E-GEOD-43682 - Transcriptome of mouse pluripotent embryonic stem cells (mESC) cultured in R2i, 2i, PD and SB conditions

Status
Released on 21 October 2013, last updated on 2 June 2014
Organism
Mus musculus
Samples (22)
Arrays (2)
Protocols (7)
Description
In this study we have analyzed the global gene expression of naïve mouse embryonic stem cells in different culture conditions including R2i (PD0325901+SB431542), 2i (PD0325901+CHIR99021), and also PD0325901+LIF and SB431542+LIF to show the similarities and differences between the conditions in maintaining pluripotency. Since the first generation of mouse embryonic stem (ES) cells, extrinsic regulation of pluripotency has been at the focus of attention. Here we show that suppression of transforming growth factor β (TGFβ) signaling could have impressive effects on self-renewal and pluripotency of mouse ES cells. We introduce a chemically defined medium with inhibitors of TGFβ and mitogen-activated protein kinase (MAPK) kinase, designated here as R2i (Royan 2 inhibitors), for highly efficient establishment of ES cell lines from various mouse strains. R2i also supports homogenous expression of Nanog and Dppa3 proteins in ES cells and shows minimal differentiation leakage. Our results uncover an appropriate condition for ES cell generation from single blastomeres of various cleavage-stage embryos. Further, the high accuracy of genome integrity after long-term cultivation in R2i illustrates an optimal condition for ES cell culture. Global transcriptomic analysis of R2i cells demonstrates that bone morphogenetic protein 4 (BMP4) signaling becomes overrepresented pursuant to TGFβ repression, which may confer further robustness to pluripotency through shielding cells from differentiation stimuli. These findings point to a new facet of ground state pluripotency by blocking differentiation pathways, without influencing the pluripotency regulatory circuitry of mouse ES cells. Whole gene expression study of 4 different mouse embryonic stem cell lines maintained under 4 different chemically defined conditions: R2i, 2i, PD and SB
Experiment type
transcription profiling by array 
Contacts
Ali Farrokhi, Ali Sharifi-Zarchi, Azam Samadian, Boris Greber, Davood Sabour, Ghasem H Salekdeh, Hamid Gourabi, Hans Schoeler, Hossein Baharvand, Marcos J Araúzo-Bravo, Mehdi Sadeghi, Mehdi Totonchi, Mohammad Pakzad, Najmesadat Masoudi, Sayedeh N Hassani, Sepideh Mollamohammadi, Shahab Mirshahvaladi, Sharif Moradi
Citation
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-43682.idf.txt
Sample and data relationshipE-GEOD-43682.sdrf.txt
Processed data (1)E-GEOD-43682.processed.1.zip
Array designsA-MEXP-1174.adf.txt, A-MEXP-1175.adf.txt
Links