Danio rerio
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA271468 | ENA |
REPOSITORIES: ENA
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Project description:Goal of the experiment was to assess the differences in gene expression between maternal zygotic ezh2 mutant zebrafish embryos and wildtype embryos at 0 and 3.3 hpf.
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Project description:The goal of the ChIP-sequencing experiments was to assess the differences in occupancy of a selection of chromatin marks and chromatin associated proteins in absence of both maternal and zygotic Ezh2 in zebrafish embryos at 24 hours post-fertilization (hpf). The goal of RNA-sequencing experiments was to ass the effect of the absence of both maternal and zygotic Ezh2 on gene expression in zebrafish embryos at 0, 3.3, and 24 hpf and link these differences with the changes in epigenetic mark occupancy.
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Project description:RNAseq of wild type and maternal-zygotic Nanog mutant (MZnanog) zebrafish embryos
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Project description:In triplicate for each condition, 12 WT and acbd6 F0 crispant Danio rerio (zebrafish) embryos were incubated with 20 μM YnMyr for 24 h, either between 48-72 hpf or 96-120 hpf. After labelling, zebrafish were washed twice with fresh egg water, deyolked, flash frozen in liquid nitrogen and stored at -80°C until further analysis.
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Project description:Sox31 is a member of the zebrafish SoxB1 subfamily, and its expression can be detected both pre- and post-MBT. To distinguish the function of its maternal and zygotic transcripts, a splice blocking morpholino (Sb MO) was designed to interfere with the processing of new, zygotically synthesised mRNAs without interfering with mRNAs of maternal origin. Developmental arrest was observed in Sb MO which could not bypass MBT. Mid-Blastula Transition (MBT) functions as a time window for zygotic genome activation and maternal mRNA degradation. To uncover whether the “zygotic up” and “maternal down” event during MBT is retarded in Sb morphants, we performed microarray experiment at the end of MBT (about 4.3 hours post fertilication/4.3 hpf) to compare mRNAs from Sb morphants and control embryos. In one experiment, three flocks of zebrafish eggs were injected with the Sox19b morpholino immediately after fertilization, while another three control populations were injected with placebo. At 4.3 hpf, these six flocks of embryos were sent for gene expression profiling with six Affymetrix Zebrafish Genome Arrays. In another experiment, we compared two wildtype embryo samples at 4h (post-MBT) against two wildtype samples at 2.5 h (pre-MBT).
2011-10-12 | E-GEOD-32914 | biostudies-arrayexpress
Project description:In triplicate for each condition, 12 WT and acbd6 F0 crispant Danio rerio (zebrafish) embryos were incubated with 20 μM YnMyr for 24 h, either between 48-72 hpf or 96-120 hpf. After labelling, zebrafish were washed twice with fresh egg water, deyolked, flash frozen in liquid nitrogen and stored at -80°C until further analysis.
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Project description:3,3’,5.5’-Tetrabromobisphenol A (TBBPA) is a widely used brominated flame-retardant utilized in the production of electronic devices and plastic paints. The objective of this study is to use zebrafish as a model and determine the effects of TBBPA exposure on early embryogenesis. We initiated TBBPA exposures (0, 10, 20 and 40μM) at 0.75 h post fertilization (hpf) and monitored early developmental events such as cleavage, blastula and epiboly that encompass maternal-to-zygotic transition (MZT) and zygotic genome activation (ZGA). Our data revealed that TBBPA exposures induced onset of developmental delays by 3 hpf (blastula). By 5.5 hpf (epiboly), TBBPA-exposed (10-20 μM) embryos showed concentration-dependent developmental lag by up to 3 stages or 100% mortality at 40 μM. Interestingly, while continued 0.75- 48 hpf TBBPA exposures (10 μM) led to severely deformed embryos, replacing exposure solution with chemical-free media at 6 hpf mitigated this effect, with 100% normal embryos at 48 hpf. To examine the genetic basis of TBBPA-induced delays, we conducted mRNA-sequencing on embryos exposed to 0 or 40 μM TBBPA from 0.75 hpf to 2, 3.5 or 4.5 hpf. Read count data showed that while TBBPA exposures had no overall impacts on maternal or maternal-zygotic genes, collective read counts for zygotically activated genes were lower in TBBPA treatment at 4.5 hpf compared to time-matched controls, suggesting that TBBPA delays ZGA. Gene ontology assessments for both time- and stage-matched differentially expressed genes revealed TBBPA-induced inhibition of chromatin assembly- a process regulated by histone modifications. Since acetylation is the primary histone modification system operant during early ZGA, we hypothesized that TBBPA inhibits histone acetylation, resulting in lack of open chromatin within promoters of zygotic genes and delaying ZGA. Therefore, we co-exposed embryos to 20 μM TBBPA and 100 μM N-(4-Chloro-3-(trifluoromethyl)phenyl)-2-ethoxybenzamide (CTB) -a histone acetyltransferase activator that promotes histone acetylation- and showed that TBBPA-CTB co-exposures from 0.75- 3 hpf significantly reversed TBBPA-only developmental delays, suggesting that TBBPA-induced phenotypes are indeed driven by repression of histone acetylation. Collectively, our work demonstrates that TBBPA disrupts ZGA and early developmental morphology, potentially by inhibiting histone acetylation. Future studies will focus on mechanisms of TBBPA-induced chromatin modifications.
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Project description:Defl1 knockdown gene expression in Zebrafish 12.5 hpf embryos
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