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Series GSE43682 Query DataSets for GSE43682
Status Public on Oct 21, 2013
Title Transcriptome of mouse pluripotent embryonic stem cells (mESC) cultured in R2i, 2i, PD and SB conditions
Organism Mus musculus
Experiment type Expression profiling by array
Summary 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.
 
Overall design Whole gene expression study of 4 different mouse embryonic stem cell lines maintained under 4 different chemically defined conditions: R2i, 2i, PD and SB
 
Contributor(s) Hassani SN, Totonchi M, Sharifi-Zarchi A, Mollamohammadi S, Pakzad M, Moradi S, Samadian A, Masoudi N, Mirshahvaladi S, Farrokhi A, Greber B, Araúzo-Bravo MJ, Sabour D, Sadeghi M, Salekdeh GH, Gourabi H, Schoeler H, Baharvand H
Citation(s) 24036899
Submission date Jan 23, 2013
Last update date Jan 16, 2019
Contact name Hossein Baharvand
E-mail(s) baharvand@royaninstitute.org
Phone +9821-22339936
Organization name Royan Institute for Stem Cell Biology and Technology
Street address Hafez St., Bani Hashem St.
City Tehran
ZIP/Postal code P.O.Box: 19395-4644
Country Iran
 
Platforms (2)
GPL6885 Illumina MouseRef-8 v2.0 expression beadchip
GPL6887 Illumina MouseWG-6 v2.0 expression beadchip
Samples (22)
GSM1068156 Royan_B18_2i_R1
GSM1068157 Royan_B18_2i_R2
GSM1068158 Royan_B20_2i_R1
Relations
BioProject PRJNA187048

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE43682_ControlProbeProfile_Ref8-v2.txt.gz 90.4 Kb (ftp)(http) TXT
GSE43682_ControlProbeProfile_WG6-v2.txt.gz 44.2 Kb (ftp)(http) TXT
GSE43682_RAW.tar 18.9 Mb (http)(custom) TAR
GSE43682_SampleProbeProfile_Ref8-v2.txt.gz 2.7 Mb (ftp)(http) TXT
GSE43682_SampleProbeProfile_WG6-v2.txt.gz 2.2 Mb (ftp)(http) TXT
GSE43682_Targets_Ref8-v2.txt.gz 288 b (ftp)(http) TXT
GSE43682_Targets_WG6-v2.txt.gz 318 b (ftp)(http) TXT
GSE43682_log2_norm_Ref8-v2.txt.gz 1.5 Mb (ftp)(http) TXT
GSE43682_log2_norm_WG6-v2.txt.gz 1.4 Mb (ftp)(http) TXT
Raw data are available on Series record
Processed data included within Sample table
Processed data are available on Series record

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