Project description:In our previous study, we found zebrafish embryos treated with 5uM 11,12-EET (epoxyeicosatrienoic acid) had increased stem cell marker, runx1, expression in the AGM. EET also induced ectopic runx1 expression in the tail. To systematically study how EET regulates gene expression, we performed microarray analysis on EET-treated embryos. Zebrafish whole embryos were synchronized at fertilization. Embryos were grown at 28 degree overnight. 25 embryos per group were treated with DMSO or 5uM 11,12-EET starting from 24 hpf (hour post fertilization) until 36 hpf at 28 degree. The triplicates were from three different clutches of embryos, and split into DMSO v.s. EET for each clutch.
Project description:In our previous study, we found zebrafish embryos treated with 5uM 11,12-EET (epoxyeicosatrienoic acid) had increased stem cell marker, runx1, expression in the AGM. EET also induced ectopic runx1 expression in the tail. To systematically study how EET regulates gene expression, we performed microarray analysis on EET-treated embryos. Zebrafish whole embryos were synchronized at fertilization. Embryos were grown at 28 degree overnight. 25 embryos per group were treated with DMSO or 5uM 11,12-EET starting from 24 hpf (hour post fertilization) until 36 hpf at 28 degree. The triplicates were from three different clutches of embryos, and split into DMSO v.s. EET for each clutch. EET vs. DMSO
Project description:To uncover the genes regulated by pharmacological activation of the Glucocorticoid Receptor, we performed microarray-based expression profiling of whole zebrafish embryos at 24 and 72 hours post fertilization (hpf) after 3-hour treatment with 25 M-BM-5M of Beclomethasone, a potent glucocorticoid previously tested in zebrafish or with 0.1 % DMSO as control. Embryos at 24 and 72 hpf stages were treated with either 0.1 % DMSO or 25 M-BM-5M Beclomethasone for 3 hours in triplicate experiments and then frozen for RNA extraction.
Project description:Purpose: To identify differntially expressed transcripts in TP-0903 treated embryos that impair cranila NC EMT and cell migration in zebrafish embryos Methods: zebrafish embryos treated at 13 hpf with 5-7uM TP-0903 and DMSO for 1-, 4- and 8-hrs at 28°C. 35 embryos were collected for each treatment. Results: TP-0903 increases expression of several retinoic acid target genes including genes from within the retinoid pathway Conclusions: TP-0903 causes a direct increase in RA signaling that impairs cranial NC EMT and cell migration in zebrafihs embryos
Project description:Purpose: To identify differntially expressed transcripts in TP-0903 treated embryos that impair cranila NC EMT and cell migration in zebrafish embryos Methods: zebrafish embryos treated at 13 hpf with 5-7uM TP-0903 and DMSO for 1-, 4- and 8-hrs at 28°C. 35 embryos were collected for each treatment. Results: TP-0903 increases expression of several retinoic acid target genes including genes from within the retinoid pathway Conclusions: TP-0903 causes a direct increase in RA signaling that impairs cranial NC EMT and cell migration in zebrafihs embryos mRNA profiles of zebrafish embryos treated with TP-0903 and DMSO were generated by RNA-Seq, in quadruplicates, using Illumina Hi Seq
Project description:To uncover the genes regulated by pharmacological activation of the Glucocorticoid Receptor, we performed microarray-based expression profiling of whole zebrafish embryos at 24 and 72 hours post fertilization (hpf) after 3-hour treatment with 25 µM of Beclomethasone, a potent glucocorticoid previously tested in zebrafish or with 0.1 % DMSO as control.
Project description:We have employed the Zebrafish gene expression microarray (MZH_Zebrafish_16k_v1.0) as a discovery platform to analyze the trancriptome of 108hpf (hours post fertilization) embryos exposed from the 96hpf to 108hpf to 100µM of diethylmaleate (DEM). Four two-color microarray studies for measuring expression levels of zebrafish embryos treated with 100µM of diethylmaleate (DEM) were performed. 8 samples were analyzed in total. Four samples were treated with 0.1% DMSO as a control; four samples were treated with 100 µM of DEM and 0.1% DMSO.
Project description:The zebrafish is as a powerful vertebrate model system for modeling human disease including liver pathology. In ZFE, hepatic responses can be expected after exposure to hepatotoxicants, because hepatocytes are present from 36-hpf and at 72-hpf the liver is fully functioning. These characteristics make the whole ZFE an attractive alternative model for compound-induced hepatotoxicity screening. Therefore, the main objective of this study is to further strengthen the applicability of whole ZFE as an alternative model for hepatotoxicity testing, with a special focus on the ability to identify gene expression responses in whole ZFE that are suggestive of hepatotoxicity. Deep sequence technology is applied to assess whether hepatotoxicity-specific transcripts that are identified in livers of hepatotoxicant treated adult zebrafish can be detected in whole ZFE as well. Whole zebrafish embryo and adult zebrafish are exposed for 48 hours to human hepatotoxicants. Afterwards, the adult liver is dissected and snap frozen untill processed for RNA isolation. The whole zebrafish embryos are pooled, one sample consists of 15 embryos, and are also snap frozen untill processed for RNA isolation. For every sample RNA is isolated according to the protocol of de Jong et al (2009). and then equal amounts of every sample is pooled. The two pools (one for the adult zebrafish liver, the other for the whole zebrafish embryo) are sequenced.
Project description:Purpose: To explore the mechanism of how Tan I inhibits malignant hematopoiesis at the gene expression level Methods: 72 hpf Tg(c-mybhyper: GFP) zebrafish embryos treated with DMSO or Tan I 60 μM were collected for RNA sequencing Results: We found that 1882 genes were differentially expressed between DMSO and Tan I treatment in c-mybhyper fish embryos (p value <=0.05, |log2 fold change| >= 0.25) Conclusions: We identified MMP9 and ABCG2 as two possible downstream genes of Tan I’s effects on EZH2