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.
Project description:High-throughput chromosome conformation capture (Hi-C) data generated for cohesin-mutated (STAG2 or RAD21) and cohesin-wildtype AMLs.
Project description:Genome-wide chromosome conformation capture (Hi-C) and promoter-capture Hi-C (CHi-C) were performed during epidermal differentiation. These data indicate that dynamic and constitutive enhancer-promoter contacts combine to control gene induction during differentiation and that chromosome conformation enables discovery of new TFs with distinct roles in this process.
Project description:Genome-wide chromosome conformation capture (Hi-C) and promoter-capture Hi-C (CHi-C) were performed during epidermal differentiation. These data indicate that dynamic and constitutive enhancer-promoter contacts combine to control gene induction during differentiation and that chromosome conformation enables discovery of new TFs with distinct roles in this process.
Project description:Genome-wide chromosome conformation capture (Hi-C) and promoter-capture Hi-C (CHi-C) were performed during epidermal differentiation. These data indicate that dynamic and constitutive enhancer-promoter contacts combine to control gene induction during differentiation and that chromosome conformation enables discovery of new TFs with distinct roles in this process.
Project description:Genome-wide chromosome conformation capture (Hi-C) and promoter-capture Hi-C (CHi-C) were performed during epidermal differentiation. These data indicate that dynamic and constitutive enhancer-promoter contacts combine to control gene induction during differentiation and that chromosome conformation enables discovery of new TFs with distinct roles in this process.
Project description:Genome profiling of BMAL1,TRIM28 and H3K9me3 analyzed by ChIP-seq in JM8+/+ and Bmal1-/- mESCs. Genome profiling of FlagBMAL1 in mESCs. High throughput capture chromosome conformation analysis (Hi-C) in JM8+/+ and Bmal1-/- mESCs. mRNA-seq analysis of JM8+/+ and Clock-/- mESCs
Project description:Genome profiling of BMAL1,TRIM28 and H3K9me3 analyzed by ChIP-seq in JM8+/+ and Bmal1-/- mESCs. Genome profiling of FlagBMAL1 in mESCs. High throughput capture chromosome conformation analysis (Hi-C) in JM8+/+ and Bmal1-/- mESCs. mRNA-seq analysis of JM8+/+ and Clock-/- mESCs
Project description:Genome profiling of BMAL1,TRIM28 and H3K9me3 analyzed by ChIP-seq in JM8+/+ and Bmal1-/- mESCs. Genome profiling of FlagBMAL1 in mESCs. High throughput capture chromosome conformation analysis (Hi-C) in JM8+/+ and Bmal1-/- mESCs. mRNA-seq analysis of JM8+/+ and Clock-/- mESCs
Project description:The organisation of the genome in nuclear space is an important frontier of biology. Chromosome conformation capture methods such as Hi-C and Micro-C produce genome-wide chromatin contact maps that provide rich data containing quantitative and qualitative information about genome architecture. Most conventional approaches to genome-wide chromosome conformation capture data are limited to the analysis of pre-defined features, and may therefore miss important biological information. One constraint is that biologically important features can be masked by high levels of technical noise in the data. Here we introduce Twins, a replicate-based method for deep learning from chromatin conformation contact maps. Using a Siamese network configuration, Twins learns to distinguish technical noise from biological variation and outperforms image similarity metrics across a range of biological systems. Features extracted by Twins from Hi-C maps after perturbation of cohesin and CTCF reflect the distinct biological functions of cohesin and CTCF in the formation of domains and boundaries, respectively. Twins distance metrics are biologically meaningful, as they mirror the density of cohesin and CTCF binding. Taken together, these properties make Twins an powerful tool for the exploration of chromosome conformation capture data, such as Hi-C capture Hi-C, and Micro-C.
