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| Status |
Public on Jan 18, 2023 |
| Title |
4DNESXR4J4MS - Replicate experiments of RNA-seq on RUES2 differentiated to mesoderm |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| 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: 4DNESXR4J4MS
condition: mesoderm - day 2
submitted_by: Kris Alavattam
dataset_label: RNA-seq on human iPSCs differentiated to endothelium
contributing_labs: William Noble, UW
experiment_type: RNA-seq
url: https://data.4dnucleome.org/experiment-set-replicates/4DNESXR4J4MS/
number_of_experiments: 2
experiment: 4DNEXNQUX8R8; replicate_number: Biorep 1, Techrep 1
experiment: 4DNEXV26Q4OX; replicate_number: Biorep 2, Techrep 1
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| Citation(s) |
36493778 |
| |
| 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
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
|
| Samples (2) |
| GSM6919603 |
RNA-seq on RUES2 differentiated to mesoderm - 4DNEXNQUX8R8 |
| GSM6919605 |
RNA-seq on RUES2 differentiated to mesoderm - 4DNEXV26Q4OX |
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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 |
PRJNA919046 |
| SRA |
SRP416850 |
