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Differentiating i-Mixl1 mESCs cultured in the presence or absence of Doxycycline

ABSTRACT: We profiled gene expression changes in differentiating i-Mixl1 ES cells(Willey, Ayuso-Sacido et al., 2006, Blood 107(8): 3122-3130) cultured in the presence or absence of Doxycycline (DOX, 0.1 ug/ml, 3 replicates per treatment/time point). Total RNA was isolated from EBs harvested at day 2, 3 and 4 (DOX added 1 day after plating of ES cells). RNA (1 ug) was subjected to one round of linear amplification (RiboAmp System) to yield 10 ug of RNA. The RNA was indirectly labeled using amino allyl-dUTP('t Hoen, de Kort et al., 2003, Nucleic Acids Res. 31: e20), then conjugated with Cy3 or Cy5. The labeled RNAs were used to screen a 15K mouse developmental cDNA microarray(Tanaka, Jaradat et al., 2000, Proc. Natl. Acad. Sci. U.S.A. 97: 9127-9132). Pairwise analysis of hybridization results for EBs cultured with or without DOX was performed for samples harvested on each day. Spotfire(R) software was used for data management and filtering. Gene expression ratios were normalized after filtering the data to remove low-intensity and poor quality spots. Data obtained for replicate samples were in excellent agreement.

ORGANISM(S): Mus musculus

PROVIDER: GSE40703 | GEO | 2015/09/01

SECONDARY ACCESSION(S): PRJNA174968

REPOSITORIES: GEO

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Differentiating i-Mixl1 mESCs cultured in the presence or absence of Doxycycline

Project description:We profiled gene expression changes in differentiating i-Mixl1 ES cells(Willey, Ayuso-Sacido et al., 2006, Blood 107(8): 3122-3130) cultured in the presence or absence of Doxycycline (DOX, 0.1 ug/ml, 3 replicates per treatment/time point). Total RNA was isolated from EBs harvested at day 2, 3 and 4 (DOX added 1 day after plating of ES cells). RNA (1 ug) was subjected to one round of linear amplification (RiboAmp System) to yield 10 ug of RNA. The RNA was indirectly labeled using amino allyl-dUTP('t Hoen, de Kort et al., 2003, Nucleic Acids Res. 31: e20), then conjugated with Cy3 or Cy5. The labeled RNAs were used to screen a 15K mouse developmental cDNA microarray(Tanaka, Jaradat et al., 2000, Proc. Natl. Acad. Sci. U.S.A. 97: 9127-9132). Pairwise analysis of hybridization results for EBs cultured with or without DOX was performed for samples harvested on each day. Spotfire(R) software was used for data management and filtering. Gene expression ratios were normalized after filtering the data to remove low-intensity and poor quality spots. Data obtained for replicate samples were in excellent agreement. Six experiments total: three time points (day 2, day 3, day 4); for each time point mRNA was collected in the presence or absence of Doxycycline. Three biological replicas were collected for each of the six experiments

2015-09-01 | E-GEOD-40703 | biostudies-arrayexpress

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Transcription profiling of mouse ES cell derived brachyury+ (T) cell specific transcriptome

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 University of Cologne, Cologne, Germany. Goal of the experiment was an analysis the transcriptome of the ES-cell derived pure T-brachyury expressing CGR8 cells. Materials and methods: On day 0, EBs were made from T-brachyury ES (CGR8) cell line by hanging drop protocol. On second day, the hanging drop EBs were transferred into suspension. On third day, the EBs were treated or untreated with puromycin at a concentration of 5ug/ml for 2 days. On 5th day, the medium was changed and added medium with or without puromycin at a concentration of 2 ug/ml for 1 day. On day 6th , RNA was isolated from EBs treated or untreated with puromycin for affymetrix analysis.

2010-05-12 | E-TABM-716 | biostudies-arrayexpress

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