DC Field | Value | Language |
---|---|---|
dc.contributor.author | Kim, Ji Hun | ko |
dc.contributor.author | Titus, Katelyn R. | ko |
dc.contributor.author | Gong, Wanfeng | ko |
dc.contributor.author | Beagan, Jonathan A. | ko |
dc.contributor.author | Cao, Zhendong | ko |
dc.contributor.author | Phillips-Cremins, Jennifer E. | ko |
dc.date.accessioned | 2022-09-15T02:00:20Z | - |
dc.date.available | 2022-09-15T02:00:20Z | - |
dc.date.created | 2022-09-15 | - |
dc.date.created | 2022-09-15 | - |
dc.date.issued | 2018-06 | - |
dc.identifier.citation | METHODS, v.142, pp.39 - 46 | - |
dc.identifier.issn | 1046-2023 | - |
dc.identifier.uri | http://hdl.handle.net/10203/298543 | - |
dc.description.abstract | Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (> 6 Billion) required per library. Here, we describe 5C-ID, a new version of Chromosome-Conformation-Capture-Carbon-Copy (5C) with restriction digest and ligation performed in the nucleus (in situ Chromosome-Conformation-Capture (3C)) and ligation-mediated amplification performed with a double alternating primer design. We demonstrate that 5C-ID produces higher resolution 3D genome folding maps with reduced spatial noise using markedly lower cell numbers than canonical 5C. 5C-ID enables the creation of high-resolution, high-coverage maps of chromatin loops in up to a 30 Megabase subset of the genome at a fraction of the cost of Hi-C. | - |
dc.language | English | - |
dc.publisher | ACADEMIC PRESS INC ELSEVIER SCIENCE | - |
dc.title | 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon Copy with in situ 3C and double alternating primer design | - |
dc.type | Article | - |
dc.identifier.wosid | 000437074600006 | - |
dc.identifier.scopusid | 2-s2.0-85047268325 | - |
dc.type.rims | ART | - |
dc.citation.volume | 142 | - |
dc.citation.beginningpage | 39 | - |
dc.citation.endingpage | 46 | - |
dc.citation.publicationname | METHODS | - |
dc.identifier.doi | 10.1016/j.ymeth.2018.05.005 | - |
dc.contributor.localauthor | Kim, Ji Hun | - |
dc.contributor.nonIdAuthor | Titus, Katelyn R. | - |
dc.contributor.nonIdAuthor | Gong, Wanfeng | - |
dc.contributor.nonIdAuthor | Beagan, Jonathan A. | - |
dc.contributor.nonIdAuthor | Cao, Zhendong | - |
dc.contributor.nonIdAuthor | Phillips-Cremins, Jennifer E. | - |
dc.description.isOpenAccess | N | - |
dc.type.journalArticle | Article | - |
dc.subject.keywordAuthor | 3D genome folding | - |
dc.subject.keywordAuthor | Higher-order chromatin organization | - |
dc.subject.keywordAuthor | Chromosome-Conformation-Capture-Carbon-Copy | - |
dc.subject.keywordAuthor | 5C | - |
dc.subject.keywordAuthor | Double alternating 5C primer design | - |
dc.subject.keywordAuthor | In situ 3C | - |
dc.subject.keywordAuthor | Low cell number | - |
dc.subject.keywordAuthor | Embryonic stem cells | - |
dc.subject.keywordPlus | 5C TECHNOLOGY | - |
dc.subject.keywordPlus | DROSOPHILA GENOME | - |
dc.subject.keywordPlus | CHROMATIN | - |
dc.subject.keywordPlus | ORGANIZATION | - |
dc.subject.keywordPlus | DOMAINS | - |
dc.subject.keywordPlus | ARCHITECTURE | - |
dc.subject.keywordPlus | PRINCIPLES | - |
dc.subject.keywordPlus | ELEMENTS | - |
dc.subject.keywordPlus | CELLS | - |
dc.subject.keywordPlus | NEIGHBORHOODS | - |
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