Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of mouse embyronic stem cell line CGR8 during the first 10 days of differentiation into embryoid bodies

ABSTRACT: This experiment is part of the FunGenES project (FunGenES - Functional Genomics in Embryonic Stem Cells partially funded by the 6th Framework Programme of the European Union, http://www.fungenes.org). The experiment was conducted at University of Cologne, Cologne, Germany. Goal of the experiment was RNA expression profiling in the first 10 days of differentiation in CGR8 cells. Materials and methods: CGR8 cells were cultivated as EBs without addition of selective reagents in hanging drop cultures in a timecourse experiment. After 7 days, EBs were plated in gelatin-coated 6-well plates. RNA was prepared from ES cells (day 0), EBs (day 1 to 7) and plated EBs (day 10). Culture conditions: ES cells were differentiated via hanging drop protocol into embryoid bodies. RNA isolation method: The RNA isolation was carried out following standard methods (on column, RNeasy Mini kit, Qiagen)

ORGANISM(S): Mus musculus

SUBMITTER: Oliver Hummel

PROVIDER: E-TABM-672 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation.

Schulz Herbert H Kolde Raivo R Adler Priit P Aksoy Irène I Anastassiadis Konstantinos K Bader Michael M Billon Nathalie N Boeuf Hélène H Bourillot Pierre-Yves PY Buchholz Frank F Dani Christian C Doss Michael Xavier MX Forrester Lesley L Gitton Murielle M Henrique Domingos D Hescheler Jürgen J Himmelbauer Heinz H Hübner Norbert N Karantzali Efthimia E Kretsovali Androniki A Lubitz Sandra S Pradier Laurent L Rai Meena M Reimand Jüri J Rolletschek Alexandra A Sachinidis Agapios A Savatier Pierre P Stewart Francis F Storm Mike P MP Trouillas Marina M Vilo Jaak J Welham Melanie J MJ Winkler Johannes J Wobus Anna M AM Hatzopoulos Antonis K AK

PloS one 20090903 9

Embryonic stem (ES) cells have high self-renewal capacity and the potential to differentiate into a large variety of cell types. To investigate gene networks operating in pluripotent ES cells and their derivatives, the "Functional Genomics in Embryonic Stem Cells" consortium (FunGenES) has analyzed the transcriptome of mouse ES cells in eleven diverse settings representing sixty-seven experimental conditions. To better illustrate gene expression profiles in mouse ES cells, we have organized the ...[more]

PMID: 19727443

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Project description:This experiment is part of the FunGenES project (FunGenES - Functional Genomics in Embryonic Stem Cells partially funded by the 6th Framework Programme of the European Union, http://www.fungenes.org). The experiment was conducted at the University Nice Sophia-Antipolis, Nice, France. The aim of this project is to identify new regulators, and new markers of the early steps of adipocyte commitment.Addition of RA on early-differentiating mES cells (Hanging drops, Day 3) orientates their commitment to the adipocyte lineage, while inhibiting myogenesis. The effect of RA on adipogenesis is mediated by retinoic acid receptor beta (RARb), since it can be mimiked by the addition of CD2314 compound, a specific agonist of this receptor isotype. In contrast, mES cell adipogenesis can be bloked by artificial activation of the Wnt pathway using GSK3 inhibitors such as lithium, or Bio.To decipher the genetic pathways that control the early steps of adipogenesis, we have compared the transcriptome of mES cells stimulated to differentiate using adipogenesis-enhancing (CD2314) or -inhibitory (BIO, or CD2314+BIO) treatments (treatment between day 3 and day 6). We have analysed the transcriptome of these cells at day 3 (before treatment), at day 6 (just after stimulation or inhibition of the early steps of adipocyte commitment) and at day 11 (to investigate later regulators of adipogenesis). Materials and methods: CGR8 at different time point during adipogenic differentiation. - Induction of differentiation by removal of LIF at day 0, hanging drops from day 0 to 3. - At day 3, harvesting of the hanging drops, and start adipogenesis-enhancing (CD2314) or -inhibitory (BIO, or CD2314+BIO) treatments (treatment from day 3 to 6, EBs in suspension on petri dishes).- At day 6, harvesting of the EBs and plating on gelatin-treated TC plates in normal culture medium ( GMEM+10%serum).- At Day 7, treatment with final inducers of adipogenic differentiation (Insuline, T3, BRL). Same medium until end point of differentiation (Day 21). Relationships between samples: day03= CGR8, day 3 of differentiation, hanging drops from day 0 (removal of LIF) and 3. day06_0= day 6 of differentiation, control condition from day 3 to 6 (GMEM+serum)day06_bio= day 6 of differentiation, treatment with Bio from day 3 to day 6. day06_cd= day 6 of differentiation,treatment with CD2314 from day 3 to day 6.day06_cd_bio= day 6 of differentiation,treatment with CD2314 plus Bio from day 3 to day 6.Day11_0= day 11 of differentiation, cells in control condition from day 3 to 6 (GMEM+serum).Day11_bio= day 11 of differentiation, cells treated with Bio from day 3 to day 6.Day11_cd= day 11 of differentiation,cells treated with CD2314 from day 3 to day 6.Day11_cd_bio= day 11 of differentiation,cells treated with CD2314 plus Bio from day 3 to day 6.Treatments: - At day 3, addition of adipogenesis-enhancing (CD2314) or -inhibitory (BIO, or CD2314+BIO) treatments (treatment from day 3 to 6).- At Day 7, treatment with final inducers of adipogenic differentiation (Insuline, T3, BRL). O= No treatment CD= treatment w Culture conditions; - Hanging drops from day 0 to Day 3.- Suspension culture between day 3 to 6, Petri dishes.- Plating on gelatine from day 6 to end point.

Dataset Information

Transcription profiling of mouse embyronic stem cell line CGR8 during the first 10 days of differentiation into embryoid bodies

Publications

The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation.

Similar Datasets

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