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Series GSE91072 Query DataSets for GSE91072
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
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.
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).
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
Street address 615 Charles E. Young Drive South
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (15)
GSM2420529 UCLA 1 P13 CNV
GSM2420530 UCLA 2 P14 CNV
GSM2420531 UCLA 3 P13 CNV
BioProject PRJNA356825

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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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