Homo sapiens strain:K562, AD519, AD519d, AD598, AD598d
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ABSTRACT:
PROVIDER: PRJNA752941 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The spatiotemporal chromatin reorganization during hematopoietic differentiation has not been well characterized, which partly limited by the large amounts of starting cells for the current high-throughput chromatin conformation capture approaches. Here, we introduce a low-input Hi-C method, tagHi-C, to capture the chromatin structures in hundreds of cells. We proved tagHi-C was a feasible and reproducible approach
2020-11-10 | GSE161082 | GEO
Project description:The spatiotemporal chromatin reorganization during hematopoietic differentiation has not been well characterized, which partly limited by the large amounts of starting cells for the current high-throughput chromatin conformation capture approaches. Here, we introduce a low-input Hi-C method, tagHi-C, to capture the chromatin structures in hundreds of cells. We proved tagHi-C was a feasible and reproducible approach.
2020-08-01 | GSE152918 | GEO
Project description:Current methods for analysing chromosome conformation in mammalian cells are either insensitive and low resolution or low throughput. Since the methods are expensive and relatively difficult to perform and analyse they are not widely used outside of specialised laboratories. Here we have re-designed the Capture-C method producing a new approach, called next generation (NG) Capture-C, which solves most of the current setbacks in analysing chromosome conformation. NG Capture-C produces unprecedented levels of sensitivity and reproducibility, which can be used to analyse any number of genetic loci and/or many samples in a single experiment. NG Capture is straightforward to perform, requiring only standard reagents and access to basic next generation sequencing platforms. The complete and detailed protocol presented here, with new publically available tools for library design and data analysis, will allow most laboratories to analyse chromatin conformation at levels of sensitivity and throughput that were previously impossible.
2015-11-16 | GSE67959 | GEO
Project description:An Upgraded Method of High-throughput Chromosome Conformation Capture (Hi-C 3.0) in Plants
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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.
2016-12-10 | E-MTAB-4719 | biostudies-arrayexpress
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
Project description:Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This hampers the investigation of chromatin structure in rare cell populations. We present two new low-input Capture-C protocols that generate high-quality, reproducible interaction profiles from fewer than 20,000 cells, and show that these are not biased by PCR amplification or the degree of formaldehyde fixation.
2017-11-20 | GSE99257 | GEO
Project description:CiFi: Accurate long-read chromosome conformation capture sequencing with low-input requirements
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Project description:We analyzed the 3D genome organization via the High-throughput/resolution chromosome conformation capture (Hi-C) data generated from lipid overload-induced HCC cells.
2025-12-04 | GSE273061 | GEO