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H3K27ac and H3K4me3 ChIP-seq in Oryzias latipes

ABSTRACT: Here we analyze key epigenetic marks from medaka (O. latipes) during the vertebrate phylotypic period (stage 24).

ORGANISM(S): Oryzias latipes

PROVIDER: GSE46351 | GEO | 2014/03/25

SECONDARY ACCESSION(S): PRJNA198798

REPOSITORIES: GEO

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H3K27ac and H3K4me3 ChIP-seq in Oryzias latipes

Project description:Here we analyze key epigenetic marks from medaka (O. latipes) during the vertebrate phylotypic period (stage 24). Chromatin immuno-precipitation with histone 3 lysine 27 acetylation and histone 3 lysine 4 trimethylation antibodies.

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Project description:We assess gene expression patterns upon 17beta-estradiol (E2) exposure to Japanese medaka (Oryzias latipes) in order to appere the E2 effects using DNA microarray analysis. Larval medaka were exposed to 0, 3, 30 and 100 ng/L of E2 and concentration-dependent changes in gene expressions were examined using Agilent medaka DNA microarrays. At 7 day, fish were sacrificed and mRNA was extracted for gene expression analysis. In an effort to link gene expression changes to effects on higher levels of biological organization, sex characteristics, gonadal histology, GSI, and egg production and fertility were examined. In microarray experiments, the correlation factors between the controls were from 0.91 to 1.00 among control samples. We observed highly induced O. latipes Gene Indices (OLGI) related to egg-yolk protein such as vitellogenin and L-SF precursor etc., which were significantly affected in a concentration-dependent manner by E2 exposure. To clarify the function of expressed genes by E2 treatments, we selected statistically expressed genes from the microarray experiments. We found 190 genes and 72 genes which were statistically expressed in E2 treatment as induced and repressed genes, respectively. In the induced gene list, there were characteristic induced-genes in the categories of lipid metabolism, stress (oxidative stress, DNA and protein damage), and apoptosis with MAPK pathway. On the other hands, there were characteristic repressed genes in the categories of heat shock protein. Our result may suggest that gene expressions in yolk medaka is able to be used for detection of E2 effect by DNA microarray analysis. Larval medaka were exposed to 0, 3, 30 and 100 ng/L of E2 and concentration and time-dependent changes in gene expressions were examined using Agilent medaka DNA microarrays. At 7 day, three independent samples (one sample contained thirty whole medakas) were sacrificed and mRNA was extracted for gene expression analysis.

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