RNA-seq of depdc5-/-, tsc2-/-, depdc5-/- x tsc2-/- and wildtype zebrafish larvae
Ontology highlight
ABSTRACT: Transcriptome analysis of the heads of 5 dpf epdc5-/-, tsc2-/-, depdc5-/- x tsc2-/- and wildtype zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a-/- zebrafish larvae.
Project description:Transcriptome analysis of the heads of 6 dpf sv2a-/-, sv2a+/- and sv2a+/+ zebrafish larvae to provide insights into the neuropathological processes underlying the observed epileptic phenotype in sv2a-/- zebrafish larvae.
Project description:Expression microarray of livers from 4 dpf control zebrafish larvae, larvae treated with azacytidine, and ahcy mutant larvae Comparison of expression from livers obtained from ahcy+/+ treated with vehicle, ahcy+/+ treated with azacytidine, and ahcy-/- treated with vehicle. We treated larvae starting at 2 dpf with 1 mM azacytidine or vehicle control. Livers were removed at 4 dpf, RNA isolated, and double amplified.
Project description:Label-free mass spectrometry-based quantitative proteomics was applied to a larval zebrafish spinal cord injury model, which allows axon regeneration and functional recovery within two days (days post lesion; dpl) after a spinal cord transection in 3 day-old larvae (dpf). Proteomic profiling of the lesion site was performed at 1 dpl and 2 dpl as well as corresponding age-matched unlesioned control tissue (4 dpf as control for 1 dpl; 5 dpf as control for 2 dpl).
Project description:ATF6 is a key regulator of the unfolded protein response. Through use of zebrafish and cultured cells we demonstrate that ATF6 drives fatty liver disease by interaction with fatty acid synthase (FASN). Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tg(fabp10:nls-mCherry) control larvae, 2 batches of ethanol-treated Tg(fabp10:nls-mCherry) larvae, and 1 batch of Tg(fabp10:nAtf6-cherry; cmlc2:GFP). Each batch was purified for preparation of high-throughput sequencing libraries.
Project description:cdipt is an essential gene in the synthesis of phosphatidylinositol (PtdIns) in the zebrafish, Danio rerio. The zebrafish mutant cdipt^hi559Tg (ZL782) carries a retroviral insertion which inactivates cdipt. Homozygous mutants exhibit hepatocellular endoplasmic reticulum (ER) stress and non-alcoholic fatty liver disease (NAFLD) pathologies at 5 days post fertilization (dpf). This study reveals a novel link between PtdIns, ER stress, and steatosis. We compared whole animal gene expression profiles of hi559 mutant larvae with phenotypically wild type larvae from a heterozygote incross in triplicate.
Project description:Genome-wide microarray analysis of the effects of swim-training on caudal fin development in zebrafish larvae. Zebrafish were subjected to swim-training from 5 days post fertilization (dpf) until 10 dpf. Subsequently, we performed a genome-wide microarray analysis on the caudal fins of control and trained fish at 10 dpf. The goal of the project was to investigate the effects of swim-training on the gene expression level during caudal fin development in zebrafish larvae. Two-condition experiment: control vs trained fish. RNA was isolated from pooled caudal fins of 15 control fish (in duplo: pooled control samples (C2 and C3)) and of 15 trained fish (in duplo: pooled trained samples( T2 and T3)). Subsequently, each pooled RNA sample of control and trained caudal fins was labeled with Cy3 and Cy5 in order to correct for dye bias. We included a technical replicate of the labeled C2 and T2 samples.
Project description:RNA-seq of wild-type Tüpfel long fin (TLF) zebrafish embryos developmentally exposed to three addictive drugs - 5 µM nicotine, 1.14 µM oxycodone and 5 µM amphetamine. Each of the 24 samples (6 samples per drug, plus 6 control samples) represents RNA from a pool of seven 5 dpf zebrafish embryos, exposed to the drug between 1 dpf and 5 dpf.
Project description:Polycomb group (PcG) proteins are transcriptional repressors important to maintain cell identity during embryonic development. Ezh2, the catalytic subunit of the Polycomb Repressive Complex 2, is responsible for placing the epigenetic repressive mark histone H3 lysine 27 trimethylation (H3K27me3). In contrast to results in mouse models, zebrafish embryos mutant for both maternal and zygotic ezh2 (MZezh2) can form a normal body plan at 1 day post fertilization (dpf) but die at 2 dpf, exhibiting pleiotropic phenotypes. To elucidate the specificity of PcG-mediated repression during early zebrafish development, we conducted in depth analysis of the transcriptome, epigenome, and proteome of the MZezh2 mutant embryos at 1 dpf. We found that, despite modifications in the epigenetic landscape, transcriptome and proteome analysis revealed only minor changes in gene and protein expression levels.
Project description:Zebrafish males undergo a juvenile ovary to testis type gonadal transformation process. To understand how juvenile ovary-to-testis transformation in zebrafish is genetically regulated, we compared the transcriptomes of juvenile ovary (JO) and juvenile ovotestis (JOT) samples at 35 dpf using the Gonad Uniclone Microarray v1 (ArrayExpress ID: A-MEXP-838). We also analyzed the transcriptomes of the 32 dpf JO, 32 dpf JOT, 34 dpf JOT, and 36 dpf JOT gonads using the slightly modified Gonad Uniclone Microarray v2 and together with the 35 dpf JO and 35 dpf JOT samples, compared the JO samples against the JOT samples to identify genes that could be potentially involved in the gonad transformation process.