EXPERIMENT_TITLE: GSM3262959: day02.HiC.Rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n. All libraries were constructed using standard illumina TruSeq LT library prep.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The three-dimensional chromatin architecture plays a critical role in the establishment of cell-type-specific gene regulatory networks in eukaryotic cells.  How pluripotent stem cells (PSC) alter their chromatin architecture to direct cell fate specification remains to be elucidated.  Here, using a human PSC cardiomyocyte differentiation model, we analyze the dynamic reorganization of chromatin structure and gene regulatory networks during key transitional stages of cardiomyocyte development.  We show that many human PSC-specific topologically associating domains (TADs) are driven by active transcription of the primate-specific retroviruses HERVH.  These HERVH are silenced at the earliest stages of differentiation , accompanied by loss of TAD borders and subsequent merging of cognate TADs during differentiation, which leads to repression of gene expression within these domains .  In line with these findings, deletion of select HERVHs results in elimination of corresponding TAD boundaries in human PSCs. We further discovered developmental stage-specific chromatin loop interactions that predict target genes of cardiac-related trait/disease non-coding genetic variants.  Overall, our results not only highlight a novel role for endogenous retroviruses in shaping species-specific PSC chromatin architecture during evolution but also provide a genomic blueprint for understanding the impact of non-coding variants in congenital and adult heart disease/traits. Overall design: hESCs are differentiated into cardiomyocyte. We used a transgenic H9 hESC line expressing a H2B-GFP fusion protein under control of the ventricular cardiomyocyte specific MYL2 promoter. We collected samples at six critical time points during differentiation: human embryonic stem cells (hESC) (Day 0), hESC mesodermal cells (Day 2), hESC-cardiac mesodermal cells (Day 5), hESC-cardiac progenitor cell (Day 7), hESC-primitive cardiomyocytes (Day 15) and hESC-ventricular cardiomyocytes (Day 80). We performed HiC, ATAC-seq, RNA-seq, and ChIP-seq for H3K27ac, H3K27me3, H3K4me1, H3K4me3, H3K9me3 and CTCF for every time point, each with two biological replicates. We also made CRISPR edited deletion at two HERV-H loci and performed RNA-seq and Hi-C, each with two replicates.
SAMPLE_TITLE: day02.HiC.Rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "ES derived mesoderm"}, {"TAG": "tissue", "VALUE": "ES derived mesoderm"}, {"TAG": "differentiation time", "VALUE": "day02"}, {"TAG": "genotype", "VALUE": "H9 MLC2v:H2B"}]
Pool_Member_@attributes_sample_title: day02.HiC.Rep2
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