4DNES8R5RDVD - Replicate experiments of DNase Hi-C on RUES2 with DNaseI

Vascular endothelial cells are a mesoderm-derived lineage with many essential functions, including angiogenesis and coagulation. The gene-regulatory mechanisms underpinning endothelial specialization are largely unknown, as are the roles of chromatin organization in regulating endothelial cell transcription. To investigate the relationships between chromatin organization and gene expression, we induced endothelial cell differentiation from human pluripotent stem cells and performed Hi-C and RNA-sequencing assays at specific time points. Long-range intrachromosomal contacts increase over the course of differentiation, accompanied by widespread heteroeuchromatic compartment transitions that are tightly associated with transcription. Dynamic topologically associating domain boundaries strengthen and converge on an endothelial cell state, and function to regulate gene expression. Chromatin pairwise point interactions (DNA loops) increase in frequency during differentiation and are linked to the expression of genes essential to vascular biology. Chromatin dynamics guide transcription in endothelial cell development and promote the divergence of endothelial cells from cardiomyocytes. Overall design: lab: Chuck Murry, UW award: 1U54DK107979-01 accession: 4DNES8R5RDVD condition: undifferentiated - day 0 submitted_by: Kris Alavattam dataset_label: DNase Hi-C on human iPSCs differentiated to endothelium contributing_labs: William Noble, UW experiment_type: DNase Hi-C url: https://data.4dnucleome.org/experiment-set-replicates/4DNES8R5RDVD/ number_of_experiments: 2 experiment: 4DNEXGWVDZL5; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEX561P4FA; replicate_number: Biorep 2, Techrep 1 Series supplementary files: *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/c091e2ab-51df-4bfe-aebe-bebc5f79e87e/ genome_assembly: GRCh38 derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI7DIPZH6.pairs.gz, 4DNFIZU6KA1G.pairs.gz description: This is an output file of the Hi-C processing pipeline file_type: contact list-combined file_format: pairs file name: 4DNFI9G526S3.pairs.gz *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/c091e2ab-51df-4bfe-aebe-bebc5f79e87e/ genome_assembly: GRCh38 derived_from: 4DNFI823LSII.chrom.sizes, 4DNFI7DIPZH6.pairs.gz, 4DNFIZU6KA1G.pairs.gz description: This is an output file of the Hi-C processing pipeline file_type: contact matrix file_format: mcool file name: 4DNFIOML8JZK.mcool *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/7a0376ad-efca-4ac0-b9ae-ec5fba386a87/ genome_assembly: GRCh38 derived_from: 4DNFIOML8JZK.mcool description: Boundaries calls on Hi-C contact matrices file_type: boundaries file_format: bed file name: 4DNFIGKQQYO6.bed.gz *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/7a0376ad-efca-4ac0-b9ae-ec5fba386a87/ genome_assembly: GRCh38 derived_from: 4DNFIOML8JZK.mcool description: Diamond insulation scores calls on Hi-C contact matrices file_type: insulation score-diamond file_format: bw file name: 4DNFI6LFESL2.bw *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/0632d35f-9799-4258-a23f-7ca1edefd294/ genome_assembly: GRCh38 derived_from: 4DNFIOML8JZK.mcool, 4DNFI7MCA4R6.bedGraph.gz description: Compartments signals on Hi-C contact matrices file_type: compartments file_format: bw file name: 4DNFI7QUHGB5.bw