Protocol for predicting the single-cell network-based gene activity landscape during human B cell development
Summary: Owing to inconsistencies in human B cell classification and the difficulty in distinguishing heterogeneous subpopulations, we present a protocol to construct gene regulatory networks and gene activity landscapes for human B cell developmental stages. We describe steps for acquiring bone mar...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-03-01
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| Series: | STAR Protocols |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166725000206 |
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| author | Xin Huang Xuetong Hou Yizhen Li Jun J. Yang Jiyang Yu |
| author_facet | Xin Huang Xuetong Hou Yizhen Li Jun J. Yang Jiyang Yu |
| author_sort | Xin Huang |
| collection | DOAJ |
| description | Summary: Owing to inconsistencies in human B cell classification and the difficulty in distinguishing heterogeneous subpopulations, we present a protocol to construct gene regulatory networks and gene activity landscapes for human B cell developmental stages. We describe steps for acquiring bone marrow data; conducting single-cell downstream analysis; and leveraging the St. Jude Algorithm for the Reconstruction of Accurate Cellular Networks (SJARACNe), Network-based Bayesian Inference of Drivers (NetBID2), and single-cell Mutual Information-based Network Engineering Ranger (scMINER) algorithms for network-based analysis. Our protocol elucidates the biological characteristics of developmental stages in human B cells.For complete details on the use and execution of this protocol, please refer to Huang et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-3cf16f66ca6645ccb0b9d9f670f6759a |
| institution | Kabale University |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-3cf16f66ca6645ccb0b9d9f670f6759a2025-02-09T05:01:24ZengElsevierSTAR Protocols2666-16672025-03-0161103614Protocol for predicting the single-cell network-based gene activity landscape during human B cell developmentXin Huang0Xuetong Hou1Yizhen Li2Jun J. Yang3Jiyang Yu4Precision Research Center for Refractory Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China; Corresponding authorInstitute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, Anhui 230601, ChinaDepartment of Hematology, Children’s Hospital of Soochow University, Soochow University, Suzhou, Jiangsu 215003, China; Pediatric Hematology & Oncology Key Laboratory of Higher Education Institutions in Jiangsu Province, Suzhou, Jiangsu 215003, ChinaPediatric Hematology & Oncology Key Laboratory of Higher Education Institutions in Jiangsu Province, Suzhou, Jiangsu 215003, China; Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; Hematological Malignancies Program, St. Jude Children’s Research Hospital, Memphis, TN 38105, USADepartment of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; Corresponding authorSummary: Owing to inconsistencies in human B cell classification and the difficulty in distinguishing heterogeneous subpopulations, we present a protocol to construct gene regulatory networks and gene activity landscapes for human B cell developmental stages. We describe steps for acquiring bone marrow data; conducting single-cell downstream analysis; and leveraging the St. Jude Algorithm for the Reconstruction of Accurate Cellular Networks (SJARACNe), Network-based Bayesian Inference of Drivers (NetBID2), and single-cell Mutual Information-based Network Engineering Ranger (scMINER) algorithms for network-based analysis. Our protocol elucidates the biological characteristics of developmental stages in human B cells.For complete details on the use and execution of this protocol, please refer to Huang et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S2666166725000206bioinformaticsimmunologysingle Cellsystems biology |
| spellingShingle | Xin Huang Xuetong Hou Yizhen Li Jun J. Yang Jiyang Yu Protocol for predicting the single-cell network-based gene activity landscape during human B cell development STAR Protocols bioinformatics immunology single Cell systems biology |
| title | Protocol for predicting the single-cell network-based gene activity landscape during human B cell development |
| title_full | Protocol for predicting the single-cell network-based gene activity landscape during human B cell development |
| title_fullStr | Protocol for predicting the single-cell network-based gene activity landscape during human B cell development |
| title_full_unstemmed | Protocol for predicting the single-cell network-based gene activity landscape during human B cell development |
| title_short | Protocol for predicting the single-cell network-based gene activity landscape during human B cell development |
| title_sort | protocol for predicting the single cell network based gene activity landscape during human b cell development |
| topic | bioinformatics immunology single Cell systems biology |
| url | http://www.sciencedirect.com/science/article/pii/S2666166725000206 |
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