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Related Experiment Video

Updated: May 15, 2025

Author Spotlight: Integrating Organoid Models with Single-Cell and Spatial Transcriptomics Technologies

Author Spotlight: Integrating Organoid Models with Single-Cell and Spatial Transcriptomics Technologies

Published on: March 29, 2024

Micro-region transcriptomics profiling of cerebral organoids using a capillary-based microdissection system.

Kaiqiang Ye¹, Yunxia Guo^1,2, Ning Chang¹

¹State Key Laboratory of Digital Medical Engineering, School of Biological Science & Medical Engineering, Southeast University, Nanjing, Jiangsu, China. xwzhao@seu.edu.cn.

Analytical Methods : Advancing Methods and Applications

|April 11, 2025

Summary

This summary is machine-generated.

A new capillary-based system efficiently isolates micro-regions from cerebral organoids for spatial transcriptomics (ST). This method maps cell types and gene expression, revealing developmental changes in neural progenitor cells and astrocytes.

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Published on: November 13, 2011

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Last Updated: May 15, 2025

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Non-Laser Capture Microscopy Approach for the Microdissection of Discrete Mouse Brain Regions for Total RNA Isolation and Downstream Next-Generation Sequencing and Gene Expression Profiling |

Non-Laser Capture Microscopy Approach for the Microdissection of Discrete Mouse Brain Regions for Total RNA Isolation and Downstream Next-Generation Sequencing and Gene Expression Profiling |

Published on: November 13, 2011

Area of Science:

Neuroscience
Genomics
Developmental Biology

Background:

Preserving spatial information in transcriptomics is crucial for understanding cellular fates.
Precise isolation of micro-regions of interest (mROIs) for spatial transcriptomics (ST) is challenging.

Purpose of the Study:

To develop an efficient method for spatial transcriptomics analysis in cerebral organoids.
To profile cellular composition and gene expression in specific mROIs.
To investigate spatial developmental trajectories in cerebral organoids.

Main Methods:

Established a capillary-based tissue microdissection system (CMS) for mROI acquisition.
Performed mRNA sequencing (CMS-seq) on isolated mROIs from cerebral organoids.
Annotated cell types (NPCs, IPs, neurons, astrocytes) and analyzed gene expression at different developmental stages (days 20 and 60).
Utilized Gene Ontology (GO) and KEGG pathway analysis for differentially expressed genes.

Main Results:

Successfully acquired mROIs from cultured cerebral organoids using CMS.
Annotated neural progenitor cells, intermediate progenitors, mature neurons, and astrocytes at days 20 and 60.
Observed distinct gene expression patterns in astrocytes at different stages (SPARC at day 20, NTRK2 at day 60).
Identified increased neural development at day 60 via GO and KEGG analysis.
Constructed a spatial cell-type annotation map for mROIs.

Conclusions:

The developed CMS provides an efficient method for ST analysis in cerebral organoids.
This technique enables detailed mapping of cell types and gene expression within organoids.
The study facilitates further exploration of spatial developmental trajectories in the brain.