EXPERIMENT_TITLE: GSM6061786: Hi-C THP1_macrophages_0240min_R3; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were crosslinked with 1% formaldehyde in RPMI fro 10 minutes with gentle shaking. Cells were then quenched with 10% 2.0 M cold glycine for 5 minutes. Media was then removed and cells were scraped into cold PBS. Cells from each flask (containing 20 million cells total) was divided into 4 tubes of approximately 5 million cells each. Cells were spun down at 526 G for 5 minutes, resuspended in PBS and respun to wash residual formaldehyde. Cells were then frozen in liquid nitrogen and stored at -80 for library preparation Libraries were prepared using the in situ Hi-C protocol as described in Rao et al. 2014. For each sample, two frozen cell pellets (5 million cells each) were used to generate separate libraries as technical replicates. Samples were sheared on a Covaris LE 220 (DF 25, PIP 500, 200 cycles/burst, 90 seconds). Illumina TruSeq Nano (Set A) indices were used, and libraries were pooled to 10 nM. Paired-end 150-bp reads were sequenced on one or two lanes of an Illumina NovaSeq S4.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: 3D chromatin structure, enhancers, and gene transcription function together to regulate cellular differentiation, establish cellular identity, and respond to external stimuli; however, the functional interplay between these regulatory elements remains incompletely understood. To infer potential causal relationships, we mapped 3D chromatin architecture, histone H3 K27 acetylation, chromatin accessibility, and gene expression across eight narrowly-spaced time points of macrophage activation. Enhancers and genes that were connected by a loop exhibited stronger correlation between histone H3K27 acetylation and expression than can be explained by distance or proximity alone, suggesting that the presence of a chromatin loop may facilitate functional regulatory connections via methods beyond simply increasing their frequency of physical proximity. Changes in enhancer acetylation preceded changes in gene expression by 30-60 minutes further supporting a causal relationship. Changes in gene expression exhibit a directional bias at differential loop anchors. The anchors of gained enhancer-promoter loops are associated with increased gene expression of genes oriented away from the center of the loop. Surprisingly, lost enhancer-promoter loops were also associated with increased gene expression, particularly within the bounds of the loop. Analysis of absolute levels of transcription revealed that lost loops were characterized by particularly high levels of internal transcription. Taken together, these results are consistent with a reciprocal relationship between looping and transcription. In this model, loops can enhance transcription by facilitating enhancer-promoter contacts, but also high levels of transcription can negatively impact loop strength by antagonizing loop extrusion mechanisms. Overall design: Genome-wide time course of chromatin structure (in situ Hi-C) in human THP-1-derived macrophages treated with LPS/IFNg for 0, 0.5, 1, 1.5, 2, 4, 6, and 24 hours. Coupled with datasets for gene expression (RNA-Seq), and enhancer activity (ATAC-Seq, H3K27ac ChIP-Seq).
SAMPLE_TITLE: Hi-C THP1_macrophages_0240min_R3
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "THP1-derived resting macrophages"}, {"TAG": "treatment", "VALUE": "4 hr LPS/IFNg"}, {"TAG": "cell line", "VALUE": "THP1 monocytes (differentiated to macropahges)"}, {"TAG": "biological replicate", "VALUE": "2"}, {"TAG": "technical replicate", "VALUE": "1"}]
Pool_Member_@attributes_sample_title: Hi-C THP1_macrophages_0240min_R3
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