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| Status |
Public on Mar 01, 2016 |
| Title |
Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming [HiC-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
We studied genome topology dynamics during reprogramming of different somatic cell types with highly distinct genome conformations. We find large-scale TAD repositioning and alterations of tissue-restricted genomic neighborhoods and chromatin loops, effectively erasing the somatic cell specific genome structures while establishing an embryonic stem cell-like 3D genome. Yet, early passage iPSCs carry topological hallmarks that enable discerning their cell-of-origin. These hallmarks are not remnants of somatic chromosome topologies. Instead, the distinguishing topological features are acquired during reprogramming, as we also find for cell-of-origin dependent gene expression patterns.
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| Overall design |
Hi-C was performed in somatic cells (NSC, macrophages, MEFs and pre-B cells) and their corresponding early and late induced pluripotent stem cells. In addition Hi-C was performed in E14 embryonic stem cells
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| Contributor(s) |
de Wit E, de Laat W |
| Citation(s) |
26971819 |
| |
| Submission date |
Jan 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Elzo de Wit |
| Phone |
+31 30 2121 800
|
| Organization name |
Hubrecht Institute
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
| |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (33)
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| This SubSeries is part of SuperSeries: |
| GSE76481 |
Cell-of-origin specific 3D genome structure acquired during somatic cell reprogramming |
|
| Relations |
| BioProject |
PRJNA307548 |
| SRA |
SRP068009 |
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