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| Status |
Public on Dec 15, 2016 |
| Title |
Copy number variant (CNV) and Single nucleotide polymorphism (SNP) of UCLA hESC lines |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
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| Summary |
Female human ESC-lines can carry active X-chromosomes (Xa) or an XIST-RNA- coated inactive X-chromosome (Xi XIST+ ). Additionally, many ESC-lines have abnormal X-chromosome-inactivation (XCI)-states where the Xi no longer expresses XIST-RNA and has transcriptionally active regions (eroded Xi=Xe). The fate of each XCI-state upon differentiation is unclear because individual lines often contain a mixture of XCI-states. Here, we established homogeneous XiXa, XeXa, and XaXa ESC-lines. We found that these lines were unable to initiate XIST-expression and X-chromosome- wide silencing upon differentiation indicating that the ESC XCI-state is maintained in differentiated cells. Consequently, differentiated XeXa and XaXa cells displayed higher levels of X-linked gene-expression than XiXa cells. Although global transcriptional compensation between X-chromosomes and autosomes is not required for female ESC-differentiation, the degree of X-chromosome- silencing influences differentiation efficiencies. Our data suggest that the Xi XIST+ Xa state is inherent to human ESCs and that all other XCI-states, including XaXa, are abnormal and arise during ESC-derivation or maintenance.
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| Overall design |
Genomic DNA from ESC lines and differentiated cardiomyocyte derivatives was extracted according to standard protocols. Genomic stability was analyzed on an Affymetrix genome-wide SNP 6.0 array as per manufacturers instructions at the UCLA microarray core. The analysis was performed as described (Greenman et al., 2010).
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| Contributor(s) |
Patel S, Bonora G, Kim R, Chronis C, Sahakyan A, Langerman J, Fitz-Gibbon S, Rubbi L, Skelton R, Ardehali R, Pellegrini M, Lowry W, Clark A, Plath K |
| Citation(s) |
27989715 |
| Submission date |
Dec 09, 2016 |
| Last update date |
Nov 27, 2018 |
| Contact name |
Kathrin Plath |
| Organization name |
University of California, Los Angeles
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| Street address |
615 Charles E. Young Drive South
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platforms (1) |
| GPL6801 |
[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA356825 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE91072_RAW.tar |
3.5 Gb |
(http)(custom) |
TAR (of CEL, CSV) |
| Processed data provided as supplementary file |
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