{"doi":"10.1016/j.xpro.2024.103375","title":"Protocol for comparative gene expression data analysis between brains and organoids using a cloud-based web app","abstract":"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 • User-friendly cloud-based web app for brain and organoid manifold alignment • Guidance on the preparation of user input using gene expression data and metadata • Steps for alignment featuring 3D interactive plots and downloadable data files • Instructions to obtain clustering analysis results with interactive plots and heatmaps Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. 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.","journal":"STAR Protocols","year":2024,"id":504575,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9451,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1355438,"name":"Pubudu Kumarage","orcid":null,"position":1,"is_corresponding":false},{"id":1037791,"name":"Soraya O. Sandoval","orcid":"0000-0002-5911-5940","position":2,"is_corresponding":false},{"id":286644,"name":"Xinyu Zhao","orcid":"0000-0002-5128-4424","position":3,"is_corresponding":false},{"id":249243,"name":"Daifeng Wang","orcid":"0000-0001-9190-3704","position":4,"is_corresponding":false},{"id":1061437,"name":"Xiang Huang","orcid":"0000-0002-4456-5893","position":0,"is_corresponding":true}],"reference_count":9,"raw_metadata":null,"created_at":"2026-07-19T02:10:39.578471Z","pmid":"39392746","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}