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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 15, 2018 |
| Title |
The promoter interactome of cardiomyocytes differentiated from human embryonic stem cells links regulatory elements to cardiac gene promoters |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Long-range chromosomal interaction is an important mechanism by which differentiating cells organise three dimensional promoter-enhancer networks to regulate lineage-specifying, developmental, regulatory genes1,2. Distal promoter contacts in pluripotent stem and specialised cell types, such as foetal liver cells, form co-regulated gene networks correlated with their biological functions1. Promoter interactomes of 17 primary blood cell types also reflect high cell-type specificity3. The lineage-specifying promoter interactions can be constrained by polycomb repressive complexes and genes with specialised functions will be selectively released from this poised network during cell fate specification or differentiation2. The cis-regulatory contact upon lineage commitment is also a dynamic process that includes acquisition and loss of specific promoter interactions4. We characterise 5126 promoter-enhancer interactions specific to cardiomyocytes differentiated from human embryonic stem cells (hESC-CM) by performing a differential promoter capture Hi-C (PCHi-C)5 approach that allows physical promoter-enhancer contacts in hESC-CM to be identified against the background level of embryonic stem cells’ interactions. This approach enables us to extract key genomic regulators and their target genes highly specific to the cardiovascular development and functions.
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| Overall design |
Performed capture Hi-C on cardiomyocytes differentiated from human embryonic stem cells (hESC-CM). There were three biological replicates.
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| Contributor(s) |
Choy M, Javierre BM, Baross SL, Liu Y, Williams SG, Wingett SW, Akbarov A, Wallace C, Spivakov M, Fraser P, Keavney BD |
| Citation(s) |
29955040 |
| Submission date |
Jul 03, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Steven William Wingett |
| E-mail(s) |
steven.wingett@mrc-lmb.cam.ac.uk
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| Organization name |
MRC Laboratory of Molecular Biology
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| Department |
Cell Biology
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| Street address |
Francis Crick Avenue, Cambridge Biomedical Campus
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| City |
Cambridge |
| State/province |
Cambs |
| ZIP/Postal code |
CB2 0QH |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL15433 |
Illumina HiSeq 1000 (Homo sapiens) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA392878 |
| SRA |
SRP110964 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE100720_Merged.CHiCAGO.washU.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE100720_RAW.tar |
3.5 Mb |
(http)(custom) |
TAR (of TXT) |
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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