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2,182 results for “organoid”
Efficient gene expression in human stem cell derived-cortical organoids using adeno associated virus
<p><strong>Supplementary figure 6. Neuronal network activity in human cortical organoid</strong>. Videos of AAV-mediated expression of the calcium indicator jGCaMP7 under the human synapsin promoter for control (aCSF), glutamate, gabazine and TTX treated cortical organoids.</p>
Coexisting mechanisms of luminogenesis in pancreatic cancer-derived organoids
<p>Source data and source code for "Coexisting mechanisms of luminogenesis in pancreatic cancer-derived organoids".</p>
Data and code for paper: Design Optimization of Geometric-Confined Cardiac Organoids Enabled by Machine Learning Techniques
<p>Collection of the code for the generation of figures, analysis and data for the paper: <strong>Design Optimization of Geometric-Confined Cardiac Organoids Enabled by Machine Learning Techniques.</strong></p> <p>Ensemble learning classifiers, PACMAP & Trimap code in python file. All figures and additional analysis in R code. </p> <p> </p>
Nasal organoids as optimal models for studying structure and function of primary nasal epithelial cell cultures - DIA-MS Dataset
Open the record for dataset details and reuse information.
Meta-analysis of scRNA-seq Co-expression in Human Neural Organoids Reveals High Variability in Recapitulating Primary Tissue
<p>Contains all code and data for Werner and Gillis, Meta-analysis of scRNA-seq Co-expression in Human Neural Organoids Reveals High Variability in Recapitulating Primary Tissue, 2024. </p> <p>Additionally, the code and data for this paper can be found at https://github.com/JonathanMWerner/meta_organoid_analysis with an easy to view github markdown file containing all the code used to generate all figure panel plots at https://github.com/JonathanMWerner/meta_organoid_analysis/blob/main/figure_plots_with_data_code.md.</p> <p>Due to file size limits on github, there are several data files not available on github, but are available here on zenodo in the data_for_plots.zip file, see below:</p> <pre>umap_embeddings_Fig2A.Rdata<br>cross_dataset_aggregated_exp_metaMarker_all_fetal_SuppFig1B_Fig2E.Rdata<br>organoid_egad_results_ranked_6_26_24_Fig3D.Rdata<br>fetal_egad_results_ranked_6_26_24_Fig3D.Rdata<br>org_eigenvec_matrices_SuppFig3CD.Rdata</pre> <p><br>The R package developed for this paper is available at https://github.com/JonathanMWerner/preservedCoexp</p>
Single-cell analysis of patient-derived PDAC organoids reveals cell state heterogeneity and a conserved developmental hierarchy
<p>scRNA-seq read count matrices from patient-derived PDAC organoids.</p>
Organoid Eppendorf 1 Mesolens 8March23
<p>Mesolens image dataset from organoid 1</p>
Data and statistical analysis for: Response to Elexacaftor/Tezacaftor/Ivacaftor in intestinal organoids derived from patients with cystic fibrosis
<p>Data and code to reproduce all statistical analyses and figure in the manuscript "Response to Elexacaftor/Tezacaftor/Ivacaftor in intestinal organoids derived from patients with cystic fibrosis".</p> <p>The dataset is stored in the file `area_data.csv`, the columns are:</p> <ul> <li>`well` The ID of the well within the plate the measurement was taken</li> <li>`time` time from start of measurement</li> <li>`area` area of the organoids</li> <li>`patient` Anonymized ID of the patient</li> <li>`date` Date when the experiment was performed (date and patient ID identify the plate)</li> <li>`filename` The filename in raw data (not published) this plate was stored in. (uniquely identifies a plate)</li> <li>`mix` Identifies one od two variants of plate layouts used</li> <li>`replicate` ID of technical replicate (two technical replicates were done for each condition on the same plate)</li> <li>`type` The main condition - one of "TEZ/IVA", "ELX/TEZ/IVA", "FskOnly" (Control, only forskolin)</li> <li>`fsk_concentration` concentration of forskolin (μM)</li> </ul> <p>The file "organoids.Rmd" reproduces the analyses, other files are supporting to let the main analysis run.</p> <p>The analysis is written in R markdown.</p> <p> </p>
Spermatogonial Differentiation Via Testicular Organoid
ClinicalTrials.gov study NCT06841861. IPD Sharing: NO. Countries: 1. Publications: 16.
Primary Organoid Models and Combined Nucleic Acids Therapeutics for Anti-HPV Treatments
ClinicalTrials.gov study NCT04278326. IPD Sharing: Not stated. Countries: 1. Publications: 5.
SOTO: Treatment Sensitivity of Organoids to Predict Treatment Outcome
ClinicalTrials.gov study NCT05400239. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Patient-derived Organoids Drug Screen in Pancreatic Cancer
ClinicalTrials.gov study NCT05351983. IPD Sharing: NO. Countries: 1. Publications: 8.
Pharmacotyping of Pancreatic Patient-derived Organoids
ClinicalTrials.gov study NCT05196334. IPD Sharing: NO. Countries: 1. Publications: 13.
Patient-derived Organoids of Lung Cancer to Test Drug Response
ClinicalTrials.gov study NCT03979170. IPD Sharing: NO. Countries: 1. Publications: 1.
Hepatocellular Carcinoma Liver Organoids
ClinicalTrials.gov study NCT06355700. IPD Sharing: NO. Countries: 1. Publications: 6.
Organoid-guided Personalized Treatment of Pleural Effusion
ClinicalTrials.gov study NCT06959173. IPD Sharing: NO. Countries: 1. Publications: 19.
In Vitro Organoid Drug Sensitivity-Guided Treatment for Advanced Pancreatic Neuroendocrine Tumor
ClinicalTrials.gov study NCT06246630. IPD Sharing: NO. Countries: 1. Publications: 10.
Selecting Chemotherapy With High-throughput Drug Screen Assay Using Patient Derived Organoids in Patients With Refractory Solid Tumours (SCORE)
ClinicalTrials.gov study NCT04279509. IPD Sharing: NO. Countries: 1. Publications: 2.
Patient-derived Organoid Drug Sensitivity Guided Treatment for Drug-resistant Recurrent Non-Small Cell Lung Cancer
ClinicalTrials.gov study NCT06406608. IPD Sharing: Not stated. Countries: 1. Publications: 10.
Prospective Clinical Validation of Next Generation Sequencing (NGS) and Patient-Derived Tumor Organoids (PDO) Guided Therapy in Patients with Advanced/ Inoperable Solid Tumors
ClinicalTrials.gov study NCT06077591. IPD Sharing: NO. Countries: 1. Publications: 11.
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.