EXPERIMENT_TITLE: GSM5534878: Hi-C H9 replicate 3; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For Hi-C, nuclei were extraced after fixing using a cell lysis buffer. All Hi-C libraries were constructed following illumina insctructions accompanying Truseq sample preparation kit.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: High-resolution mapping of the gene regulatory chromatin interactions from noisy Hi-C contact heatmaps remains a major challenge in 3D genome research due to the complex bias structure and severe data sparsity. Here we present DeepLoop, which addresses this problem by combining a rigorous bias correction strategy (HiCorr) and deep learning-based signal enhancement techniques. We demonstrated that DeepLoop can robustly identify high-resolution chromatin interactions from low-depth and single cell Hi-C data. With DeepLoop, we for the first-time mapped the genetic and epigenetic determinants of human homolog-specific chromatin loops in GM12878 cells at 5kb-resolution. We nominated two new imprinting loci with unbalanced DNA folding in additional to the well-known H19/IGF2 locus. Interestingly, we also found that the sub-TAD loops at the DXZ4 “megadomain” boundary escapes X-inactivation, but the loops at the FIRRE “superloop” locus do not escape. Unexpectedly, DeepLoop detected four previously unknown Mb-sized heterozygous structure variants in the GM12878 genome, including two large inversions causing allele-specific gene expression via enhancer rewiring. Finally, DeepLoop also pinpointed dozens of loop regulatory SNPs that often have transcriptional consequences. Taken together, DeepLoop expands the use of Hi-C to provide genome-wide insights into the genetics of 3D genome at loop resolution. Overall design: DeepLoop robustly identify high-resolution chromatin loops regardless of noise and depth. Each text file (300K) contains a chromatin loop calling list from Hi-C data for one cell type.
SAMPLE_TITLE: Hi-C H9 replicate 3
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "H9"}, {"TAG": "cell type", "VALUE": "embryonic stem cells"}, {"TAG": "cell line", "VALUE": "H9"}, {"TAG": "treatment", "VALUE": "no treat"}, {"TAG": "protocol", "VALUE": "Hi-C"}, {"TAG": "restriction enzyme", "VALUE": "HindIII"}]
Pool_Member_@attributes_sample_title: Hi-C H9 replicate 3
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