Transcriptional analysis of forebrain plus optic cup from zebrafish embryos after BMP4 overexpression
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
SUBMITTER: Juan Mateo
PROVIDER: E-MTAB-10085 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Estrogen signaling is important for vertebrate embryonic development. Here we have used zebrafish (Danio rerio) as a vertebrate model to identify estrogen regulated genes during the first 4 days of development. Zebrafish embryos were exposed to 1 M-BM-5M 17M-NM-2-estradiol from 3 hours post fertilization to 4 days post fertilization, harvested daily and subjected to RNA extraction for transcriptome analysis using microarrays. Estrogen responsive genes were analyzed with hierarchical clustering followed by gene function and tissue expression analysis. Markedly distinct sets of genes were up and down-regulated by estrogen treatment at different time points. Among these genes, only the well-known estrogenic marker vtg1 was co-regulated at all time points. Despite this, the biological functional categories targeted by estrogen were similar throughout zebrafish development. Estrogen responsive genes were enriched mainly in the liver, pancreas and brain. In conclusion, our data shows that in zebrafish distinct cohorts of E2 responsive genes are expressed in a tissue specific manner at different developmental stages. However, the biological pathways that are affected are conserved. 30 embryos were pooled as one sample and exposed to 1 M-NM-<M E2 or vehicle (0.1% DMSO) at approximately 3 hours post fertilization (hpf). At different time points, 1 dpf (24 hpf), 2 dpf (48 hpf), 3 dpf (72 hpf) and 4 dpf (104 hpf), embryos were collected for total RNA extractions. Time points 1 and 2 dpf were performed in biological triplicates of independent pools of RNA while time points 3 and 4 dpf were performed in quadruplicates.
2013-12-31 | E-GEOD-42766 | biostudies-arrayexpress
Project description:RNA-seq was performed to reveal the RNA expression profile at two different stages (shield and tail-bud stage) in the embryogenesis of zebrafish (wild type strain AB). Zebrafish embryos were collected at the shield stage and tail-bud stage, which correspond to 6 hours post fertilization (hpf) and 10 hpf, respectively. Total RNA was extracted with miRNeasy Mini Kit, libraries for sequencing were prepared with TruSeq stranded mRNA library prep kit (Illumina), and paired-end sequencing was performed using NovaSeq 6000 (Illumina).
2022-01-14 | E-MTAB-10167 | biostudies-arrayexpress
Project description:In order to discover the targets of Foxj1, we made transgenic zebrafish in which Foxj1 is ubiquitously overexpressed in response to heat [Tg(hsp70::foxj1a)]. Transgenic embryos and wild type control embryos were collected, given two heat shocks (at 18 hours post fertilization (hpf) and 20 hpf), then analyzed at 22 hpf. Gene expression profiles of embryos overexpressing Foxj1a were compared to gene expression profiles of wild type embryos using Nimblegen whole transcriptome zebrafish microarrays.
2014-08-31 | E-MTAB-2815 | biostudies-arrayexpress
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
2012-07-27 | E-GEOD-39707 | biostudies-arrayexpress
Project description:We use the zebrafish embryo model to study the innate immune response against Staphylococcus epidermidis. Therefore, we injected S. epidermidis (and three controls groups) into the yolk at 2 hpf and samples at mutiple timepoints. Gene expression profiles were obtained at 6, 30, 54, 78, 102 and 126 hpi by microarrays. The results show that the gram-positive bacterium S. epidermidis induces a late immune response with a strong response at 102 hpi. This microarray study was designed to determine the gene expression profile during infection with Staphylococcus epidermidis. RNA was isolated from groups of embryos (20) at 6 timepoints during the infection. Wildtypes zebrafish embryos were micro-injected into the yolk (2hpf) with (1) 20 CFU of S. epidermdis O-47 mCherry bacteria suspended in PVP (Polyvinylpyrrolidone), (2) mock-injected with PVP as a control, (3) Needle insertion as control, (4) Non-injected as a control. After injections embryos were transferred into fresh egg water and incubated at 28M-BM-0C. At 8 hpf (6 h post infection), 32 hpf (30 h post infection), 56 hpf (54 h post infection), 80 hpf (78 h post infection), 104 hpf (102 h post infection) or 128 hpf (126 h post infection) twenty embryos per treatment group were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent. All treatment groups were analyzed using a common reference approach.
2013-04-01 | E-GEOD-37227 | biostudies-arrayexpress
Project description:Investigation of whole genome expression pattern of 24 hours post fertilization Danio rerio embryos exposed to bisphenol A, 17β-estradiol, or 0.1% DMSO vehicle control This data represents 2 experiments using 2 separate microarrays. Microarray 1 [Low]: Embryos were exposed to 0.1 µM BPA, 0.1 µM E2, or control from 8 hpf to 24 hpf. Three biological replicates were collected for each treatment. 40 embryos were pooled to comprise a replicate. Microarray 2 [High]: Embryos were exposed to 80 µM BPA, 15 µM E2, or control from 8 hpf to 24 hpf. Two biological replicates were collected for each treatment. 40 embryos were pooled to comprise a replicate. These 2 microarray experiments are cross-comparable, as described in the associated publication.
2013-03-25 | E-GEOD-38960 | biostudies-arrayexpress
Project description:During early neurogenesis, multiple whole animal gene expression profiling studies revealed widespread changes in developmental mRNA and miRNA abundance in ethanol-exposed embryos. Consistent with a role for miRNAs in neurobehavioral development, miRNA target prediction analyses identified multiple miRNAs misexpressed in the ethanol exposed cohorts that were also predicted to target inversely expressed transcripts known to influence brain morphogenesis. [mRNA] A twelve chip study using total RNA recovered from pools of 75 tropical 5D zebrafish embryos at 24 hours post fertilization (hpf). Embryos were exposed to control embryo medium, 100 mM ethanol, or 300 mM ethanol from 4-24 hpf, with four-fold biological redundancy per condition. A single 12x135K Nimblegen array was used to measure the expression level of 38,489 genes from Danio rerio using 60-mer probes, with three-fold technical redundancy. [miRNA] A twelve chip study using miRNA recovered from pools of 75 tropical 5D zebrafish embryos at 12, 24, 36, and 48 hours post fertilization (hpf). Embryos were exposed to control embryo medium or 300 mM ethanol from 4-24 hpf, with two-fold biological redundancy per condition. Control samples were pooled and hybridized to a single array. 12 miRZebrafish arrays (based on MirBase release 12.0) were used to measure the expression level of 218 mature miRNA from Danio rerio, with 12-fold technical redundancy.
2011-09-30 | E-GEOD-30497 | biostudies-arrayexpress
Project description:Congenital malformations are a prevalent cause of infant mortality in the United States and their induction has been linked to a variety of factors, including exposure to teratogens. However, the molecular mechanisms of teratogenicity are not fully understood. MicroRNAs are an important group of small, non-coding RNAs that regulate mRNA expression. MicroRNA roles in early embryonic development are well established, and their disruption during development can cause abnormalities. We hypothesized that developmental exposure to teratogens such as valproic acid alters microRNA expression profiles in developing embryos. Valproic acid is an anticonvulsant and mood-stabilizing drug used to treat epilepsy, bipolar disorder and migraines. To examine the effects of valproic acid on microRNA expression during development, we used zebrafish embryos as a model vertebrate developmental system. Zebrafish embryos were continuously exposed to valproic acid (1 mM) or vehicle control (ethanol) starting from 4 hours post-fertilization (hpf) and sampled at 48 and 96 hpf to determine the miRNA expression profiles prior to and after the onset of developmental defects. At 96 hpf, 95% of the larvae showed skeletal deformities, abnormal swimming behavior, and pericardial effusion. Microarray expression profiling was done using Agilent zebrafish miRNA microarrays. Microarray results revealed changes in miRNA expression at both the time points. Thirteen miRNAs were differentially expressed at 48 hpf and 22 miRNAs were altered at 96 hpf. Among them, six miRNAs (miR-16a, 18c, 122, 132, 457b, and 724) were common to both time points. Bioinformatic target prediction and examination of published literature revealed that these miRNAs target several genes involved in the normal functioning of the central nervous system. These results suggest that the teratogenic effects of valproic acid could involve altered miRNA expression. Small RNA profiles were deteremined in valproic acid exposed zebrafish embryos using Agilent miRNA microarrays
2013-06-19 | E-GEOD-48054 | biostudies-arrayexpress
Project description:Exposure experiments with the non-aromatizable fish androgen, 11-ketotestosterone in the range of 0.05-5000 nM were conducted in order to identify potential androgen-responsive genes in zebrafish embryos by microarray analysis. Zebrafish embryos were treated from 96 hpf to 120 hpf in a single experiment with three controls (embryonic medium). Microarray studies were performed using a Custom 8x60k Gene Expression Microarrays (Amadid G4102A, based on the ensembl zebrafish genome version 3) from total RNA with low input labelling and hybridization kit (Agilent Technologies) and one-color design according to the manufacturer instructions. Fluorescent intensities of individual microarray spots were extracted using the Agilent Feature Extraction software. Raw microarray data were converted to log2 values and quantile-normalized. For further statistical analysis, fold changes in relation to the mean of the controls were calculated for each treatment. Zebrafish embryos were treated from 96 hpf to 120 hpf in a single experiment with three controls and 11 concentrations of 11-ketotestosterone ranging from 0.05-5000 nM.
2014-09-30 | E-GEOD-59499 | biostudies-arrayexpress
Project description:Investigation of whole genome expression pattern of 60 and 72 hours post fertilization Danio Rerio embryos exposed to TMT and vehicle control Embryos were exposed to 10uM TMT or control from 48hpf to 60 or 72 hpf. Three replicates were collected for each time point. 40 embryos were pooled to comprise a replicate.
2011-03-23 | E-GEOD-28131 | biostudies-arrayexpress