SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data [preprint]
UMass Chan Affiliations
Program in Molecular MedicineDocument Type
PreprintPublication Date
2022-12-19Metadata
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Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometer and tens of kilobase 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 obtained comparable results of chromatin loops across datasets generated from diverse imaging technologies.Source
SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data. Lindsay Lee, Hongyu Yu, Bojing Blair Jia, Adam Jussila, Chenxu Zhu, Jiawen Chen, Liangqi Xie, Antonina Hafner, Caterina Strambio-De-Castillia, Alistair Boettiger, Bing Ren, Yun Li, Ming Hu. bioRxiv 2022.12.16.520793; doi: https://doi.org/10.1101/2022.12.16.520793DOI
10.1101/2022.12.16.520793Permanent Link to this Item
http://hdl.handle.net/20.500.14038/51490Notes
This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.Related Resources
Now published in Nature Communications, https://doi.org/10.1038/s41467-023-40658-3.Rights
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Except where otherwise noted, this item's license is described as The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.