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| Status |
Public on Jan 26, 2017 |
| Title |
Human embryonic stem cells do not change their X-inactivation status during differentiation [RNA-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Female human ESC-lines can carry active X-chromosomes (Xa) or an XIST-RNA-coated inactive X-chromosome (XiXIST+). Additionally, many ESC lines have abnormal X-chromosomeinactivation (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. Employing RNA-FISH, RNA-sequencing and DNA methylation analyses, 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 XiXIST+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 |
RNA-seq was used to measure the expression state of X-linked and autosomal genes in undifferentiated human embryonic stem cells with different X-chromosome states and their differentiated cells.
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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, Pelligrini M, Lowry B, Clark A, Plath K |
| Citation(s) |
27989715 |
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| Submission date |
Oct 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kathrin Plath |
| Organization name |
UCLA
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| Street address |
615 Charles E. Young Drive South
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| City |
Los Angeles |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (41)
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| This SubSeries is part of SuperSeries: |
| GSE88933 |
Human embryonic stem cells do not change their X-inactivation status during differentiation |
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| Relations |
| BioProject |
PRJNA349151 |
| SRA |
SRP091767 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE88931_RNA-seq_MergedReadCounts.tsv.gz |
78.3 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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