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SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data

dc.contributor.authorLee, Lindsay
dc.contributor.authorYu, Hongyu
dc.contributor.authorJia, Bojing Blair
dc.contributor.authorJussila, Adam
dc.contributor.authorZhu, Chenxu
dc.contributor.authorChen, Jiawen
dc.contributor.authorXie, Liangqi
dc.contributor.authorHafner, Antonina
dc.contributor.authorMishra, Shreya
dc.contributor.authorWang, Duan Dennis
dc.contributor.authorStrambio-De-Castillia, Caterina
dc.contributor.authorBoettiger, Alistair
dc.contributor.authorRen, Bing
dc.contributor.authorLi, Yun
dc.contributor.authorHu, Ming
dc.date.accessioned2024-07-02T14:35:29Z
dc.date.available2024-07-02T14:35:29Z
dc.date.issued2023-08-12
dc.identifier.citationLee L, Yu H, Jia BB, Jussila A, Zhu C, Chen J, Xie L, Hafner A, Mishra S, Wang DD, Strambio-De-Castillia C, Boettiger A, Ren B, Li Y, Hu M. SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data. Nat Commun. 2023 Aug 12;14(1):4873. doi: 10.1038/s41467-023-40658-3. PMID: 37573342; PMCID: PMC10423204.en_US
dc.identifier.eissn2041-1723
dc.identifier.doi10.1038/s41467-023-40658-3en_US
dc.identifier.pmid37573342
dc.identifier.urihttp://hdl.handle.net/20.500.14038/53538
dc.description.abstractMultiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometers and up to several kilobases in resolution in single cells. However, computational methods to reliably identify chromatin loops from such imaging datasets are still lacking. Here we present a Single-Nucleus Analysis Pipeline for multiplexed DNA FISH (SnapFISH), to process the multiplexed DNA FISH data and identify chromatin loops. SnapFISH can identify known chromatin loops from mouse embryonic stem cells with high sensitivity and accuracy. In addition, SnapFISH obtains comparable results of chromatin loops across datasets generated from diverse imaging technologies. SnapFISH is freely available at https://github.com/HuMingLab/SnapFISH .en_US
dc.language.isoen
dc.relationThis article is based on a previously available preprint in bioRxiv, https://doi.org/10.1101/2022.12.16.520793.en_US
dc.relation.ispartofNature Communicationsen_US
dc.relation.urlhttps://doi.org/10.1038/s41467-023-40658-3en_US
dc.rightsOpen Access: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/ licenses/by/4.0/. © The Author(s) 2023; Attribution 4.0 Internationalen_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.titleSnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH dataen_US
dc.typeJournal Articleen_US
dc.source.journaltitleNature communications
dc.source.volume14
dc.source.issue1
dc.source.beginpage4873
dc.source.endpage
dc.source.countryUnited States
dc.source.countryUnited States
dc.source.countryUnited States
dc.source.countryUnited States
dc.source.countryUnited States
dc.source.countryUnited States
dc.source.countryUnited States
dc.source.countryEngland
dc.identifier.journalNature communications
refterms.dateFOA2024-07-02T14:35:31Z
dc.contributor.departmentProgram in Molecular Medicineen_US


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Open Access: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/ licenses/by/4.0/. © The Author(s) 2023; Attribution 4.0 International
Except where otherwise noted, this item's license is described as Open Access: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/ licenses/by/4.0/. © The Author(s) 2023; Attribution 4.0 International