EXPERIMENT_TITLE: GSM4119011: Capture Hi-C, Primary CD4+ T-cells, unstimulated, replicate 1; 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). Genomic regions of interest were captured using biotinylated RNA baits (Agilent Technologies). Primary human CD4+ T-cells were isolated from PBMCs using an EasySep T-cell isolation kit (StemCell)
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Genome-wide association studies have identified genetic variation contributing to complex disease risk but assigning causal genes and mechanisms has been more challenging, as disease-associated variants are often found in distal regulatory regions with cell-type specific behaviours. Here, the simultaneous correlation of ATAC-seq, Hi-C, Capture Hi-C and nuclear RNA-seq data, in the same stimulated T-cells over 24 hours, allowed the assignment of functional enhancers to genes. We show how small magnitude changes in DNA interaction and activity dynamics are correlated with much larger changes to dynamics in gene expression and that the strongest correlations are observed within 200 kb of promoters. Using rheumatoid arthritis as an exemplar T-cell mediated disease, we demonstrate interactions of expression quantitative trait locus SNPs with target genes and confirm assigned genes or show complex interactions for 20% of disease associated loci. Finally, we confirm one of the putative causal genes using CRISPR/Cas9. Overall design: Examine dynamics between open chromatin, chromosome interactions and gene expression in stimulated T cells over 24 hours
SAMPLE_TITLE: Capture Hi-C, Primary CD4+ T-cells, unstimulated, replicate 1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Primary CD4+ T-cells"}, {"TAG": "stimulation", "VALUE": "none"}, {"TAG": "restriction enzyme", "VALUE": "HindIII"}]
Pool_Member_@attributes_sample_title: Capture Hi-C, Primary CD4+ T-cells, unstimulated, replicate 1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Capture Hi-C, Primary CD4+ T-cells, unstimulated, replicate 1
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