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| Status |
Public on Dec 01, 2013 |
| Title |
VGLL4 is a novel regulator of survival in human embryonic stem cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Human embryonic stem cells (hESCs) are maintained in a self-renewing state by an interconnected network of mechanisms that sustain pluripotency, promote proliferation and survival, and prevent differentiation. We sought to find novel genes that could contribute to one or more of these processes by using a gain-of-function screen of a large collection of human open reading frames. We identified Vestigial-like 4 (VGLL4), a co-transcriptional regulator with no previously described function in hESCs, as a positive regulator of survival in hESCs. Specifically, VGLL4 overexpression in hESCs significantly decreases cell death in response to dissociation stress. Additionally, VGLL4 overexpression enhances hESC colony formation from single cells. These effects may be attributable, in part, to a decreased activity of initiator and effector caspases observed in the context of VGLL4 overexpression. Additionally, we show an interaction between VGLL4 and the Rho/Rock pathway, previously implicated in hESC survival. This study introduces a novel gain-of-function approach for studying hESC maintenance and presents VGLL4 as a previously undescribed regulator of this process.
The goal of this experiment was to compare the global transcriptional profile of hESCs overexpressing VGLL4 to wild-type hESCs in order to understand the transcriptional differences behind the phenotype exhibited by VGLL4-overexpressing cells. This list was then used for subsequent analysis where genes were filtered individually, but also per sample, such that only genes with a pvalue of detection of less than 0.05 on at least 5 of the samples were kept. Next, the SAM statistical suite was used to generate a list of genes that are expressed at a significantly higher level in the 4 Vgll4 samples compared to the 4 WT samples using an FDR of 7% for discovery purposes.
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| Overall design |
RNA was purified from total cultures of HUES6 human embryonic stem cells (wildtype vs cells overexpressing VGLL4 from a lentiviral vector). Samples were collected in quadruplicates (biological replicates) using a Qiagen RNeasy kit and 200 ng of starting material were used as input for the Illumina TotalPrep Amplification Kit. Human ES cells were grown in the presence of mouse embryonic fibroblasts.
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| Contributor(s) |
Tajonar A, Maehr R, Hu G, Sneddon JB, Rivera-Feliciano J, Cohen DE, Elledge SJ, Melton DA |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Feb 22, 2013 |
| Last update date |
Aug 13, 2018 |
| Contact name |
Adriana Tajonar |
| Organization name |
Harvard University
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| Street address |
3707 Poinciana Drive
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| City |
Santa Clara |
| State/province |
California |
| ZIP/Postal code |
95051 |
| Country |
USA |
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| Platforms (1) |
| GPL10558 |
Illumina HumanHT-12 V4.0 expression beadchip |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA190189 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE44590_RAW.tar |
26.2 Mb |
(http)(custom) |
TAR |
| GSE44590_non-normalized.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
| GSE44590_normalized.txt.gz |
4.1 Mb |
(ftp)(http) |
TXT |
| GSE44590_raw.txt.gz |
4.1 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data are available on Series record |
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