Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1328194 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Restriction site Associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allow RAD tags to serve as genetic markers spread at a high-density throughout the genome. Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping. First, we show that these markers can be identified and typed on pre-existing microarray formats. Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers. We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and utilizing an enriched RAD marker array for the threespine stickleback. The high number of RAD markers enabled localization of a previously identified region, as well as a second novel region also associated with the lateral plate phenotype. Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and non-model systems. Keywords: microarray genotyping
2007-01-24 | GSE5773 | GEO
Project description:RAD-seq data was used to generate SNP candidates for the development of a SNP parentage assignment panel.
| PRJEB17687 | ENA
Project description:The delta smelt (Hypomesus transpacificus) is an endangered pelagic fish species endemic to the Sacramento-San Joaquin estuary, California, and considered an indicator of ecosystem health. The experimental combination of molecular biomarkers with higher level condition indicators may allow for interpretation of responses in a functional context that can be used to predict detrimental outcomes caused by contaminant exposure. Copper is a contaminant of concern in Californian waterways that may affect the development and survival of this endangered species. We have developed and applied a delta smelt microarray in order to screen for probable candidate molecular biomarkers that may be used in monitoring programs. Functional classifications of microarray responses are presented along with quantitative Polymerase Chain Reaction (qPCR) assessments measuring effects upon neuromuscular, digestive and immune responses in delta smelt exposed to copper. Differences in sensitivity were measured between juvenile and larval delta smelt (LC¬5096h= 25.2 and 80.4 ?g/L Cu2+ respectively). Swimming velocity declined with higher exposure concentrations in a dose-dependent manner, though were not statistically significant to controls. Genes encoding for aspartoacylase (ASPA), hemopexin, alpha-actin and calcium regulation proteins were significantly affected by exposure and were functionally interpreted with measured swimming responses. Effects on digestion were measured by upregulation of chitinase and downregulation of amylase, whilst downregulation of tumor necrosis factor indicated a probable compromised immune system.
2010-08-18 | GSE23238 | GEO
Project description:The delta smelt (Hypomesus transpacificus) is an endangered pelagic fish species endemic to the Sacramento-San Joaquin estuary, California, and considered an indicator of ecosystem health. The experimental combination of molecular biomarkers with higher level condition indicators may allow for interpretation of responses in a functional context that can be used to predict detrimental outcomes caused by contaminant exposure. Copper is a contaminant of concern in Californian waterways that may affect the development and survival of this endangered species. We have developed and applied a delta smelt microarray in order to screen for probable candidate molecular biomarkers that may be used in monitoring programs. Functional classifications of microarray responses are presented along with quantitative Polymerase Chain Reaction (qPCR) assessments measuring effects upon neuromuscular, digestive and immune responses in delta smelt exposed to copper. Differences in sensitivity were measured between juvenile and larval delta smelt (LC¬5096h= 25.2 and 80.4 ?g/L Cu2+ respectively). Swimming velocity declined with higher exposure concentrations in a dose-dependent manner, though were not statistically significant to controls. Genes encoding for aspartoacylase (ASPA), hemopexin, alpha-actin and calcium regulation proteins were significantly affected by exposure and were functionally interpreted with measured swimming responses. Effects on digestion were measured by upregulation of chitinase and downregulation of amylase, whilst downregulation of tumor necrosis factor indicated a probable compromised immune system. We utilized 3 replicates for exposed samples and 3 replicates for controls, both of which were hybridized to a reference pool. Each replicate contained 4 pooled larval delta smelt. The Reference pool consisted of delta smelt samples from this experiment and a number of prior tests. No dye swaps were performed due to limited material. Supplementary file linked below reports candidate differentially expressed cDNAs. Data represented as filtered, normalized, Log-2 Alexa (547/555) ratios.
2010-08-18 | E-GEOD-23238 | biostudies-arrayexpress
Project description:Rainbow smelt (Osmerus mordax) are freeze-resistant fish that accumulate glycerol and produce an antifreeze protein during winter. Quantitative reverse transcription-PCR (qPCR) and subtractive hybridization studies have revealed a few genes in smelt liver to be differentially regulated in winter in comparison with the fall when water temperatures are warmer. In order to further define the suite of processes that are regulated seasonally, we undertook a large-scale analysis of gene expression by hybridization of smelt cDNA to the salmonid 16K cGRASP cDNA microarray. These microarray experiments were conducted as a focused sieving exercise, which identified informative genes for further study in the microarray samples and over a seasonal sampling series using quantitative reverse-transcription PCR.
2010-01-31 | GSE17961 | GEO
Project description:We exposed adult delta smelt to treatments of increased salinities to quantify the transcriptomic responses involved in coping with osmotic stress
2015-12-31 | GSE72772 | GEO