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High resolution 3D chromatin maps of human primary monocytes [Hi-C]

ABSTRACT: High resolution 3D chromatin maps of human primary monocytes [Hi-C]

PROVIDER: PRJNA663570 | ENA |

REPOSITORIES: ENA

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High resolution 3D chromatin maps of human primary monocytes [Hi-C]

Project description:Although the Hi-C maps in cultured immune cell has been reported, there still lacks 3D landscape of human primary monocytes. The peripheral blood from two health people and two SLE patients was collected and CD14+ monocytes were selected to perform Hi-C, RNA-seq, ATAC-seq and ChIP-seq. The raw data of THP1 cell Hi-C library was also used in comparison. We firstly presented the 3D genome structure heterogeneity in human primary monocytes. Significantly diversity of chromatin interaction in HLA complex region might regulates many immunologic processes. The chromatin loop regulation around CD16 and its relevant expression pattern indicated the CD16 associated monocyte functions are dominated regulated by this variable TAD boundary.

2022-01-01 | GSE157971 | GEO

High resolution 3D chromatin maps of human primary monocytes [ATAC-Seq]

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High resolution 3D chromatin maps of human primary monocytes [RNA-Seq]

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High resolution 3D chromatin maps of human primary monocytes [ChIP-Seq]

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High resolution 3D chromatin maps of human primary monocytes

Project description:High resolution 3D chromatin maps of human primary monocytes

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High resolution 3D chromatin maps of human primary monocytes [ATAC-Seq]

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High resolution 3D chromatin maps of human primary monocytes [ChIP-Seq]

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High resolution 3D chromatin maps of human primary monocytes [RNA-Seq]

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Robust Hi-C maps of enhancer-promoter interactions reveal the function of non-coding genome in neural development and diseases

Project description:Genome-wide mapping of chromatin interactions at high resolution remains experimentally and computationally challenging. Here we used a low-input “easy Hi-C” protocol to map the 3D genome architecture in human neurogenesis and brain tissues and also demonstrated that a rigorous Hi-C bias-correction pipeline (HiCorr) can significantly improve the sensitivity and robustness of Hi-C loop identification at sub-TAD level, especially the enhancer-promoter (E-P) interactions. We used HiCorr to compare the high-resolution maps of chromatin interactions from 10 tissue or cell types with a focus on neurogenesis and brain tissues. We found that dynamic chromatin loops are better hallmarks for cellular differentiation than compartment switching. HiCorr allowed direct observation of cell-type- and differentiation-specific E-P aggregates spanning large neighborhoods, suggesting a mechanism that stabilizes enhancer contacts during development. Interestingly, we concluded that Hi-C loop outperforms eQTL in explaining neurological GWAS results, revealing a unique value of high-resolution 3D genome maps in elucidating the disease etiology.

2020-07-31 | GSE116825 | GEO

High-resolution Hi-C maps in EV and ZFP661-3HA OE mESCs

Project description:In this assay, we aimed to investigate the impacts of ZFP661 on the permeability of CTCF barriers to chromatin interactions. To achieve this, we generated high-resolution Hi-C maps using empty vector (EV) control and ZFP661-3HA overexpressing (OE) mESCs. Our findings demonstrate that ZFP661 suppresses the trapping of cohesin at the CTCF barriers and modulates their permeability.

2023-05-09 | GSE231867 | GEO

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