Sangam: A Confluence of Knowledge Streams

Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models

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dc.contributor EPSRC - Engineering and Physical Sciences Research Council
dc.contributor ERC - European Research Council
dc.contributor Brackley, Chris A
dc.creator Brackley, Chris A
dc.creator Brown, Jill M
dc.creator Waithe, Dominic
dc.creator Babbs, Christian
dc.creator Davies, James
dc.creator Hughes, Jim R
dc.creator Buckle, Veronica J
dc.creator Marenduzzo, Davide
dc.date 2016-01-08T16:41:02Z
dc.date 2016-01-08T16:41:02Z
dc.date.accessioned 2023-02-17T20:53:44Z
dc.date.available 2023-02-17T20:53:44Z
dc.identifier Brackley, Chris A; Brown, Jill M; Waithe, Dominic; Babbs, Christian; Davies, James; Hughes, Jim R; Buckle, Veronica J; Marenduzzo, Davide. (2016). Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models, [dataset]. https://doi.org/10.7488/ds/1306.
dc.identifier https://hdl.handle.net/10283/1882
dc.identifier https://doi.org/10.7488/ds/1306
dc.identifier.uri http://localhost:8080/xmlui/handle/CUHPOERS/244141
dc.description The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation within a single cell, and the mechanisms leading to the observed interactions are still largely obscure. We present a polymer modelling scheme based on the assumption that chromosome architecture is maintained by protein bridges which form chromatin loops. To test the model we perform FISH experiments and also compare with Capture-C data. Starting merely from the locations of protein binding sites, our model accurately predicts the experimentally observed chromatin interactions, revealing a population of 3D conformations.
dc.description Experimental data sets, simulation data sets and files used to perform simulations are provided in gzipped tarballs. The README gives brief details of each zipped file, and each of these contains a further README with full details.
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dc.language eng
dc.relation http://arxiv.org/pdf/1601.02822.pdf
dc.relation CA Brackley, JM Brown, D Waithe, C Babbs, J Davies, JR Hughes, VJ Buckle, and D Marenduzzo "Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models" In Submission (2016)
dc.rights Creative Commons Attribution 4.0 International Public License
dc.subject chromosome conformation
dc.subject polymer model
dc.subject fluorescence in situ hybridization
dc.subject Physical Sciences
dc.title Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models
dc.type dataset
dc.coverage UK
dc.coverage UNITED KINGDOM


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accession_numbers.txt 1.483Kb text/plain View/Open
alphaglobin_mES_simulations.tar.gz 50.08Mb application/gzip View/Open
alphaglobin_Ter119_FISHdata.tar.gz 3.8Kb application/gzip View/Open
alphaglobin_Ter119_simulations.tar.gz 100.1Mb application/gzip View/Open
alphaglobin_Ter119CTCFKO_simulations.tar.gz 50.07Mb application/gzip View/Open
alphaglobin_Ter119DHSKO_simulations.tar.gz 7.474Mb application/gzip View/Open
alphaglobin_Ter ... ailR2KO_simulations.tar.gz 50.10Mb application/gzip View/Open
alphaglobin_Ter119moredetailWT_simulations.tar.gz 50.10Mb application/gzip View/Open
betaglobin_mES_simulations.tar.gz 50.03Mb application/gzip View/Open
betaglobin_Ter119_simulations.tar.gz 50.05Mb application/gzip View/Open
betaglobin_Ter119CTCFKO_simulations.tar.gz 50.00Mb application/gzip View/Open
betaglobin_Ter119DHSKO_simulations.tar.gz 7.484Mb application/gzip View/Open
Fig1.tar.gz 2.782Mb application/gzip View/Open
Fig2.tar.gz 16.01Mb application/gzip View/Open
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Fig7.tar.gz 24.69Mb application/gzip View/Open
mitoferrin1_CapCdata.tar.gz 1.649Mb application/gzip View/Open
mitoferrin1_mES_simulations.tar.gz 50.07Mb application/gzip View/Open
mitoferrin1_Ter119_simulations.tar.gz 50.06Mb application/gzip View/Open
README 4.094Kb text/plain View/Open
SIFigS10.tar.gz 448bytes application/gzip View/Open
SIFigS11.tar.gz 759bytes application/gzip View/Open
SIFigS12.tar.gz 1.518Mb application/gzip View/Open
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SIFigS8.tar.gz 13.16Mb application/gzip View/Open
SIFigS9.tar.gz 24.68Mb application/gzip View/Open

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