Project description:Zebrafish CNS-PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA-seq.
Project description:Using 2 male and 2 female zebrafish (pool of 6) brain samples, we generated base-resolution DNA methylation maps to document sex-specific epigenetic differences. Here we generated single-nucleotide resoultion DNA methylation map of 4 zebrafish brain samples using Reduced Representation Bisulfite Sequencing (RRBS)
Project description:Purpose: Identify zebrafish control and csf1r-mutant brain transcriptomes Methods: RNA sequencing was performed on whole brain of control (3x), csf1ra-/- microglia (3x) and csf1ra-/-;b+/- microglia (3x) and csf1ra-/-;b-/- zebrafish. 10-20 million reads per sample were obtained. Reads were mapped to zebrafish genome GRC10. Results: We identified that microglia gene expression was reduced in csf1ra-/-;b+/- and csf1ra-/-;b-/;- mutant transcriptomes.
Project description:we report a transgenic zebrafish line using destabilized fluorescent protein, Venus-NLS-PEST (VNP), driven by the promoter of a key circadian clock gene, nr1d1. This system allows us to monitor the development of single-cell circadian rhythm in live zebrafish larva in a cell-type specific manner. To identify the cell types expressing nr1d1:VNP in the whole brain, we conducted single cell RNA-seq (scRNA-seq) of ~15,000 cells dissociated from the brain of Tg(nr1d1:VNP) larval fish at 6.5dpf. Among them, 6514 cells were identified with number of genes > 500 and used for the following analysis. 26 cells clusters were classified from scRNAseq, and manually annotated by comparing the marker genes with the adult zebrfiash whole brain single cell RNA-seq data. The mRNA of nr1d1:VNP was enriched in photoreceptors in pineal gland, granule cells and purkinje cells in cerebellum, habenula cells as well as non-neuron cell.
Project description:Zebrafish populations recently collected from the wild differ from domesticated populations in anxiety-related behaviors. We measured anxiety-related behaviors in wild and domesticated zebrafish populations and performed a multi-brain region transcriptional comparison using microarrays to try to understand the genetic changes that accompany behavioral adaptation to domestication. We performed a microarray analysis comparing the midbrain and telencephalon brain regions of male and female adult zebrafish from four populations varying in domestication history (Wild: Nadia (N) and Pargana (P), and Domesticated: Scientific Hatchery (S) and Transgenic Mosaic 1 (T)). We collected 16 samples per brain region (4 samples per zebrafish population, with 1 telencephalon sample missing for the S population). We attempted to maintain equal sex ratios within each zebrafish population, but this was not always possible due to sex biases within some populations.
Project description:Adult zebrafish (Tübingen strain, sex not specified) at approximately 1 year of age were analysed. For experiments conducted under low oxygen conditions, nitrogen gas was bubbled through water to deplete oxygen before exposure of individual fish to the medium. Oxygen concentrations were measured using a dissolved oxygen meter (DO 6+, EUTECH instruments, Singapore). The dissolved oxygen level for hypoxia treatment was measured to be 1.20 ± 0.6 mg/l, whereas normal ambient oxygen levels were 6.6 ± 0.45 mg/l. Zebrafish were exposed to the hypoxic medium for 3 hours. Briefly, after each hypoxia trial, the animals were euthanized by hypothermic shock and then decapitated to remove the brain. Total RNA was extracted from samples mentioned above using the QIAGEN RNeasy mini kit (QIAGEN, GmbH, Hilden, Germany) and stored at â??80°C before further analysis. RNA concentration was determined with a NanoVueâ?¢ UVâ??vis spectrophotometer (GE Healthcare Life Sciences, Fairfield, USA). RNA integrity and quality were then estimated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and the RNA integrity number (RIN) index was calculated for each sample. Only RNAs with a RIN number >7.0 were processed further. Microarray analysis of gene expression was performed using the Zebrafish Gene 1.0 ST Array (Affymetrix Inc. Santa Clara, CA). Briefly, 300ng of total RNA derived from a single adult brain was converted to amplified sense strand cDNA using the Ambion WT Expression Kit (Life Technologies, Carlsbad, CA). The resulting sense cDNA was fragmented and Biotin end-labelled using the Affymetrix Genechip WT Terminal Labeling Kit prior to hybridisation to the array at 45 °C for 16 hours. Two treatments including hypoxia and normoxia were studied. Each treatment had three biological replicates (i.e. three fish exposed to hypoxia and three fish exposed to normoxia). Six samples were analysed. Microarray analysis of gene expression was performed using the Zebrafish Gene 1.0 ST Array. The signal intensity of the chip was scanned using a GeneChipR Scanner 3000TG and analysed using Expression Console software (www. Affymetrix.com). CEL files were imported and intensities adjusted by RMA background correction and quantile normalization.
Project description:Aim of the study was to examine the expression of calsequestrin isoforms in zebrafish adult brain. By quantitative PCR we found three RNA transcripts coding for Casq1a, Casq1b and Casq2. In brain homogenate, two protein isoforms were detected by western blotting and mass spectrometry. Whole brain fractionation experiments revealed that Casq2 isoform was enriched in a heavy fraction containing microsomes and synaptic membranes, while Casq1a was recovered also in a light cytosolic-enriched fraction. By immunofluorescence, we found that calsequestrins show different cellular localization and we confirmed heterogeneous cell expression of Casq1a and Casq2 mRNA by in situ hybridization. Both isoforms were expressed in cerebellum, and cerebellum-like structures of the brain, Casq2 more concentrated in Purkinje cells, and Casq1 equally distributed in granular and Purkinje cells. At sub cellular level, in Purkinje cells, Casq2 was localized in cell bodies, dendrites and axons, while Casq1 was restricted to cell bodies and axons. Data are discussed in relation to the heterogeneous cellular and subcellular distribution of other Calcium store markers of cerebellum and are evaluated with respect to the relevance of calsequestrins in neuron-specific functional activity.