Single Cell Organoids

Single-cell organoids are three-dimensional, miniature tissue models generated from one isolated stem or progenitor cell, enabling researchers to study how individual cells produce organized biological structures. In a supportive three-dimensional matrix and defined culture conditions, the starting cell proliferates, differentiates, and self-organizes through intrinsic programs and cell-signaling interactions. These models help connect cellular behavior with tissue formation and function while reducing the complexity of conventional multicellular samples. In biology, single-cell organoids support studies of development, regeneration, disease mechanisms, and drug responses, and can reveal how cellular heterogeneity influences tissue-level outcomes.

Single Cell Organoids - Related Videos

Research

JoVE Journal - Cancer Research

Generation and Single-Cell Transcriptomic Analysis of Hepatocellular Carcinoma Organoids following Drug Treatment

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2026

This protocol outlines a streamlined method for generating hepatocellular carcinoma organoids, applying drug treatment, and performing single-cell RNA sequencing before and after treatment to characterize treatment-associated transcriptional changes.

Research

JoVE Journal - Cancer Research
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Multiparametric Tumor Organoid Drug Screening Using Widefield Live-Cell Imaging for Bulk and Single-Organoid Analysis

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Cited by 16 •

2022

This protocol describes a semi-automated method for medium- to high-throughput organoid drug screenings and microscope-agnostic, automated image analysis software to quantify and visualize multiparametric, single-organoid drug responses to capture intratumor heterogeneity.

Live-Cell Imaging and Single-Cell Tracking to Monitor Clonal Dynamics and Fate Transitions in Human and Murine Intestinal Organoids

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2026

We describe confocal imaging and tracking pipelines applied to two reporter strategies: mosaic organoids for resolving individual cell behavior and fate reporter organoids for monitoring cell type transitions in human and murine intestinal organoids.

Generation and Downstream Analysis of Single-Cell and Single-Nuclei Transcriptomes in Brain Organoids

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2024

Here, we introduce a comprehensive protocol for the generation and downstream analysis of human brain organoids using single-cell and single-nucleus RNA sequencing.

Generating Mature Cerebellar Organoids From Induced Pluripotent Stem Cells Using Single-Use Bioreactors

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2025

This video demonstrates a technique for generating mature cerebellar organoids from induced pluripotent stem cells (iPSCs) using a single-use 3D bioreactor. The bioreactor facilitates iPSC aggregate formation, which then undergoes treatment with a series of culture media enriched in growth factors and chemokines that induce the differentiation of the iPSC aggregates into mature cerebellar organoids. Subsequently, the organoids are harvested and cryopreserved for further analysis.

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