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Series GSE72676 Query DataSets for GSE72676
Status Public on Mar 01, 2016
Title Co-expression networks in generation of induced pluripotent stem cells
Organism Homo sapiens
Experiment type Expression profiling by array
Summary We developed an adenoviral vector, in which Yamanaka’s four reprogramming factors (RFs) were controlled by individual CMV promoters in a single cassette (Ad-GFP-SOcMK). This permitted coordinated expression of RFs (SOX2, OCT3/4, c-MYC and KLF4) in a cell for a transient period of time, synchronizing the reprogramming process with the majority of transduced cells assuming induced pluripotent stem cell (iPSC)-like characteristics as early as 3 days. These reprogrammed cells resembled human ES cells with regard to morphology, biomarker expression, and could be differentiated into cells of the germ layers in vitro and in vivo. These iPSC-like cells, however, failed to expand into larger iPSC colonies. The short and synchronized reprogramming process allowed us to study global transcription changes within short time intervals. Weighted Gene Co-Expression Network analysis (WGCNA) identified sixteen large gene co-expression modules, each including members of gene ontology categories involved in cell differentiation and development. In particular, the brown module contained a significant number of ES cell marker genes, whereas the turquoise module contained cell-cycle related genes that were downregulated in contrast to upregulation in human ESCs. Strong coordinated expression of all 4 RFs via adenoviral transduction may constrain stochastic processes and lead to silencing of genes important for cellular proliferation.
Overall design Cells were dedifferentiated and gene expression assessed at 13 timepoints
Contributor(s) Paul S, Pflieger L, Dansithong W, Gao F, Coppola G, Pulst S
Citation(s) 26892236
Submission date Sep 02, 2015
Last update date Nov 27, 2018
Contact name Giovanni Coppola
Phone 310-794-4172
Organization name UCLA
Department Psychiatry and Neurology
Lab Neurogenetics
Street address 1524 Gonda, 695 Charles Young Drive South
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
Platforms (1)
GPL13607 Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Feature Number version)
Samples (16)
GSM1868006 GE iPS 0 day
GSM1868007 GE iPS 0.7 day
GSM1868008 GE iPS 1.2 day
BioProject PRJNA294632

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Supplementary file Size Download File type/resource
GSE72676_RAW.tar 200.6 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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