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3CDB specifications


Unique identifier OMICS_11493
Name 3CDB
Alternative name Chromosome Conformation Capture
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes


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Publication for Chromosome Conformation Capture

3CDB citations


Chromosome scale assembly of the Monopterus genome

PMCID: 5946948
PMID: 29688346
DOI: 10.1093/gigascience/giy046

[…] 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 […]


Computational Methods for Assessing Chromatin Hierarchy

Comput Struct Biotechnol J
PMCID: 5910504
PMID: 29686798
DOI: 10.1016/j.csbj.2018.02.003

[…] 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 […]


Structural and spatial chromatin features at developmental gene loci in human pluripotent stem cells

Nat Commun
PMCID: 5696376
PMID: 29158493
DOI: 10.1038/s41467-017-01679-x

[…] 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 […]


Developmentally regulated higher order chromatin interactions orchestrate B cell fate commitment

Nucleic Acids Res
PMCID: 5737614
PMID: 28977418
DOI: 10.1093/nar/gkx722

[…] 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 […]


Trichoderma reesei complete genome sequence, repeat induced point mutation, and partitioning of CAZyme gene clusters

Biotechnol Biofuels
PMCID: 5496416
PMID: 28690679
DOI: 10.1186/s13068-017-0825-x

[…] 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 […]


Epigenomic profiling of primary gastric adenocarcinoma reveals super enhancer heterogeneity

Nat Commun
PMCID: 5052795
PMID: 27677335
DOI: 10.1038/ncomms12983

[…] 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 […]

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3CDB institution(s)
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
3CDB funding source(s)
This work was supported by grants from the National High Technology Development 863 Program of China (2014AA021103); the National Nature Science Foundation of China (NSFC, 31271398, 91540114 and 91131012); National Basic Research Program of China (the 973 Program, 2014CB542002) and the 100 Talents Project.

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