EXPERIMENT_TITLE: GSM2692024: hESC-CM biological replicate 3; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: hESC-CM were fixed by 2% formaldehyde (Agar Acientifics; R1026) for 10 min at room temperature, quenched by cold 0.125 M glycine (5 min at room temperature followed by 15 min on ice), flash frozen in liquid nitrogen and stored at -80˚C. Then as dscribed in Javierre, B.M. et al. Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters. Cell 167, 1369-1384 (2016). As dscribed in Javierre, B.M. et al. Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters. Cell 167, 1369-1384 (2016).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Long-range chromosomal interaction is an important mechanism by which differentiating cells organise three dimensional promoter-enhancer networks to regulate lineage-specifying, developmental, regulatory genes1,2. Distal promoter contacts in pluripotent stem and specialised cell types, such as foetal liver cells, form co-regulated gene networks correlated with their biological functions1. Promoter interactomes of 17 primary blood cell types also reflect high cell-type specificity3. The lineage-specifying promoter interactions can be constrained by polycomb repressive complexes and genes with specialised functions will be selectively released from this poised network during cell fate specification or differentiation2. The cis-regulatory contact upon lineage commitment is also a dynamic process that includes acquisition and loss of specific promoter interactions4. We characterise 5126 promoter-enhancer interactions specific to cardiomyocytes differentiated from human embryonic stem cells (hESC-CM) by performing a differential promoter capture Hi-C (PCHi-C)5 approach that allows physical promoter-enhancer contacts in hESC-CM to be identified against the background level of embryonic stem cells' interactions. This approach enables us to extract key genomic regulators and their target genes highly specific to the cardiovascular development and functions. Overall design: Performed capture Hi-C on cardiomyocytes differentiated from human embryonic stem cells (hESC-CM).  There were three biological replicates.
SAMPLE_TITLE: hESC-CM biological replicate 3
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Cardiomyocytes differentiated from human embryonic stem cells (hESC-CM)"}, {"TAG": "cell line", "VALUE": "WA09 (H9)"}, {"TAG": "cell type", "VALUE": "Cardiomyocytes differentiated from human embryonic stem cells"}]
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