EXPERIMENT_TITLE: GSM3110158: siControl_REP2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: In addition to mediating sister chromatid cohesion, cohesin plays a central role in DNA looping and segmentation of the genome into contact domains (TADs). Two variant cohesin complexes that contain either STAG/SA1 or SA2 are present in all cell types. Here we addressed their specific contribution to genome architecture in non-transformed human cells. We found that cohesin-SA1 drives stacking of cohesin rings at CTCF-bound sites and thereby contributes to the stabilization and preservation of TAD boundaries. In contrast, a more dynamic cohesin-SA2 promotes cell type-specific contacts between enhancers and promoters within TADs independently of CTCF. SA2 loss, a condition frequently observed in cancer cells, results in increased intra-TAD interactions, likely altering the expression of key cell identity genes. Overall design: ChIP-seq for cohesin subunits SMC1, SA1 and SA2 was performed in 3 different cell lines (MCF10A, HMEC, HCAEC) and peak calling was done against the input sample from the corresponding cell line. RNA-seq was performed in triplicates in MCF10A cells control depleated from SA1, SA2 or CTCF by means of Dharmacon SMART pool siRNAs. HiC-seq was performed in two replicates in MCF10A cells control and depleated from SA1 and SA2 by means of Dharmacon SMART pool siRNAs. 4C-seq was performed in MCF10A cells control and depleated from SA2 or CTCF.
SAMPLE_TITLE: siControl_REP2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Human Mammary Epithelial Cells"}, {"TAG": "cell type", "VALUE": "MCF10A -Transformed nontumorigenic"}, {"TAG": "experiment", "VALUE": "MCF10A cells were arrested in G1 by means of high confluency culture (150,000 cells per cm2). Hi-C was performed as described (Serra et al., 2017) using MboI enzyme. Two library replicates per condition were sequenced (>200 million reads each)."}]
Pool_Member_@attributes_sample_title: siControl_REP2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: siControl_REP2
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