4DNES6MT2D6K - Replicate experiments of DNase Hi-C on RUES2 differentiated to endothelial progenitor cell 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: 4DNES6MT2D6K condition: endothelial progenitor - day 6 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/4DNES6MT2D6K/ number_of_experiments: 2 experiment: 4DNEXMBTNXDO; replicate_number: Biorep 1, Techrep 1 experiment: 4DNEX1G8JPA2; replicate_number: Biorep 2, Techrep 1 Series supplementary files: *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/e5aa930c-3432-4241-afbc-e16825a67abd/ genome_assembly: GRCh38 derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIA8K6KY2.pairs.gz, 4DNFI1CFBP14.pairs.gz description: This is an output file of the Hi-C processing pipeline file_type: contact list-combined file_format: pairs file name: 4DNFITUM51JH.pairs.gz *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/e5aa930c-3432-4241-afbc-e16825a67abd/ genome_assembly: GRCh38 derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIA8K6KY2.pairs.gz, 4DNFI1CFBP14.pairs.gz description: This is an output file of the Hi-C processing pipeline file_type: contact matrix file_format: mcool file name: 4DNFI3CTXDI2.mcool *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/7ce02156-7855-42b4-99d4-518d05bf3442/ genome_assembly: GRCh38 derived_from: 4DNFI3CTXDI2.mcool description: Boundaries calls on Hi-C contact matrices file_type: boundaries file_format: bed file name: 4DNFI7TJG9K9.bed.gz *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/7ce02156-7855-42b4-99d4-518d05bf3442/ genome_assembly: GRCh38 derived_from: 4DNFI3CTXDI2.mcool description: Diamond insulation scores calls on Hi-C contact matrices file_type: insulation score-diamond file_format: bw file name: 4DNFI51TV9E1.bw *************** workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/a3af3d78-fc80-45bd-b01f-3c03e5d3f530/ genome_assembly: GRCh38 derived_from: 4DNFI3CTXDI2.mcool, 4DNFI7MCA4R6.bedGraph.gz description: Compartments signals on Hi-C contact matrices file_type: compartments file_format: bw file name: 4DNFIYKU74YL.bw

血管内皮细胞是源自中胚层的细胞谱系，具备多种核心生物学功能，包括血管生成与凝血调控。目前学界对于支撑内皮细胞特化的基因调控机制尚不清楚，而染色质组织在内皮细胞转录调控中发挥的作用同样尚未明确。为探究染色质组织与基因表达之间的关联，我们从人类多能干细胞中诱导内皮细胞分化，并在特定时间点开展Hi-C（高通量染色体构象捕获，High-throughput Chromosome Conformation Capture）与RNA测序（RNA-sequencing）分析。
分化进程中，染色质长程染色体内相互作用逐渐增强，伴随广泛的异染色质-常染色质区室转换，该过程与转录调控紧密相关。动态拓扑关联结构域（topologically associating domain, TAD）边界逐步强化并收敛至内皮细胞状态，进而调控基因表达。染色质成对位点相互作用（DNA环，DNA loops）的发生频率在分化过程中升高，且与血管生物学核心基因的表达存在显著关联。染色质动态变化调控内皮细胞发育过程中的转录程序，并推动内皮细胞与心肌细胞的谱系分化分离。
整体实验设计：
实验室：Chuck Murry，华盛顿大学（University of Washington, UW）
资助项目编号：1U54DK107979-01
登录号：4DNES6MT2D6K
实验条件：内皮祖细胞 - 第6天
提交人：Kris Alavattam
数据集标签：针对诱导分化为内皮细胞的人类诱导多能干细胞（induced pluripotent stem cells, iPSCs）的DNase Hi-C实验
合作实验室：William Noble，华盛顿大学（University of Washington, UW）
实验类型：DNase Hi-C
数据链接：https://data.4dnucleome.org/experiment-set-replicates/4DNES6MT2D6K/
实验数量：2
实验1：4DNEXMBTNXDO；重复编号：生物学重复1，技术重复1
实验2：4DNEX1G8JPA2；重复编号：生物学重复2，技术重复1

系列补充文件：
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工作流运行链接：https://data.4dnucleome.org/workflow-runs-awsem/e5aa930c-3432-4241-afbc-e16825a67abd/
基因组组装版本：GRCh38
来源文件：4DNFI823LSII.chrom.sizes、4DNFIA8K6KY2.pairs.gz、4DNFI1CFBP14.pairs.gz
描述信息：本文件为Hi-C处理流程的输出结果
文件类型：接触列表-合并文件
文件格式：pairs
文件名：4DNFITUM51JH.pairs.gz
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工作流运行链接：https://data.4dnucleome.org/workflow-runs-awsem/e5aa930c-3432-4241-afbc-e16825a67abd/
基因组组装版本：GRCh38
来源文件：4DNFI823LSII.chrom.sizes、4DNFIA8K6KY2.pairs.gz、4DNFI1CFBP14.pairs.gz
描述信息：本文件为Hi-C处理流程的输出结果
文件类型：接触矩阵文件
文件格式：mcool
文件名：4DNFI3CTXDI2.mcool
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工作流运行链接：https://data.4dnucleome.org/workflow-runs-awsem/7ce02156-7855-42b4-99d4-518d05bf3442/
基因组组装版本：GRCh38
来源文件：4DNFI3CTXDI2.mcool
描述信息：基于Hi-C接触矩阵的边界调用结果
文件类型：边界文件
文件格式：bed
文件名：4DNFI7TJG9K9.bed.gz
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工作流运行链接：https://data.4dnucleome.org/workflow-runs-awsem/7ce02156-7855-42b4-99d4-518d05bf3442/
基因组组装版本：GRCh38
来源文件：4DNFI3CTXDI2.mcool
描述信息：基于Hi-C接触矩阵的菱形绝缘评分调用结果
文件类型：绝缘评分-菱形文件
文件格式：bw
文件名：4DNFI51TV9E1.bw
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工作流运行链接：https://data.4dnucleome.org/workflow-runs-awsem/a3af3d78-fc80-45bd-b01f-3c03e5d3f530/
基因组组装版本：GRCh38
来源文件：4DNFI3CTXDI2.mcool、4DNFI7MCA4R6.bedGraph.gz
描述信息：基于Hi-C接触矩阵的区室信号结果
文件类型：区室文件
文件格式：bw
文件名：4DNFIYKU74YL.bw