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Experiment 1: Overexpression experiments at 30% epiboly MZspg and WT embryos with or without protein synthesis inhibition

ABSTRACT: Overexpression experiments with or without protein synthesis inhibition were performed to investigate transcriptional targets of Klf4, FoxD3, and Nanog-like in the blastula stage embryos (4.7 hours postfertilization) of wild type or MZspg background. Experiments were performed in biological triplicates. Cy3 and Cy5 channels were splitted in Genedata Expressionist and Analyst software, quantile normalised and used for independent comparisons.

ORGANISM(S): Danio rerio

SUBMITTER: Wolfgang Driever

PROVIDER: E-GEOD-44982 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Experiment 2: Klf2a, Klf2b and FoxD3 overexpression experiments at 30% epiboly MZspg and WT embryos with or without protein synthesis inhibition

Project description:Overexpression experiments with or without protein synthesis inhibition were performed to investigate transcriptional targets of Klf2a, Klf2b and FoxD3 in the blastula stage embryos (4,7 hours postfertilization) of wild type or MZspg backgroumd Experiments were performed in biological duplicates. Cy3 and Cy5 channels were splitted in Genedata Analyst software, quantile normalised and used for independent comparisons.

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Experiment 4: Affymetrix validation array

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Experiment 3: Klf2a and Klf2b loss-of-function experiments at 30% epiboly Wild Type zebrafish embryos

Project description:Morpholino injections were performed to investigate transcriptional targets of Klf2a, and Klf2b in the blastula stage embryos (4,7 hours postfertilization) of wild type zebrafish embryos. Experiments were performed in biological duplicates. Cy3 and Cy5 channels were splitted in Genedata Analyst software, quantile normalised and used for independent comparisons.

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Experiment 4: Klf4, FoxD3, FoxD5 and combined FoxD3 and FoxD5 loss-of-function experiments at 30% epiboly Wild Type zebrafish embryos

Project description:Morpholino injections were performed to investigate transcriptional targets of Klf4, FoxD3 and FoxD5 in the blastula stage embryos (4,7 hours postfertilization) of wild type zebrafish embryos. Experiments were performed in biological duplicates or triplicates. Cy3 and Cy5 channels were splitted in Genedata Analyst software, quantile normalised and used for independent comparisons.

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Zebrafish embryos exposed to the model hedgehog pathway inhibitor cyclopamine, as well as to the potential hedghog pathway disrupters SANT-2 and GANT-61.

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Gene expression in unfertilized eggs and the MBT stage of zebrafish embryos

Project description:Very little is known on the nature of epigenetic states in developing zebrafish despite its growing importance as a model organism in developmental biology. We report histone modifications on promoters of pluripotency genes in zebrafish embryos at the mid-late blastula transition (MBT+) stage. We identify three classes of expressed genes based on these profiles: (1) those with a promoter occupied by marks of active genes without any repressive marks; (2) those co-occupied by both activating and repressive modifications; of these genes, klf4 was notably found to be mosaically expressed in the embryo, possibly accounting for this epigenetic pattern; (3) those occupied by repressive marks with, surprisingly, little not acetylated H3K9 or H4. Culture of embryo-derived cells results in a switch from histone acetylation to K9 and K27 trimethylation on genes transcriptionally inactivated, resulting in a profile similar to that of fibroblasts. All promoters retain H3K4me3, indicating no correlation between H3K4me3 occupancy and gene expression. Our results illustrate a complex chromatin state on the promoter of pluripotency-associated genes in the zebrafish embryo, shortly after the embryonic genome is turned on. We assessed gene expression in unfertilized eggs and the MBT stage of zebrafish embryos (~ 3.5 hpf) using a 44K custom designed chip from Agilent (3 and 4 replicates, respectively). Genes of interest were extracted and evaluated according to expression dynamics and levels.

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