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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mouse ES and iPS cells

ABSTRACT: Induced pluripotent stem (iPS) cells were produced from reprogramming of somatic cells, and they are shown to possess pluripotent properties similar to embryonic stem (ES) cells. Here we used microarrays to detail the global expression pattern among the ES cells and iPS cells, as well as the original mouse embryo fibroblast (MEF), to identify important players involved in the reprogramming process. Experiment Overall Design: Mouse ES cell cultures, as well as selected iPS cell lines and the original MEF cells they were derived from, were used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates for each sample were processed. GeneChips were processed and data were analyzed as previously described (Zeng et al., Dev Biol 20004).

ORGANISM(S): Mus musculus

SUBMITTER: Fanyi Zeng

PROVIDER: E-GEOD-16925 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from mouse ES and iPS cells

Project description:Induced pluripotent stem (iPS) cells were produced from reprogramming of somatic cells, and they are shown to possess pluripotent properties similar to embryonic stem (ES) cells. Here we used microarrays to detail the global expression pattern among the ES cells and iPS cells, as well as the original mouse embryo fibroblast (MEF), to identify important players involved in the reprogramming process. Mouse ES cell cultures, as well as selected iPS cell lines and the original MEF cells they were derived from, were used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates for each sample were processed. GeneChips were processed and data were analyzed using the RMA package of Bioconductor.

2010-05-28 | E-GEOD-21515 | biostudies-arrayexpress

Expression data from mouse ES and iPS cells

2009-08-03 | GSE16925 | GEO

Expression data from mouse ES and iPS cells

2010-05-13 | GSE21515 | GEO

Genome-wide mapping of miRNAs expressed in embryonic stem cells and pluripotent stem cells generated by different reprogramming strategies

Project description:We report the miRNA profiling in MEF cells, ES cells and three Pluripotent Stem Cells obtained by three different reprogramming approaches from MEF cells based on Solexa sequencing. iPS cells are reprogrammed by four factors (OSKM) from MEF cells. NT-ESCs were established by reprogramming MEF cells into ESCs using nuclear transfer. NT-iPSCs were established to reflect the combination of nuclear transfer and iPS technologies. iPSCs, NT-ESCs, and NT-iPSCs were exactly derived from the same MEF cells. The results indicate NT-ESCs give expression to the unique miRNAs other than both ESCs and iPSCs while pluripotent cells acquire or retain the pluripotent specific miRNAs compared with MEF. Furthermore, the comparison of different reprogramming cells suggests that several miRNAs have key roles in distinctly developmental potential reprogrammine cells. Small RNA profiles of MEF, ES, iPS, NT-ES and NT-iPS cells were generated by Solexa sequencing. MEF and ES cells were performed in triplicate. iPS, NT-ES and NT-iPS cells were sequenced in duplicate.

2014-07-05 | E-GEOD-52950 | biostudies-arrayexpress

Genome-wide mapping of miRNAs expressed in embryonic stem cells and pluripotent stem cells generated by different reprogramming strategies

2014-07-05 | GSE52950 | GEO

Transcription profi;ing of mouse induced pluripotent stem cells vs MEF cells to investigate culturing conditions

Project description:We present a robust serum-free system for the rapid and efficient reprogramming of mouse somatic cells by Oct4, Sox2 and Klf4. The elimination of fetal bovine serum and oncogene c-Myc allowed reprogramming cells to be detected as early as Day 2 and reached greater than 10% of the population at Day 7 post retroviral transduction. The resulting iPS colonies were isolated with high efficiency to establish pluripotent cell lines. Based on this method, we further developed iPS-SF1 as a dedicated reprogramming medium for chemical screening and mechanistic investigations. Comparasion of iPS cell lines derived from serum-free culture condition, MEF cells cultured in serum and serum-free condition and ES cell lines was shown. Experiment Overall Design: Selected induced pluripotent stem cell lines and its original mouse embroynic fibroblast were comparaed to defined mouse embroynic stem cell lines: R1 and CGR8.

2009-03-28 | E-GEOD-15267 | biostudies-arrayexpress

Transcriptome analysis during somatic cell reprogramming

Project description:By combining deep sequencing with high-throughput quantitative RT-PCR, we reveal that somatic splicing profiles are reorganized to pluripotent splicing profiles during reprogramming from mouse embryonic fibroblasts (MEFs) to induced pluripotent stem (iPS) cells. The splicing pattern in pluripotent stem cells resembles that in testis, and the regulatory regions have specific characters in length and sequence. These results indicate that the dynamic alteration in splicing is an integral part of the molecular network involved in the reprogramming process. Sequencing data from MEF, two iPS cell lines and one ES cell line. RT-PCR data will be represented within Figures or Tables in published manuscripts.

2013-10-17 | E-GEOD-46149 | biostudies-arrayexpress

Expression data of induced pluripotent stem cell

2009-03-18 | GSE15267 | GEO

Inducible iPS Cells Support Full-term Development of Tetraploid BlastocystâComplemented Embryos

Project description:Differentiated somatic cells can be reprogrammed into induced pluripotent stem (iPS) cells by forced expression of four transcription factorsâOct4, Sox2, Klf4, and c-Myc. However, it remains undetermined whether the reprogrammed iPS cells are fully pluripotent, resembling normal embryonic stem (ES) cells, given that no iPS cell lines have been shown to possess the capability to autonomously generate full-term mice after injection into tetraploid blastocysts. Here, we provide evidence demonstrating that iPS cells induced by the four transcription factors can be fully pluripotent and that full-term mice can be produced from complemented tetraploid blastocysts. This work serves as a proof of principle that iPS cells can generate full term embryos by tetraploid complementation. We compared the gene expression profile of iPS cell, ES cell and MEF. ES cell and MEF served as control for iPS cell. Three biological repeats were included for each line.

2010-08-18 | E-GEOD-17004 | biostudies-arrayexpress

Transcription profiling of mouse differentiated, partially- and fully-reprogrammed MEFs/B-cells

Project description:Expression profiles generated during dissection of the molecular mechanisms underlying direct reprogramming of somatic cells to a pluripotent state (induced pluripotent stem cells, iPS). Experiment Overall Design: 2 technical replicates of B lymphocytes, partially reprogrammed (MCV8, MCV6, BIV1), MEF-iPS(Oct4) and B-iPS(Nanog) cell lines.

2008-06-18 | E-GEOD-10871 | biostudies-arrayexpress

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