ABSTRACT: The aim of this study was to identify genes that are regulated by Bmp signaling with the zebrafish heart at the heart cone stage around 21-23 hours post fertilization. In total, 4 samples based on cDNA from extracted cardiac tissue were analyzed: 2 samples of Tg(hsp70l:bmp2b)fr13 transgenic embryos heatshocked at 18 hpf and 2 WT control samples.
Project description:The aim of this study was to identify genes that are regulated by ccm2 signaling with the zebrafish heart at around 72 hours post fertilization. In total, 4 samples based on cDNA from extracted cardiac tissue were analyzed: 2 samples of ccm2 m201 mutant embryos and 2 WT control samples.
Project description:Heart formation requires input from two populations of progenitor cells - the first and second heart fields - that differentiate at distinct times and create different cardiac components. The cardiac outflow tract (OFT) is built through recruitment of late-differentiating, second heart field (SHF) -derived cardiomyocytes to the arterial pole of the heart. Mechanisms responsible for selection of an appropriate number of OFT cells from the SHF remain unclear, although several lines of evidence emphasize the importance of FGF signaling in promoting this process. Here, we examine the impact of inhibition of FGF signaling on cardiac transcription profiles in an effort to identify genes operating downstream of FGF during OFT development. We compared hearts from embryos treated with the FGFR inhibitor SU5402 to the hearts from sibling embryos treated with DMSO. Two replicates were performed.
Project description:Key tissues of the adult female parasite involved in nutritional uptake and reproduction were examined using a novel gene discovery approach that combined laser microdissection microscopy and microarray analyses. Gastrodermis, vitelline glands and ovary were microdissected from unfixed, frozen sections of the Asian species, Schistosoma japonicum. Total RNA was isolated from the enriched tissue preparations and microarray analyses undertaken to generate tissue specific gene expression profiles. Single colour adult female schistosome laser microdissection microarray data with technical replicates in duplicate: Gastrodermis (gut); vitelline glands (vitelline); ovary; and whole section (control).
Project description:To define the differential gene regulation of adult Schistosoma japonicum in response to host insulin, we utilised a parasite microarray with 38,444 probes representing 19,222 genes. We cultured male and female adult worms were exposed to insulin and glucose; and then parasites were collected at three time-points. There were 1,437 probes (1101 genes) up or down regulated (±1.5 fold change) by insulin after 0.5, 3, 24 hours, with the majority, 712 probes (577 genes) and 623 probes (486 genes) were up-regulated at 24 hour of adding insulin in males and females respectively compared with the control (without insulin). Single colour microarray, insulin treated adult Schistosoma japonicum with technical replicates in duplicate: Separate male and female worms exposed to insulin at 0, 0.5, 3, 24 hours. This study includes 6 control samples for separate male and female worms cultured without insulin at 0, 0.5, 3, 24 hours.
Project description:We have examined the gene expression profile of the transformation of the blood fluke Schistosoma mansoni from the cercarial to schistosomula stages. Specifically cercariae were mechanically transformed and then cultured for 3 hours or 5 days, and then total RNA was isolated and microarray analysis performed. A second experiment compares the effect that the presence of red blood cell in the culturing conditions has over the 3 hour and 5 day periods have on the parasite. Agilent custom designed microarray was used. One colour experimental design. One biological replicate was labelled and then two technical replicates (hybridisations) performed for each sample. A total of 5 samples were examined, cercariae, 3 hrs +RBCs, 5 days + RBCs, 3 hrs â??RBCs and 5 days â?? RBCs.
Project description:We identified a novel paralog of the antioxidant response element transcription factor, Nrf2 in zebrafish. To determine whether the paralogs Nrf2a and Nrf2b regulate different sets of genes, we performed loss-of-function experiments followed by microarray-based gene expression profiling, performed on embryos in which expression of Nrf2a, Nrf2b, or both paralogs was knocked down. Embryos at the 1-4 cell stage were injected with 3-5 nl of a control morpholino (MO) or gene-specific MO to knockdown Nrf2a, Nrf2b, or a Nrf2a+b combination. At 48 hpf, triplicate groups of 5 embryos were exposed to 2 M-BM-5M of tert butyl hydroquinone or 2% DSMO for 4 hours. At 52 hpf, embryos were fixed in RNA Later and stored at -80M-BM-0C. RNA was extracted, bioanalyzed, labeled with Cy3 and hybridized to the Agilent V3 4x44K zebrafish microarray (cat. #G2519F-026437) at the Genome Technology Core of the Whitehead Institute (Cambridge, MA). Raw array data obtained from the Whitehead Institute were extracted using Agilent's feature extraction software using background detrending (spatial and multiplicative).Prior to normalization, Cy3 values below 5 were set to 5. The data were then normalized using the non-linear scaling method based on rank invariant probes. After normalization but before statistical analyses, probes not significantly above background in all microarrays were removed (3147 probes in all; based on AgilentM-bM-^@M-^Ys 2.6 standard deviation method). None of the probes were saturated for Cy3 signal on any microarray, so no further filtering was applied. There were a total of 40,456 probes for statistical analyses. Statistical tests were performed using MeV v4. Data were log transformed and median centered for each probe. An ANOVA was run for morpholino injection, with p-value based on 1000 permutations of the data and alpha of 0.01. The probes found significant in the ANOVA were subsequently examined using Rank Product (RP) analysis to identify probes up- and down-regulated by the MO injection For each RP test, a two-class unpaired RP analysis was performed using 100 permutations of the data with a false discovery rate (FDR) M-bM-^IM-$10%.
Project description:This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 days post fertilisation, extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole heart(s) and sent for sequencing along with 3 groups of 200 uninjured hearts, extracted and processed identically. RNA sequencing, quality control and alignment was performed by the commercial company GENEWIZ.
Project description:The zebrafish (Danio rerio) is a popular animal model in studies of vertebrate development and organogenesis. Recent research has shown a similarity of approximately 70% between the human and zebrafish genomes and of 84% in human disease-causing genes, specifically. Zebrafish embryos have a number of desirable features, including transparency, a large size, and rapid embryogenesis. Protein phosphorylation is a well-known post-translational modification (PTM), which performs various biological functions. Recent mass spectrometry (MS) developments have enabled the study of global phosphorylation patterns by using MS-based proteomics coupled with TiO2 phosphopeptide enrichment. In the present study, we identified 3,500 non-redundant phosphorylation sites on 2,166 phosphoproteins and 1,564 quantified phosphoproteins in zebrafish embryos.
Project description:Retinoic acid (RA) and 2,3,7,8-tetrachlorodibenzo-p-dioxin activate distinct ligand-dependent transcription factors, and both cause cardiac malformation and heart failure in zebrafish embryos. We hypothesized that they cause this response by hyperactivating a common set of genes critical for heart development. To test this, we used microarrays to measure transcripts changes in hearts isolated from zebrafish embryos 1,2,4 and 12 h after exposure to 1μM RA. We used hierarchical clustering to compare the transcriptional responses produced in the embryonic heart by RA and TCDD. We could identify no early responses in common between the two agents. However, at 12 h both treatments produced a dramatic downregulation of a common cluster of cell cycle progression genes, which we term the Cell Cycle Gene Cluster (CCGC). This was associated with a halt in heart growth. These results suggest that RA and TCDD ultimately trigger a common transcriptional response associated with heart failure, but not through the direct activation of a common set of genes. Among the genes rapidly induced by RA was Nr2F5, a member of the COUP-TF family of transcription repressors. We found that induction of Nr2F5 was both necessary and sufficient for the cardiotoxic response to RA. Experiment Overall Design: For RA study, total of 24 samples were collected and analyzed by microarray. Samples of zebrafish embryonic hearts were collected at four timepoints: 1, 2, 4, 12 hours post RA dosing. For each timepoint, there are three replicates of microarray studies. Each replicate includes microarray studies of one sample of RA treated heats and one sample of vehicle control (DMSO) treated hearts.
Project description:Forebrain and optic cups were microdissected from zebrafish embryos at 21 hours post-fertilization (hpf) after heat-shock at 15 hpf to induce overexpression of BMP in heterozygous tg(hsp70l:bmp4) embryos vs wild type controls.