Organoid Processing
Organoid Processing - Related Videos
08:07
Culturing, Freezing, Processing, and Imaging of Entire Organoids and Spheroids While Still in a Hydrogel
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Cited by 1 •
2022
The present study describes methodologies for culturing, freezing, thawing, processing, staining, labeling, and examining entire spheroids and organoids under various microscopes, while they remain intact in a hydrogel within a multipurpose device.
05:11
Organoid Electroporation: A Method to Transfect Plasmid DNA into Gastrointestinal Organoids
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2023
This video describes the electroporation protocol for transfecting large plasmids into three-dimensional gastrointestinal organoids to prove its universal functionality in different entities, namely pancreatic ductal adenocarcinoma (PDAC), colorectal cancer (CRC), cholangiocarcinoma (CCC), and gastric cancer (GC) organoids.
05:45
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.
05:38
Generation of Apical-Out Intestinal Organoids and Assessment of Organoid Proliferation Rate Using EdU-Labeling
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Cited by 1 •
2025
Here, we describe a protocol for generating apical-out intestinal organoids from standard matrix-embedded organoid cultures. It also outlines the subsequent incorporation of EdU into actively proliferating cells and the semiautomatic quantification of EdU-positive cells.
10:43
Modeling Oral-Esophageal Squamous Cell Carcinoma in 3D Organoids
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Cited by 10 •
2022
This protocol describes the key steps to generate and characterize murine oral-esophageal 3D organoids that represent normal, preneoplastic, and squamous cell carcinoma lesions induced via chemical carcinogenesis.
FAQs
The downstream assay determines whether organoids should remain intact, be dissociated into individual cells, or be fixed, embedded, and sectioned. Intact preparations support examination of overall architecture, while dissociation enables analysis of cell composition. Fixed and sectioned material supports microscopy of spatial organization. Matching processing to the assay helps retain the features needed for reliable biological interpretation.
Dissociation separates the three-dimensional culture into individual cells, shifting analysis toward cellular composition rather than preserved tissue architecture. This can support molecular profiling or comparisons of cell populations, but it does not provide the same spatial information as an intact or sectioned preparation. The choice therefore depends on whether the experiment prioritizes individual-cell characteristics or organization within the organoid.
Fixation and embedding prepare organoids for sectioning, allowing researchers to examine internal regions rather than only the outer surface. Sectioned material can reveal spatial organization, cellular composition, and structural development through microscopy. Careful handling during these stages is important because the usefulness of the resulting images depends on retaining relevant cellular and architectural features.
A typical workflow begins by collecting organoids from culture and then selecting a preparation according to the planned analysis. Samples may be dissociated for individual-cell studies or fixed and embedded before sectioning for structural examination. The processed material is then directed to microscopy, molecular profiling, or functional comparison, with handling chosen to preserve the features relevant to each assay.
Processed organoids can provide information about spatial organization, cell composition, and structural development. Depending on the workflow, they can also support microscopy, molecular profiling, and functional comparisons across experimental conditions. These outcomes allow investigators to connect three-dimensional growth with measurable biological features rather than relying only on observations made during culture.
In biology, processing links organoid models to questions about tissue development, disease mechanisms, drug responses, and regenerative biology. Comparing appropriately processed samples across conditions can reveal changes in structure, composition, or function. The value of these comparisons depends on consistent handling, because differences in preparation may affect how cellular and architectural features are observed.