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2,182 results for “organoid”
Annotated mouse intestinal organoid dataset (YOLO format)
<p>Dataset of 840 light-transmitted images taken with EVOS FL microscope (Thermo Fisher) at objective 4X of mouse intestinal organoids grown at different densities and from multiple stages of culture. The dataset has a total of 23066 annotations<strong>. </strong>The images were manually annotated using the python library labelImg and exported for Yolo format as text files. The four classes of organoids in the text files are coded with integers: 0 for organoid0, 1 for organoid1, 2 for organoid3, and 3 for spheroid. The dataset images were split into a training and validation set consisting of 756 and 84 images using the python library module splitfolders. See publication ( doi:<a href="https://doi.org/10.1242/dmm.049756">10.1242/dmm.049756</a>) for more details. </p> <p><strong>Annotations</strong></p> <table> <tbody> <tr> <td> <p><strong>Class </strong></p> </td> <td> <p><strong>Description</strong></p> </td> <td> <p><strong> Label</strong></p> </td> </tr> <tr> <td> <p>Cystic organoid</p> </td> <td> <p>Very early stage, small, cystic, non-budding organoids with thick walls</p> </td> <td> <p><em>Organoid0</em></p> </td> </tr> <tr> <td> <p>Early organoid</p> </td> <td> <p>Early, budding organoids with 1-2 crypts</p> </td> <td> <p><em>Organoid1</em></p> </td> </tr> <tr> <td> <p>Late organoid</p> </td> <td> <p>Large, budding organoids with 3 or more crypt units</p> </td> <td> <p><em>Organoid3</em></p> </td> </tr> <tr> <td> <p>Spheroid</p> </td> <td> <p>Large, circular, thin-walled organoids representing, e.g. fetal, regenerating, tumorigenic, or hyperstimulated organoids </p> </td> <td> <p><em>Spheroid</em></p> </td> </tr> </tbody> </table>
Trellis Single-Cell Screening Reveals Stromal Regulation of Patient-Derived Organoid Drug Responses
<p>Patient-derived organoids (PDOs) can model personalized therapy responses, however current screening technologies cannot reveal drug response mechanisms or how tumor microenvironment cells alter therapeutic performance. To address this, we developed a highly-multiplexed mass cytometry platform to measure post translational modification (PTM) signaling, DNA-damage, cell-cycle activity, and apoptosis in >2,500 colorectal cancer (CRC) PDOs and cancer associated fibroblasts (CAFs) in response to clinical therapies at single-cell resolution. To compare patient- and microenvironment-specific drug responses in thousands of single-cell datasets, we developed <em>Trellis</em> — a highly-scalable, hierarchical tree-based treatment effect analysis method. Trellis single-cell screening revealed that on-target cell-cycle blockage and DNA-damage drug effects are common, even in chemorefractory PDOs. However, drug-induced apoptosis is rare, patient-specific, and aligns with cancer cell PTM signaling. We find that CAFs can regulate cancer cell plasticity — shifting proliferative stem cells to slow-cycling revival stem cells via YAP to protect cancer cells from chemotherapy.</p> <p> </p> <p>This repo contains the processed scRNA-seq Scanpy AnnData objects generated from the study. More information describing the data can be found at: https://github.com/TAPE-Lab/Ramos-et-al-Trellis</p>
Brainwaves Monitoring via Human Midbrain Organoids Microphysiological Analysis Platform: MAP
<p>This dataset corresponds to the research manuscript entitled "Brainwaves Monitoring via Human Midbrain Organoids Microphysiological Analysis Platform: MAP"</p>
Patient-Derived Tumor Organoid and Fibroblast Assembloid Models for interrogation of the tumor microenvironment in Esophageal Adenocarcinoma
<p>This repository contains original microscopy data from the Sharpe et al. paper, "Patient-Derived Tumor Organoid and Fibroblast Assembloid Models for interrogation of the tumor microenvironment in Esophageal Adenocarcinoma" in Cell Reports Methods 2024.</p> <p>All whole slide images were obtained using an LM dotSlide slide scanning microscope in Olympus .vsi format and can be opened using the BioFormats library (for example, in QuPath). Wholemount immunofluorescent stains were imaged on a Leica SP8 laser-scanning confocal microscope and are presented as .IMS files, which allows for visualization and further analysis of the 3D data in Imaris (Oxford Instruments).</p> <p>Data are arranged in subfolders based on the figure they came from (Figures 1-4).</p>
The Culture of Advanced or Recurrent Ovarian Cancer Organoids and Drug Screening
ClinicalTrials.gov study NCT05290961. IPD Sharing: NO. Countries: 1. Publications: 14.
The Culture of Advanced/Recurrent/Metastatic Colorectal Cancer Organoids and Drug Screening
ClinicalTrials.gov study NCT05304741. IPD Sharing: NO. Countries: 1. Publications: 7.
Extracellular Recordings from Human Brain Organoids Using High-density CMOS Arrays
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Human tau mutations in cerebral organoids induce a progressive dyshomeostasis of cholesterol
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Myelomeningocele spinal cord organoids scRNAseq
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Differential Effects of Confinement on the Dynamics of Normal and Tumor-Derived Pancreatic Ductal Organoids
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Bulk and single-cell RNA-seq of human fetal pancreatic organoids
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Human nasal epithelial organoids for therapeutic development in cystic fibrosis
<p>Table S1: Individual subject demographics and available clinical data for selected participants contributing functional data. Figure S1: Example measurement of µOCT ciliary beat frequencies, Figure S2: Organoid CFTR (green) co-localization with apical ZO-1 (red). (A) To illustrate the location of the ZO-1 staining within the organoid, an alpha-blended 3-D volume reconstruction was created with the fluorescence intensity increased to reveal the organoid’s shape and orient the reader to the location of the 2D co-localization image below. (B) Magnified view of the yellow frame in (A) to better visualize the CFTR and ZO-1 overlay, Video S1: Brightfield video of luminal movement of mucus, Video S2: µOCT video of luminal movement of mucus, Video S3: Brightfield video of luminal cilia beating, Video S4: µOCT video of cilia beating, Video S5: FIS assay of non-CF organoids, Video S6: FIS assay of F508del/P67L organoids. Video S7: FIS assay of F508del/F508del organoids.</p>
Endocannabinoid signalling in stem cells and cerebral organoids drives differentiation to deep layer projection neurons via CB1 receptors
<p>The endocannabinoid (eCB) system, <i>via</i> cannabinoid CB<sub>1</sub> receptor, regulates neurodevelopment by controlling neural progenitor proliferation and neurogenesis. CB<sub>1</sub> receptor signalling <i>in vivo</i> drives corticofugal deep layer projection neuron development through the regulation of <span>BCL11B </span>and <span>Satb2</span> transcription factors. Here, we investigated the role of eCB signalling in mouse pluripotent embryonic stem cell-derived neuronal differentiation. Characterization of the eCB system revealed increased expression of eCB-metabolizing enzymes, eCB ligands and CB<sub>1</sub> receptors along neuronal differentiation. CB<sub>1</sub> receptor knockdown inhibited neuronal differentiation of deep layer neurons and increased upper layer neuron generation, and this phenotype was rescued by CB<sub>1</sub> re-expression. Pharmacological regulation with CB<sub>1</sub> receptor agonists or elevation of eCB tone with a monoacylglycerol lipase inhibitor promoted neuronal differentiation of deep layer neurons at the expense of upper layer neurons. Patch-clamp analyses revealed that enhancing cannabinoid signalling facilitated neuronal differentiation and functionality. Noteworthy, incubation with CB<sub>1</sub> receptor agonists during human iPSC-derived cerebral organoid formation also promoted the expansion of BCL11B<sup>+</sup> neurons. These findings unveil a cell-autonomous role of eCB signalling that, <i>via</i> CB<sub>1</sub> receptor, promotes mouse and human deep layer cortical neuron development.</p>
The model for new data mapping to human endoderm-derived organoids cell atlas (HEOCA)
<p><strong>The model for new data mapping to human endoderm-derived organoids cell atlas (HEOCA).</strong></p>
Data and figures from: "Organoid research through the lens of scientometrics"
<p>This package contains data and figures related to the publication:</p> <p>Keisuke Okamura, “Organoid research through the lens of scientometrics”, <em>Jikken Igaku</em> (Experimental Medicine) Special Issue Vol. 42, No. 5 (2024).</p>
Colorectal cancer patients-derived immunity-organoid platform unveils cancer-specific tissue markers associated with immunotherapy resistance.
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Data and scripts supporting "Metabolic profiling of patient-derived organoids reveals nucleotide synthesis as a metabolic vulnerability in malignant rhabdoid tumors"
<p>This submission contains the processed sequencing data and analysis scripts, as well as the raw and processed LC-MS metabolomics files accompanying our manuscript "Metabolic profiling of patient-derived organoids reveals nucleotide synthesis as a metabolic vulnerability in malignant rhabdoid tumors" (Cell Reports Medicine, 2024)</p>
Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids
<p>Source data and source code for the graphs in "Spatiotemporal dynamics of self-organized branching pancreatic cancer-derived organoids".</p>
Label-free three-photon imaging of intact human cerebral organoids: Tracking early events in brain development and deficits in Rett Syndrome
<p>Human cerebral organoids are unique in their development of progenitor-rich zones akin to ventricular zones from which neuronal progenitors differentiate and migrate radially. Analyses of cerebral organoids thus far have been performed in sectioned tissue or in superficial layers due to their high scattering properties. Here, we demonstrate label-free three-photon imaging of whole, uncleared intact organoids (~2 mm depth) to assess early events of early human brain development. Optimizing a custom-made three-photon microscope to image intact cerebral organoids generated from Rett Syndrome patients, we show defects in the ventricular zone volumetric structure of mutant organoids compared to isogenic control organoids. Long-term imaging of live organoids reveals that shorter migration distances and slower migration speeds of mutant radially migrating neurons are associated with more tortuous trajectories. Our label-free imaging system constitutes a particularly useful platform for tracking normal and abnormal development in individual organoids, as well as for screening therapeutic molecules via intact organoid imaging.</p>
Supplemental material for: The estrogen receptor α cistrome in human endometrium and epithelial organoids
<p>Endometrial health is impacted by molecular processes that underlie estrogen responses. We assessed estrogen regulation of endometrial function by integrating the estrogen receptor alpha (ESR1) cistromes and transcriptomes of endometrial biopsies taken from the proliferative and mid-secretory phases of the menstrual cycle together with hormonally stimulated endometrial epithelial organoids. The cycle stage specific ESR1 binding sites were determined by ChIPseq and then integrated with changes in gene expression from RNAseq data to infer candidate ESR1 targets in normal endometrium. Genes with ESR1 binding in whole endometrium were enriched for chromatin modification and regulation of cell proliferation. The distribution of ESR1 binding sites in organoids was more distal from gene promoters when compared to primary endometrium and was more similar to the proliferative than the mid-secretory phase ESR1 cistrome. Inferred organoid estrogen/ESR1 candidate target genes impacted formation of cellular protrusions, and chromatin modification. Comparison of signaling impacted by candidate ESR1 target genes in endometrium vs. organoids reveals enrichment of both overlapping and distinct responses. Our analysis of the ESR1 cistromes and transcriptomes from endometrium and organoids provides important resources for understanding how estrogen impacts endometrial health and function.</p>
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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.