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| Status |
Public on Mar 28, 2014 |
| Title |
The distribution of genomic variations in human iPSCs is related to replication timing reorganization during reprogramming [Affymetrix] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
Genome variation profiling by SNP array
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| Summary |
Cell fate change involves significant genome reorganization, including change in replication timing, but how these changes are related to genetic variation has not been examined. To study how change in replication timing that occurs during reprogramming impacts the copy number variation (CNV) landscape, we generated genome-wide replication timing profiles of induced pluripotent stem cells (iPSCs) and their parental fibroblasts. A significant portion of the genome changes replication timing as a result of reprogramming, indicative of overall genome reorganization. We found that early and late replicating domains in iPSCs are differentially affected by copy number gains and losses, and that in particular CNV gains accumulate in regions of the genome that change to earlier replication during the reprogramming process. This differential relationship was present irrespective of reprogramming method. Overall, our findings reveal a functional association between reorganization of replication timing and the CNV landscape that emerges during reprogramming.
Keywords: Expression profiling by array
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| Overall design |
[Gene expression] We isolated RNA from normal human fibroblast derived iPS cells, normal human fibroblasts, and human embryonic stem cells for hybridization to the Affymetrix gene expression microarrays.
[CNV] We isolated genomic DNA from iPSCs derived with retroviral and episomal vectors and their parental fibroblast cells for hybridization to the Affymetrix Genome-Wide Human SNP 6.0 Array.
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| Contributor(s) |
Li H, Lu J |
| Citation(s) |
24685138 |
| Submission date |
Feb 26, 2014 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Hu Li |
| E-mail(s) |
li.hu@mayo.edu
|
| Organization name |
Mayo Clinic
|
| Department |
Molecular Pharmacology & Experimental Therapeutics
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| Lab |
Systems Biology and Pharmacology
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| Street address |
200 First Street, Gonda Building G19-408
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| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55904 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
| GPL6801 |
[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array |
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| Samples (14)
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| This SubSeries is part of SuperSeries: |
| GSE46848 |
The distribution of genomic variations in human iPSCs is related to replication timing reorganization during reprogramming |
|
| Relations |
| BioProject |
PRJNA239577 |
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