ArticleSTAR protocols2024
Protocol for comparative gene expression data analysis between brains and organoids using a cloud-based web app.
Xiang Huang, Pubudu Kumarage, Soraya Sandoval, Xinyu Zhao, Daifeng Wang
Abstract readComparative Study
In one paragraphArticle in STAR protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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2 · The registryThe trial behind it
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4 · The recordCorrections and comments
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5 · Who and what moneyAuthors and funding
5 authors.
Xiang HuangWaisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA.
Pubudu KumarageWaisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA.
Soraya SandovalWaisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA.
Xinyu ZhaoWaisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA.
Daifeng WangWaisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address: daifeng.wang@wisc.edu.
Funding
Understanding the molecular mechanisms that contribute to neuropsychiatric symptoms in Alzheimer DiseaseR01AG067025 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI FINKBEINER, STEVEN M, HAROUTUNIAN, VAHRAM · 2019 to 2023
$11.8MWaisman Center Intellectual and Developmental Disabilities Research CenterP50HD105353 · NICHD · UNIVERSITY OF WISCONSIN-MADISON · PI Brittany Gail Travers · 2021 to 2026
$8.5MThe Role of MDM2 in FMRP regulation of neuronal developmentR01MH116582 · NIMH · UNIVERSITY OF WISCONSIN-MADISON · PI ZHAO, XINYU · 2018 to 2022
$2.2MThe role of RNA binding protein in FXR1P in interneuronsR01MH118827 · NIMH · UNIVERSITY OF WISCONSIN-MADISON · PI ZHAO, XINYU · 2019 to 2023
$2.2MInterrogate FMRP functions in primate brain developmentR01MH136152 · NIMH · UNIVERSITY OF WISCONSIN-MADISON · PI Xinyu Zhao · 2024 to 2026
$2.2MIntegration of Experience-Induced Gene Expression and Circuit FunctionsR01NS105200 · NINDS · UNIVERSITY OF WISCONSIN-MADISON · PI JACKSON, MEYER B., ZHAO, XINYU · 2018 to 2022
$2.0MFMRP regulation of mitochondria and metabolism in mammalian brain developmentR01NS138268 · NINDS · UNIVERSITY OF WISCONSIN-MADISON · PI Xinyu Zhao · 2024 to 2026
$1.9MMachine learning analyses of single-cell multi-modal data for understanding cell-type functional genomics and gene regulationRF1MH128695 · NIMH · UNIVERSITY OF WISCONSIN-MADISON · PI WANG, DAIFENG · 2022 to 2022
$1.2MCreation of a Schwann Cell Gene Regulatory NetworkR21NS127432 · NINDS · UNIVERSITY OF WISCONSIN-MADISON · PI SVAREN, JOHN P, WANG, DAIFENG · 2022 to 2023
$401kPrediction and Validation of Oligodendrocyte Gene Regulatory Network from Multi-OmicsR21NS128761 · NINDS · UNIVERSITY OF WISCONSIN-MADISON · PI SVAREN, JOHN P, WANG, DAIFENG · 2022 to 2022
$401kCharacterization of Fragile X Syndrome 3D Cortical OrganoidsR36MH136790 · NIMH · UNIVERSITY OF WISCONSIN-MADISON · PI SANDOVAL, SORAYA OROZCO · 2024 to 2025
$91kNIA NIH HHS R01 AG067025NICHD NIH HHS P50 HD105353NIMH NIH HHS R01 MH116582NIMH NIH HHS R01 MH118827NIMH NIH HHS R01 MH136152NIMH NIH HHS R36 MH136790NIMH NIH HHS RF1 MH128695NINDS NIH HHS R01 NS105200NINDS NIH HHS R01 NS138268NINDS NIH HHS R21 NS127432NINDS NIH HHS R21 NS128761
6 · The paper itselfAbstract
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.
Indexed as
BrainOrganoidsCloud ComputingGene Expression ProfilingHumansSequence Analysis, RNASoftwarebioinformaticsdevelopmental biologygene expressionorganoids
Identifiers
PMID39392746
PMCPMC11736003
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LicenceCC BY-NC-ND
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