Protocol to profile snATAC-seq datasets and motif enrichment analysis during zebrafish early embryogenesis
Summary: The scarcity of zebrafish-specific motif databases presents a challenge to the analysis of transcription factor (TF) motif within zebrafish single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data, thus hindering the identification of regulatory elements thr...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-12-01
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| Series: | STAR Protocols |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S266616672400666X |
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| author | Jie Zhou Xueqian Yang Xiumei Lin Kaichen Zhao Xue Wang Zhiqiang Dong Chuanyu Liu Chang Liu |
| author_facet | Jie Zhou Xueqian Yang Xiumei Lin Kaichen Zhao Xue Wang Zhiqiang Dong Chuanyu Liu Chang Liu |
| author_sort | Jie Zhou |
| collection | DOAJ |
| description | Summary: The scarcity of zebrafish-specific motif databases presents a challenge to the analysis of transcription factor (TF) motif within zebrafish single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data, thus hindering the identification of regulatory elements throughout zebrafish embryonic development. Here, we provide a protocol to analyze single-nucleus chromatin accessibility dataset during zebrafish early embryogenesis. We describe steps for fragment file retrieval, sample integration, quality control, Latent Semantic Indexing (LSI) clustering, and peak calling via ArchR. Crucially, we detail procedures for zebrafish-specific motif database construction, motif enrichment, and TF footprinting analysis.For complete details on the use and execution of this protocol, please refer to Lin 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-474a02b95031497583ffd0109c57c0b3 |
| institution | OA Journals |
| issn | 2666-1667 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-474a02b95031497583ffd0109c57c0b32025-08-20T01:59:35ZengElsevierSTAR Protocols2666-16672024-12-015410350110.1016/j.xpro.2024.103501Protocol to profile snATAC-seq datasets and motif enrichment analysis during zebrafish early embryogenesisJie Zhou0Xueqian Yang1Xiumei Lin2Kaichen Zhao3Xue Wang4Zhiqiang Dong5Chuanyu Liu6Chang Liu7BGI Research, Shenzhen 518083, China; BGI Research, Hangzhou 310030, China; Corresponding authorCollege of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, ChinaBGI Research, Shenzhen 518083, China; BGI Research, Hangzhou 310030, ChinaBGI Research, Hangzhou 310030, China; College of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, ChinaBGI Research, Hangzhou 310030, ChinaCollege of Biomedicine and Health, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Center for Neurological Disease Research, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, ChinaBGI Research, Shenzhen 518083, China; Corresponding authorBGI Research, Shenzhen 518083, China; BGI Research, Hangzhou 310030, China; Corresponding authorSummary: The scarcity of zebrafish-specific motif databases presents a challenge to the analysis of transcription factor (TF) motif within zebrafish single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data, thus hindering the identification of regulatory elements throughout zebrafish embryonic development. Here, we provide a protocol to analyze single-nucleus chromatin accessibility dataset during zebrafish early embryogenesis. We describe steps for fragment file retrieval, sample integration, quality control, Latent Semantic Indexing (LSI) clustering, and peak calling via ArchR. Crucially, we detail procedures for zebrafish-specific motif database construction, motif enrichment, and TF footprinting analysis.For complete details on the use and execution of this protocol, please refer to Lin 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/S266616672400666Xbioinformaticssingle celldevelopmental biologymodel organisms |
| spellingShingle | Jie Zhou Xueqian Yang Xiumei Lin Kaichen Zhao Xue Wang Zhiqiang Dong Chuanyu Liu Chang Liu Protocol to profile snATAC-seq datasets and motif enrichment analysis during zebrafish early embryogenesis STAR Protocols bioinformatics single cell developmental biology model organisms |
| title | Protocol to profile snATAC-seq datasets and motif enrichment analysis during zebrafish early embryogenesis |
| title_full | Protocol to profile snATAC-seq datasets and motif enrichment analysis during zebrafish early embryogenesis |
| title_fullStr | Protocol to profile snATAC-seq datasets and motif enrichment analysis during zebrafish early embryogenesis |
| title_full_unstemmed | Protocol to profile snATAC-seq datasets and motif enrichment analysis during zebrafish early embryogenesis |
| title_short | Protocol to profile snATAC-seq datasets and motif enrichment analysis during zebrafish early embryogenesis |
| title_sort | protocol to profile snatac seq datasets and motif enrichment analysis during zebrafish early embryogenesis |
| topic | bioinformatics single cell developmental biology model organisms |
| url | http://www.sciencedirect.com/science/article/pii/S266616672400666X |
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