Protocol for comparative gene expression data analysis between brains and organoids using a cloud-based web app.

Area of Science:

• Developmental biology
• Computational biology
• Genomics

Background:

• Comparative analysis of brain and organoid development is crucial for understanding human biology and disease.
• Existing methods may not fully capture the complex gene expression dynamics between these systems.
• Standardized protocols are needed for robust analysis of developmental trajectories.

Purpose of the Study:

• To present a protocol for comparative gene expression analysis between brains and organoids using the Brain and Organoid Manifold Alignment (BOMA) web application.
• To enable detailed investigation of shared and distinct developmental pathways.
• To provide a method applicable to both single-cell and bulk RNA sequencing data.

Main Methods:

• Utilizing the cloud-based Brain and Organoid Manifold Alignment (BOMA) web application.
• Performing global alignment of developmental gene expression data from brains and organoids.
• Refining alignment locally using manifold learning to investigate developmental pathways.

Main Results:

• A standardized protocol for comparative gene expression analysis between brains and organoids.
• Identification of shared and distinctive developmental pathways.
• Successful application to both single-cell and bulk RNA sequencing datasets.

Conclusions:

• Brain and Organoid Manifold Alignment (BOMA) offers a robust framework for comparative developmental gene expression analysis.
• The protocol facilitates deeper insights into conserved and divergent developmental processes.
• This approach enhances the utility of organoids as models for brain development and disease.