness was carried out in 3D using the “Volume Thickness Map” tool within Dragonfly software, following segmentation of the tissue layer. Local thickness analysis allowed for the visualization and quantification of the spatial distribution and variability of thickness within the tissue engineered oral epithelium (TEOE).</p> <p>Visual representation of local thickness histograms was employed to elucidate the distribution of thickness throughout the TEOE. These histograms effectively illustrate the number of voxels associated with specific cross-sectional thickness, offering both a graphical depiction of the variation in thickness across the tissue sample, and a quantitative measure of the average thickness of the specimen.</p> <p>It's worth noting, the volumetric and non-destructive nature of the technique enabled whole-block imaging, which proved crucial in addressing challenges arising from tissue sample shrinkage. This shrinkage, a consequence of dehydration during the fixation process, can occur in some cases and lead led to the specimen wrapping. While wrapping is not a common occurrence, this analysis method allowed for the evaluation of challenging-shaped specimens, such as the wrapped one presented in Figure 4. Unlike conventional 2D methods such as classical histology, which rely on the angle of slicing and encounter limitations when dealing with non-perfectly perpendicular slicing, μCT-based XRH enables analysis of all specimens, including those with complex shapes.</p> <p> </p>
Dataset of Lipidomics of Cell Secretome Combined with the Study of Selected Bioactive Lipids in an In Vitro Model of Osteoarthritis
<p>Raw data of the paper "Lipidomics of Cell Secretome Combined with the Study of Selected Bioactive Lipids in an In Vitro Model of Osteoarthritis"</p>
In Vitro Modeling of Drug-resistant Psychiatric Disorders Using Induced Pluripotent Cells
ClinicalTrials.gov study NCT05887310. IPD Sharing: YES. Countries: 1. Publications: 0.
In Vitro Model of the Cystic Fibrosis Bronchial Epithelium Via iPS Technology
ClinicalTrials.gov study NCT03754088. IPD Sharing: Not stated. Countries: 1. Publications: 0.
In Vitro Models From Pediatric Brain Tumors
ClinicalTrials.gov study NCT06499636. IPD Sharing: NO. Countries: 1. Publications: 0.
The Effect of HIV Tat Protein on HCV Replication in an In-vitro Model System
ClinicalTrials.gov study NCT01206933. IPD Sharing: NO. Countries: 1. Publications: 0.
In Vitro Models of Liver and Pancreatic Cancer
ClinicalTrials.gov study NCT02436564. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Stools and Life Habits Collection in Heathy Volunteers/Subjects - to Provide Material for in Vitro Model Development
ClinicalTrials.gov study NCT04301973. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Protein Sorbent Properties of Montmorillonite in Vitro and in Vivo Models
ClinicalTrials.gov study NCT02124330. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Modelling host-Trypanosoma brucei gambiense interactions in vitro using human induced pluripotent stem cell-derived cortical brain organoids
GEO Series GSE225147. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Reproducibility of PD patient-specific midbrain organoid data for in vitro disease modelling (timepoints)
GEO Series GSE269316. Homo sapiens. 48 samples. Type: Expression profiling by high throughput sequencing.
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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.