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

Here, we present a protocol for using Brain and Organoid Manifold Alignment (BOMA), a cloud-based web app for comparative gene expression data analysis between brains and organoids. We describe steps for performing a global alignment of developmental gene expression data from both brains and organoids. We then detail procedures for investigating both shared and distinctive developmental pathways across brains and organoids by refining alignment locally using manifold learning. This protocol is applicable for working with single-cell and bulk RNA sequencing data. For complete details on the use and execution of this protocol, please refer to He et al.1 1