EXPERIMENT_TITLE: GSM4568362: Hi-C, HaCaT Keratinocyte cells, unstimulated; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were thawed on ice and re-suspended in 50ml ice-cold lysis buffer (10mM Tris-HCl pH 8, 10mM NaCl, 0.2% Igepal CA-630, one protease inhibitor cocktail tablet). Cells were lysed on ice for a total of 30 min, with 2x10 strokes of a dounce homogeniser with a 5 minute break between douncing. The nuclei were pelleted and permeabilised and the chromatin was digested with HindIII. Ends were marked with biotin followed by in-nucleus ligation, decrosslinking and biotin pulldown according to the previously established Hi-C protocol (Dryden et al., 2014; P. Martin et al., 2015) Sequencing libraries were generated with 6-8 cycles of PCR using Truseq single indexes (Illumina) and Phusion polymerase (NEB)
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Chromatin looping between regulatory elements and gene promoters presents a potential mechanism whereby disease risk variants affect their target genes. Here we use H3K27ac HiChIP, a method for assaying the active chromatin interactome in two cell lines: keratinocytes and skin derived CD8+ T cells. We integrate public datasets for a lymphoblastoid cell line and primary CD4+ T cells and identify gene targets at risk loci for skin-related disorders. Interacting genes enrich for pathways of known importance in each trait, such as cytokine response (psoriatic arthritis, psoriasis) and replicative senescence (melanoma). We show examples of how our analysis can inform changes in the current understanding of multiple psoriasis associated risk loci. For example, the variant rs10794648, which is generally assigned to IFNLR1, was linked to GRHL3 in our dataset, a gene essential in skin repair and development. Our findings, therefore, indicate a renewed importance of skin related factors in the risk of disease. Overall design: HiChIP and Hi-C data was generated for Keratinocytes (HaCaT) and CD8+ T cells (MyLa). Keratinocytes were also stimulated with IFN-?. We generated biological 2 replicates for each HiChIP sample and 1 replicate for each Hi-C sample. Accompanying RNA-seq data was also generated with 4 libraries for naive HaCaT, 3 for stimulated HaCaT, 1 for MyLa and 2 for GM12878 cells. The data was also uploaded to GSE68257 for a previous study but the processed files here are updated to reflect the new study.
SAMPLE_TITLE: Hi-C, HaCaT Keratinocyte cells, unstimulated
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HaCaT Keratinocyte cells"}, {"TAG": "biomaterial_provider", "VALUE": "https://www.addexbio.com/productdetail?pid=117"}, {"TAG": "cell line", "VALUE": "HaCaT Keratinocyte cell line"}, {"TAG": "stimulation", "VALUE": "none"}, {"TAG": "restriction enzyme", "VALUE": "HindIII"}]
Pool_Member_@attributes_sample_title: Hi-C, HaCaT Keratinocyte cells, unstimulated
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C, HaCaT Keratinocyte cells, unstimulated
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