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Chromosome conformation capture in mouse embryonic Rif1 null stem cells

ABSTRACT: Chromosome conformation capture in mouse embryonic Rif1 null stem cells

PROVIDER: PRJEB9106 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR855864.fastq.gz	Fastqsanger.gz
	ERR855865.fastq.gz	Fastqsanger.gz
	ERR855866.fastq.gz	Fastqsanger.gz
	ERR855867.fastq.gz	Fastqsanger.gz
	ERR855868.fastq.gz	Fastqsanger.gz

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Chromosome conformation capture in Rif1 null pMEFs

Project description:Chromosome conformation capture in Rif1 null pMEFs

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Chromosome conformation capture in mouse embryonic Rif1 null stem cells

Project description:Mammalian Rif1 defines the architecture of replication-timing domains interactions through the three-dimensional organization of the nuclear volume. Deletion of RIf1 in mammalian cells causes an initial alteration of three-dimensional chromatin organization which impacts first on replication timing and genome stability, but has long-term indirect repercussions also on gene expression.

2015-12-24 | E-MTAB-3500 | biostudies-arrayexpress

Chromosome conformation capture in Rif1 null pMEFs

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2015-12-24 | E-MTAB-3505 | biostudies-arrayexpress

Systematic evaluation of chromosome conformation capture assays

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Project description:Background: Identification of locus-locus contacts at the chromatin level provides a valuable foundation for understanding of nuclear architecture and function and a valuable tool for inferring long-range linkage relationships. As one approach to this, chromatin conformation capture-based techniques allow creation of genome spatial organization maps. While such approaches have been available for some time, methodological advances will be of considerable use in minimizing both time and input material required for successful application. Results: Here we report a modified tethered conformation capture protocol that utilizes a series of rapid and efficient molecular manipulations. We applied the method to Caenorhabditis elegans, obtaining chromatin interaction maps that provide a sequence-anchored delineation of salient aspects of Caenorhabditis elegans chromosome structure, demonstrating a high level of consistency in overall chromosome organization between biological samples collected under different conditions. In addition to the application of the method to defining nuclear architecture, we found the resulting chromatin interaction maps to be of sufficient resolution and sensitivity to enable detection of large-scale structural variants such as inversions or translocations. Conclusion: Our streamlined protocol provides an accelerated, robust, and broadly applicable means of generating chromatin spatial organization maps and detecting genome rearrangements without a need for cellular or chromatin fractionation. Application of modified version of TCC protocl using different C. elegans strains (N2 and glp-1) in L1, and adult life stages.

2016-01-20 | E-GEOD-76930 | biostudies-arrayexpress

Characterization of chromosomal architecture in Arabidopsis thaliana by Chromosome Conformation Capture

Project description:Background: The packaging of long chromatin fibres in the nucleus poses a major challenge, as it must fulfil both physical and functional requirements. Until recently, insight into the chromosomal architecture of plants was mainly provided by cytogenetic studies. Complementary to these analyses, chromosome conformation technologies promise to refine and improve our view on chromosomal architecture and to provide a more generalised description of nuclear organization. Results: Employing circular chromosome conformation capture (4C), this study describes chromosomal architecture in Arabidopsis nuclei from a genome-wide perspective. Surprisingly, the linear organisation of chromosomes is reflected in the genome-wide interactome. In addition, we studied the interplay of the interactome and epigenetic marks and report that the heterochromatic knob on the short arm of chromosome 4 (hk4s) maintained a pericentromere-like interaction profile and interactome despite its euchromatic surrounding. Conclusion: Despite the extreme condensation that is necessary to pack the chromosomes into the nucleus, the Arabidopsis genome appears to be packed in a predictive manner, according to the following criteria: (i) heterochromatin and euchromatin represent two distinct interactomes, (ii) interactions between chromosomes correlates with the linear position on the chromosome arm, and (iii) distal chromosome regions have a higher potential to interact with other chromosomes. This study includes circular chromosome conformation capture (4C) sequencing information of 13 samples, present in two batches, each present in duplicates (A and B). The individual 4C sequencing information can be retrieved by the 4C primer sequence, given in the 4C primer information file.

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Project description:Chromosome Conformation Capture (4C seq) at the rs9929218 locus in colorectal cancinogensis

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Systematic evaluation of chromosome conformation capture assays [1D]

Project description:Systematic evaluation of chromosome conformation capture assays [1D]

| PRJNA698732 | ENA

A Streamlined Tethered Chromosome Conformation Capture Protocol

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Project description:Here, we developed a novel chromosome conformation capture (3C) method for capturing the 3D spatial contacts of endogenous genomic loci without a need for crosslinking. This method, i3C, was applied to multiple loci in two different human primary (ENCODE) cell lines, HUVEC and IMR90, and in the absence or presence of a proinflammatory stimulus (TNFalpha). Coupled to high throughput sequencing on an Illumina HiSeq200 platform, i3C generated aprrox. 8 million single-end reads per experiment.

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