Show simple item record

dc.contributor.authorLando, Daviden
dc.contributor.authorBasu, Srinjanen
dc.contributor.authorStevens, Tim Jen
dc.contributor.authorRiddell, Andrewen
dc.contributor.authorWohlfahrt, Kaien
dc.contributor.authorCao, Yangen
dc.contributor.authorBoucher, Wayneen
dc.contributor.authorLeeb, Martinen
dc.contributor.authorAtkinson, Liam Pen
dc.contributor.authorLee, Stevenen
dc.contributor.authorHendrich, Brianen
dc.contributor.authorKlenerman, Daviden
dc.contributor.authorLaue, Ernesten
dc.date.accessioned2018-02-28T17:45:27Z
dc.date.available2018-02-28T17:45:27Z
dc.date.issued2018-05en
dc.identifier.issn1754-2189
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/273627
dc.description.abstractFluorescence imaging and chromosome conformation capture assays such as Hi-C are key tools for studying genome organization. However, traditionally they have been carried out independently making integration of the two types of data difficult to perform. By trapping individual cell nuclei inside the well of a 384 well glass bottomed plate with an agarose pad, we have established a protocol that allows both fluorescence imaging and Hi-C processing to be carried out on the same single cell. The protocol identifies 30,000 to 100,000 chromosome contacts per single haploid genome in parallel with fluorescence images. Contacts can be used to calculate intact genome structures to better than 100 kb resolution, which can then be directly compared with the images. Preparation of 20 single-cell Hi-C libraries using this protocol takes 5 days of bench work by researchers experienced in molecular biology techniques. Image acquisition and analysis requires basic understanding of fluorescence microscopy, while some bioinformatics knowledge is required to run the sequence processing tools described here.
dc.format.mediumPrint-Electronicen
dc.languageengen
dc.publisherSpringer Nature
dc.subjectCells, Cultureden
dc.subjectChromosomesen
dc.subjectChromatinen
dc.subjectAnimalsen
dc.subjectMiceen
dc.subjectImaging, Three-Dimensionalen
dc.subjectMolecular Biologyen
dc.subjectMolecular Conformationen
dc.subjectSingle-Cell Analysisen
dc.subjectOptical Imagingen
dc.subjectMouse Embryonic Stem Cellsen
dc.titleCombining fluorescence imaging with Hi-C to study 3D genome architecture of the same single cell.en
dc.typeArticle
prism.endingPage1061
prism.issueIdentifier5en
prism.publicationDate2018en
prism.publicationNameNature protocolsen
prism.startingPage1034
prism.volume13en
dc.identifier.doi10.17863/CAM.17117
dcterms.dateAccepted2017-12-18en
rioxxterms.versionofrecord10.1038/nprot.2018.017en
rioxxterms.versionAM*
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserveden
rioxxterms.licenseref.startdate2018-05en
dc.contributor.orcidLando, David [0000-0001-5783-8769]
dc.contributor.orcidBasu, Srinjan [0000-0002-1080-979X]
dc.contributor.orcidStevens, Tim J [0000-0001-6475-2074]
dc.contributor.orcidWohlfahrt, Kai [0000-0002-0970-5539]
dc.contributor.orcidLeeb, Martin [0000-0001-5114-4782]
dc.contributor.orcidLee, Steven [0000-0003-4492-5139]
dc.contributor.orcidHendrich, Brian [0000-0002-0231-3073]
dc.contributor.orcidKlenerman, David [0000-0001-7116-6954]
dc.contributor.orcidLaue, Ernest [0000-0002-7476-4148]
dc.identifier.eissn1750-2799
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idMRC (MR/M010082/1)
pubs.funder-project-idEC FP7 CP (277899)
pubs.funder-project-idMRC (MR/P019471/1)
pubs.funder-project-idWellcome Trust (206291/Z/17/Z)
pubs.funder-project-idWellcome Trust (098021/Z/11/Z)
pubs.funder-project-idMRC (MC_PC_12009)
pubs.funder-project-idWellcome Trust (082010/Z/07/Z)
rioxxterms.freetoread.startdate2018-10-19


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record