Comparison of Hi-C results using in-solution versus in-nucleus ligation
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ABSTRACT: Chromosome conformation capture (3C) and derivative (4C, 5C and Hi-C) methods employ ligation of diluted cross-linked chromatin complexes, intended to favor proximity-dependent, intra-complex ligation. We previously described an alternative Hi-C protocol with ligation in preserved nuclei rather than in solution. Here we directly compare Hi-C methods employing "in-nucleus ligation" and the standard "in-solution ligation". The results show that in-nucleus ligation captures chromatin interactions more consistently over a wider range of distances, and significantly reduces both experimental noise and bias. Thus in-nucleus ligation not only simplifies the experimental procedures, but also produces higher quality data with benefits for the entire range of 3C applications.
ORGANISM(S): Mus musculus Homo sapiens
PROVIDER: GSE70181 | GEO | 2015/08/12
SECONDARY ACCESSION(S): PRJNA287806
REPOSITORIES: GEO
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