3CDB

[…] sequencing (LRseq) [] approach, contiguity-preserving transposase sequencing (fragScaff) [], and various assembly algorithms [, ]. Recently, chromatin interactions, such as high-throughput/resolution chromosome conformation capture, have been used to assemble ultra-long scaffolds that can lead to a chromosome-scale assembly; however, a certain amount of error occurs when used for de novo assembly […]

[…] TAD Topology associating domains 3C Chromosome conformation capture 4C Circular chromosome conformation capture 5C Chromosome conformation capture carbon copy LMA ligation-mediated amplification DI Directionality index ID Insulation index MNase-seq micrococcal nuclease sequencing FAIRE formalde […]

[…] difications, called bivalent domains–. To examine the chromatin interaction profiles of the developmental genes (especially bivalent genes) at high resolution, we tried to perform a 4C- (circularized chromosome conformation capture) based massively paralleled sequenced method (4C-seq). Many versions of 4C-seq have been reported to overcome the disadvantages of 4C-seq described above by introducing […]

[…] observed for stable TADs (Figure , right panel; ). Collectively, these analyses demonstrate that 3D models reflect the changes in 2D interaction maps. To validate these results, we performed 3C-qPCR (Chromosome Conformation Capture) for a merged TAD (Chr12:69720000–71160000) found in pro-B cells formed as a result of coalescence of three minor TADs in pre-pro-B cells. The spatial distance between […]

[…] collectively annotated and compared ~30% genes in the JGI genomes of T. reesei, T. atroviride, and T. virens [].To reveal gene order and dynamic gene expression at the chromosome level, a genome-wide chromosome conformation capture method (referred herein as “HiC”) had been applied to close the gaps between the QM6a-v2.0 scaffolds. The HiC draft genome revealed seven superscaffolds and four short […]

[…] BSCR27, CLDN3, ABHD11 and ABHD11-AS1. ABHD11-AS1 is a long non-coding RNA was previously shown to be highly expressed in gastric cancer. To validate the Capture-C data, we also performed circularized chromosome conformation capture assays (4C) on four selected predicted super-enhancers in two GC lines (OCUM-1, SNU16) (). We observed a concordance between Capture-C and 4C data of 75%, similar to co […]