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| Status |
Public on Jan 18, 2023 |
| Title |
4DNES8R5RDVD - Replicate experiments of DNase Hi-C on RUES2 with DNaseI |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
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.
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| 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:
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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
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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
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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
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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
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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
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| Citation(s) |
36493778 |
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| Submission date |
Jan 06, 2023 |
| Last update date |
Jan 20, 2023 |
| Contact name |
4DN DCIC |
| E-mail(s) |
support@4dnucleome.org
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| Organization name |
4D Nucleome - Data Coordination and Integration Center
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| Street address |
10 Shattuck St
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (2) |
| GSM6919593 |
DNase Hi-C on RUES2 with DNaseI - 4DNEX561P4FA |
| GSM6919599 |
DNase Hi-C on RUES2 with DNaseI - 4DNEXGWVDZL5 |
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| This SubSeries is part of SuperSeries: |
| GSE222551 |
Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation |
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| Relations |
| BioProject |
PRJNA919044 |
| SRA |
SRP416844 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE222303_4DNFI6LFESL2.bw |
8.1 Mb |
(ftp)(http) |
BW |
| GSE222303_4DNFI7QUHGB5.bw |
207.6 Kb |
(ftp)(http) |
BW |
| GSE222303_4DNFI9G526S3.pairs.gz |
3.2 Gb |
(ftp)(http) |
PAIRS |
| GSE222303_4DNFIGKQQYO6.bed.gz |
205.9 Kb |
(ftp)(http) |
BED |
| GSE222303_4DNFIOML8JZK.mcool |
995.8 Mb |
(ftp)(http) |
MCOOL |
| GSE222303_RAW.tar |
3.5 Gb |
(http)(custom) |
TAR (of PAIRS) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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