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ShareScore release 0.9.0
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171 results for “brain organoids”
Murine brain organoids developmental profiling
<p>The dataset includes the RNA sequencing data generated for the study entitled "Murine cerebral organoids develop network of functional neurons and hippocampal brain region identity" by Ciarpella et al. Starting from mouse neuronal stem cells, we generate organoids to recapitulate the hippocampal structure as new platform for modeling diseases, for drug screening and for organ transplantation in regenerative medicine. Performing RNA sequencing in organoids at different stage of proliferation and maturation, we obtained a measure of the cellular diversity within the organoids, the degree of differentiation and the affinity to hippocampus or cortex tissue (reference samples). </p>
Data from: Identification of neural oscillations and epileptiform changes in human brain organoids.
<p>Seurat object containing processed single-cell RNA sequencing data described in:</p> <p>Samarasinghe, R.A., Miranda, O.A., Buth, J.E. <em>et al.</em> Identification of neural oscillations and epileptiform changes in human brain organoids. <em>Nat Neurosci</em> <strong>24, </strong>1488–1500 (2021). <a href="https://doi.org/10.1038/s41593-021-00906-5">https://doi.org/10.1038/s41593-021-00906-5</a></p> <p>Additional raw and processed data can be accessed at the Gene Expression Omnibus under accession number <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165577">GSE165577</a>. </p> <p> </p>
Source Data and Scripts - Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols
<p>Source data and scripts associated with the manuscript "<em>Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols</em>" (Naas et al. 2024, <em>bioRxiv</em>, <a href="https://doi.org/10.1101/2024.11.15.623576" rel="nofollow">DOI: 10.1101/2024.11.15.623576</a>). Corresponding scripts to reproduce all figures and tables presented in the manuscript are also available on <a href="https://github.com/jn-goe/brain_organoids_four_protocols">https://github.com/jn-goe/brain_organoids_four_protocols</a>.</p> <div> <div> <p>The therein introduced NEST-Score is available as R package on <a href="https://github.com/jn-goe/NESTScore">https://github.com/jn-goe/NESTScore</a>.</p> <p>The interactive Shiny App data explorer is available on <a href="https://vienna-brain-organoid-explorer.vbc.ac.at/">https://vienna-brain-organoid-explorer.vbc.ac.at</a>.</p> </div> </div>
Underlying data_Survey on human brain organoids [version 2]
<p> [version 2] Data on a survey of Japanese public attitudes toward human brain organoid research in Dec. 2022.</p>
Extended data_Survey on human brain organoids [version 2]
<p>[Version 2] The detail of the questionnaire, demographic information, and correlation tables of a survey of Japanese public attitudes toward human brain organoid research in Dec. 2022.</p>
A large and diverse brain organoid dataset of 1,400 cross-laboratory images of 64 trackable brain organoids from four different clones
<p>This dataset is presented in the paper <strong><span>A large and diverse brain organoid dataset of 1,400 cross-laboratory images of 64 trackable brain organoids from four different clones</span></strong></p> <p> </p> <p>This dataset encompasses two sources of data:</p> <ol> <li>A comma-separated values ('CSV') file. This file serves as a key to our dataset with one image per row. Each image is represented by its image identifier ('img_id') with the format [org_id]_[clone]_d[imaging_day]_[imaging_lab]. For each image, the CSV file also specifies the organoid size for convenience. Alternatively, the organoid size can be calculated using the ground truth organoid segmentation (org_segGT). </li> <li>For each row of the CSV file, we provide the image and org_segGT. For Lab A, the images are in JPEG format. For lab B, the images are in TIF format. Org_segGT is a manually created binary 2D NumPy array with the same size as the image (1024 x 768 for lab A, 1388 x 1040 for lab B). A value of 1 in org_segGT at position (x, y) means that the same position (x, y) in the corresponding image is covered by the organoid. The image file and the org_segGT file have the following format: [img_id].[jpg|tif] and [img_id].npy. For day 12, organoids were imaged before and after embedding from 96-well plates in 12-well plates, allowing the investigation of well-specific optical properties.</li> </ol> <p>For segmentation and growth monitoring using this dataset, please see <a href="https://github.com/deiluca/robust_monitoring_organoid_growth">https://github.com/deiluca/robust_monitoring_organoid_growth</a>.</p>
Resolving Organoid Brain Region Identities by Mapping Single-Cell Genomic Data to Reference Atlases
<p>Data underlying the figures in the publication “Resolving organoid brain region identities by mapping single-cell genomic data to reference atlases”, published in <em>Cell Stem Cell, </em><strong>2021</strong><em>, </em>28, 1148–1159.</p> <p><a href="https://www.sciencedirect.com/science/article/pii/S1934590921000655">https://www.sciencedirect.com/science/article/pii/S1934590921000655</a></p> <p>Table of contents:</p> <p><strong>1. patscreen_srt.rds</strong>; Numerical data for <em>Figure 7</em>: RNA-seq data of a patterning screen in organoids with an array of small molecules. The dataset is in the rds data format, which can be opened in the R programming language using the function `readRDS()`. Once opened, the dataset is a Seurat object (https://satijalab.org/seurat/) and contains both the transcript counts and the metadata for all samples in the screen. The raw data used in figure 7 was also deposited in ArrayExpress (<a href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-10037/">https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-10037/</a>)</p>
Extracellular Recordings from Human Brain Organoids Using High-density CMOS Arrays
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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>
Human myelinated brain organoids with integrated microglia as a model for myelin repair and remyelinating therapies
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Label-free three-photon imaging of intact human cerebral organoids: Tracking early events in brain development and deficits in Rett Syndrome
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Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution
GEO Series GSE124299. Pan troglodytes; Macaca mulatta; Homo sapiens. 3096 samples. Type: Expression profiling by high throughput sequencing; Third-party reanalysis.
In vivo intratumoral Heterogeneity in a dish: Scalable Forebrain Organoid Models of Embryonal Brain Tumors for High-Throughput Personalized Drug Discovery (human organoids+cell lines subset 1)
GEO Series GSE269254. Homo sapiens. 17 samples. Type: Expression profiling by high throughput sequencing.
Genetically Engineered Brain Organoids Recapitulate Spatial and Developmental States of Glioblastoma Progression [Xenium Spatial Transcriptomics]
GEO Series GSE283497. Homo sapiens. 6 samples. Type: Other.
Transcriptomic study of human brain organoids in Alzheimer's Disease
GEO Series GSE266358. Homo sapiens. 32 samples. Type: Expression profiling by high throughput sequencing.
A Shared Pathogenic Mechanism for Valproic Acid and SHROOM3 Knockout in a Brain Organoid Model of Neural Tube Defects
GEO Series GSE232218. Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
Identification of extensive cellular diversity and maturation of active neuronal networks in long-term cultures of human brain organoids
GEO Series GSE86153. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Gene expression profile at single cell level of human cortical brain organoids at day 20.
GEO Series GSE280890. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Brain organoids reproducibly generate the cellular diversity of the human cerebral cortex
GEO Series GSE129519. Homo sapiens. 21 samples. Type: Expression profiling by high throughput sequencing.
Morphological diversification and functional maturation of human astrocytes in glia-enriched cortical organoids transplanted in the mouse brain
GEO Series GSE185472. Homo sapiens. 12 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.