Ontology highlight
ABSTRACT:
PROVIDER: PRJNA322734 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For non-model organisms with adaptive key-innovations, patterns of regulatory evolution have been predominantly limited to targeted sequence-based analyses. Chromatin-immunoprecipitation with high-throughput sequencing (ChIP-seq) is a technology that has only been used in genetic model systems and is a powerful experimental tool to screen for active cis-regulatory elements. Here, we show that it can also be used in ecological model systems and permits genome-wide functional exploration of cis-regulatory elements. As a proof of concept, we use ChIP-seq technology in adult fin tissue of the cichlid fish Oreochromis niloticus to map active promoter elements, as indicated by occupancy of trimethylated Histone H3 Lysine 4 (H3K4me3). The fact that cichlids are one of the most phenotypically diverse and species-rich families of vertebrates could make them a perfect model system for the further in-depth analysis of the evolution of transcriptional regulation. examination of H3K4me3 in adult fin tissue of the Nile tilapia (Oreochromis niloticus)
2015-07-07 | E-GEOD-62791 | biostudies-arrayexpress
Project description:The goal of this experiment is to test the hypothesis that hypothyroid zebrafish caudal fin possess proximalized gene expression profile. Transcriptome data was generated for proximal, middle and distal adult fin tissue of hypothyroid zebrafish, with euthyroid sibling fish as control.
2022-04-12 | E-MTAB-9528 | biostudies-arrayexpress
Project description:Our main objectives were: 1) to test whether the caudal fin may be used to detect the effects of pollutant exposure by means of DNA microarray; 2) to test whether the fin may be used to detect the effects of pollutants in wild contaminated fish; 3) to investigate the mechanisms of toxicity for Cd metal. Detecting and unraveling specific effects of contaminants in a multi-stress field context remain a major challenge in ecotoxicology. The aim of this study was to apply a previously developed DNA microarray comprising 1000 candidate genes on caudal fin clips in order to assess the usefulness of a non-invasive method in ecotoxicogenomic studies in the European eel. Fin gene expression patterns of eels exposed in laboratory to Cd or a PCBs mixture were compared to test whether fin clips may be used to detect effects of these contaminants. Then, gene transcription profiles of wild fish from 3 sampling sites with differing contamination levels were compared to experimental exposures to test whether fin could detect and unravel the in situ effects of these contaminants. Also, transcriptomic profiles from liver and caudal fin of eels experimentally exposed to Cd were compared to test whether fins may be used to investigate the toxicity mechanisms of this metal. Our results showed distinct fin transcription profiles in response to Cd or PCBs exposure. In addition, the transcription profiles of eels from the most contaminated site clustered with the laboratory-exposed fish. Finally, gene transcription patterns from caudal fin and liver in Cd-exposed eels showed significant differences between the two organs and only 16 common genes were identified. Many of these genes were found to be involved in tissue development and in epigenetic mechanisms. This study thus demonstrates the applicability and usefulness of performing gene transcription assays on non-invasive tissue sampling in order to assess the effect of Cd and PCBs on the transcriptome of fish.
2014-12-01 | GSE62954 | GEO
Project description:To identify gender specific differences in gene expression during fin rgeneration, pectoral fins were amputated from both male and female adult fish. Fins were allowed to recover for 4 days in standard tank condtions then tissue was collected for RNA isolation and microarray analysis
2011-09-03 | GSE31871 | GEO
Project description:Fish and Chips: Expression Profiling in Non-traditional Model Systems Using a Cichlid Fish cDNA Microarray This series represents the 26 arrays that went into Renn et al 2004 (submitted January 16th), and one additional hybridization (GSM15240) that was not included in the publication analysis for statistical reasons.
2010-06-09 | E-GEOD-975 | biostudies-arrayexpress
Project description:Zebrafish have the remarkable ability to regenerate body parts including the heart, spinal cord and fins by a process referred to as epimorphic regeneration. Recent studies have illustrated that similar to adult zebrafish, early life stage-larvae also possess the ability to regenerate the caudal fin. A comparative genomic analysis was used to determine the degree of conservation in gene expression among the regenerating adult caudal fin, adult heart and larval fin. Results indicate that these tissues respond to amputation/injury with strikingly similar genomic responses. Comparative analysis revealed raldh2, a rate-limiting enzyme for the synthesis of Retinoic acid (RA), as one of the highly induced genes across the three regeneration platforms. Experiment Overall Design: The caudal fin of zebrafish larvae at 2days post fertilization were amputated. Caudal fin tissue at 2dpf and regenerating fins were isolated at 1, 2and 3 days post amputation. Three replicates were collected at each time point. 150 fins were pooled to comprise one replicate.
2008-04-07 | E-GEOD-10188 | biostudies-arrayexpress
Project description:Teleost fish have the remarkable ability to regenerate their body parts including heart, spinal cord, and the caudal fin, while many higher vertebrates including us humans have only a limited ability. To facilitate molecular and genetic approaches for regeneration, we previously established an assay using the fin fold of early stage larvae, which regenerate their caudal fin folds as in adult regeneration. Here, we performed transcriptional profiling of regenerating larval fin folds and identified genes with differential expression during regeneration. Gene expression profiling of zebrafish larval fin-fold regeneration was performed by comparing amputated fin fold and uncut control. Keywords: Stress response, injury response.
2008-10-01 | GSE11391 | GEO
Project description:Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For non-model organisms with adaptive key-innovations, patterns of regulatory evolution have been predominantly limited to targeted sequence-based analyses. Chromatin-immunoprecipitation with high-throughput sequencing (ChIP-seq) is a technology that has only been used in genetic model systems and is a powerful experimental tool to screen for active cis-regulatory elements. Here, we show that it can also be used in ecological model systems and permits genome-wide functional exploration of cis-regulatory elements. As a proof of concept, we use ChIP-seq technology in adult fin tissue of the cichlid fish Oreochromis niloticus to map active promoter elements, as indicated by occupancy of trimethylated Histone H3 Lysine 4 (H3K4me3). The fact that cichlids are one of the most phenotypically diverse and species-rich families of vertebrates could make them a perfect model system for the further in-depth analysis of the evolution of transcriptional regulation.
2015-07-07 | GSE62791 | GEO
Project description:The little skate, a cartilaginous fish evolutionarily distal from tetrapods, displays walking-like behavior and has conserved genetic programs and neuronal substrates for land-walking. Studies on little skate have been limited due to lack of high-quality genome assembly. Here, we generated an improved genome assembly of little skate reflecting precise gene annotation and structures and performed integrated analysis of gene expression and chromatin accessibility to investigate molecular mechanisms of fin motor neuron development. Through interspecies comparison of RNA expression, common and species-specific genes expressed in fin/limb/wing level motor neurons were identified. Moreover, by performing chromatin accessibility analysis with a pure fin motor neuron population the potential regulators controlling the gene expression in fin motor neurons were identified. Interspecies comparison of genomic data, gene expression, and chromatin accessibility assay suggest that the little skate has highly conserved gene regulatory mechanisms controlling tetrapod locomotion, which was not previously expected.
2022-10-24 | GSE180334 | GEO
Project description:Fish and Chips: Expression Profiling in Non-traditional Model Systems Using a Cichlid Fish cDNA Microarray This series represents the 26 arrays that went into Renn et al 2004 (submitted January 16th), and one additional hybridization (GSM15240) that was not included in the publication analysis for statistical reasons. Keywords: other
2004-02-05 | GSE975 | GEO