Riverine metagenome
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR195937_1.fastq.gz | Fastqsanger.gz | |||
| DRR195937_2.fastq.gz | Fastqsanger.gz | |||
| DRR195938_1.fastq.gz | Fastqsanger.gz | |||
| DRR195938_2.fastq.gz | Fastqsanger.gz | |||
| DRR195939_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
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Project description:Studying how different genotypes respond to environmental variation is essential to understand the genetic basis of adaptation. The Mexican tetra, Astyanax mexicanus, has cave and surface‐dwelling morphotypes that have adapted to entirely different environments in the wild, and are now successfully maintained in lab conditions. While this has enabled the identification of genetic adaptations underlying a variety of physiological processes, few studies have directly compared morphotypes between lab‐reared and natural populations. Such comparative approaches could help dissect the varying effects of environment and morphotype, and determine the extent to which phenomena observed in the lab are generalizable to conditions in the field. To this end, we take a transcriptomic approach to compare the Pachón cavefish and their surface fish counterparts in their natural habitats and the lab environment. We identify key changes in expression of genes implicated in metabolism and physiology between groups of fish, suggesting that morphotype (surface or cave) and environment (natural or lab) both alter gene expression. We find gene expression differences between cave and surface fish in their natural habitats are much larger than differences in expression between morphotypes in the lab environment. However, lab‐raised cave and surface fish still exhibit numerous gene expression changes, supporting genetically encoded changes in livers of this species. From this, we conclude that a controlled laboratory environment may serve as an ideal setting to study the genetic underpinnings of metabolic and physiological differences between the cavefish and surface fish.
2020-02-19 | GSE139490 | GEO
Project description:The use of profiling techniques such as transcriptomics, proteomics, and metabolomics has been proposed to improve the detection of side effects of plant breeding processes. This paper describes the construction of a food safety-oriented potato cDNA microarray (FSPM). Microarray analysis was performed on a well-defined set of tuber samples of two different potato varieties, grown under different, well-recorded environmental conditions. Data were analyzed to assess the potential of transcriptomics to detect differences in gene expression due to genetic differences or environmental conditions. The most pronounced differences were found between the varieties Sante and Lady Balfour, whereas differences due to growth conditions were less significant. Transcriptomics results were confirmed by quantitative PCR. Furthermore, the bandwidth of natural variation of gene expression was explored to facilitate biological and/or toxicological evaluation in future assessments. Keywords: experiment with factorial design factorial design; 2 potato cultivars (Sante, Lady Balfour); 2 fertilizers (dairy manure compost, chicken manure pellets); 3 plant protection treatments (copper oxychloride, comcat, water), 3 biological replicates, 48 samples
2009-02-01 | E-GEOD-11875 | biostudies-arrayexpress
Project description:Understanding the consequences of thermal and chemical variations in aquatic habitats is of importance in a scenario of global change. In ecology, the sex ratio is a major population demographic parameter. Research carried out so far on environmental perturbations on fish sex ratios has usually involved a few model species with a strong genetic basis of sex determination, analyzing juvenile or adult gonads. However, the underlying mechanisms at the time of commitment are poorly understood. The European sea bass has a mixed genetic and environmental sex determination system, which makes it naturally sensitive to environmental cues. Here, we transcriptomically analyzed developing gonads experiencing either testis or ovarian differentiation as a result of thermal and/or estrogen influences. Elevated temperature masculinized genetic females while estrogen exposure resulted in an all-female population. A total of 383 genes were differentially expressed, with an overall downregulation in the expression of genes involved both in testicular and ovarian differentiation in the estrogen-exposed fish achieved by a shutdown of the first steps of steroidogenesis. GO enrichment analysis uncovered affected pathways related to the immune response, xenobiotic metabolism, response to stimulus, signaling and growth. However, once the female phenotype was imposed gonads could continue their normal development, even taking into account that some of the resulting females were fish that otherwise would have developed as males. The data on the underlying mechanisms operating at the molecular level presented here contributes to better understanding the sex ratio response of fish species subjected to a combination of environmental perturbations.
2016-12-31 | GSE52938 | GEO
Project description:The use of profiling techniques such as transcriptomics, proteomics, and metabolomics has been proposed to improve the detection of side effects of plant breeding processes. This paper describes the construction of a food safety-oriented potato cDNA microarray (FSPM). Microarray analysis was performed on a well-defined set of tuber samples of two different potato varieties, grown under different, well-recorded environmental conditions. Data were analyzed to assess the potential of transcriptomics to detect differences in gene expression due to genetic differences or environmental conditions. The most pronounced differences were found between the varieties Sante and Lady Balfour, whereas differences due to growth conditions were less significant. Transcriptomics results were confirmed by quantitative PCR. Furthermore, the bandwidth of natural variation of gene expression was explored to facilitate biological and/or toxicological evaluation in future assessments. Keywords: experiment with factorial design
2009-02-02 | GSE11875 | GEO
Project description:Feral organisms are affected by adverse environmental factors present in their habitat. It was hypothesized that transcript expression pattern in a suitable target organ of a sentinel feral organism compared to a reference transcript population may serve as a comprehensive biomarker of these adverse effects. This study was aimed at inquiring the applicability of such biomarker and establishing a procedure for its appropriate utilization. The examined system contains dual-labeled microarray-based evaluation of the hepatic transcript expression pattern in a sentinel fish sampled in two habitats, a polluted (Haifa Bay) and a clean (Dor) site, respectively, for two years. The hepatic expression patterns were compared to a reference RNA assumed to represent specimens that have no exposure history to pollution. The sentinel fish is Lithognathus mormyrus, which inhabits a marine coastal habitat along the Mediterranean coast of Israel. The hepatic transcript expression patterns were evaluated using a 1152-clone cDNA microarray, biased towards pollution-affected genes. The LIMMA software was used to calculate the log2 ratios of expressions (M) and to identify the differentially expressed genes in each sample (adjusted P<0.01). Keywords: Response of fish hepatic gene expression pattern to environmental conditions.
2009-12-01 | GSE14673 | GEO
Project description:Gene expression is a complex quantitative trait partially regulated by genetic variation in DNA sequence. Population differences in gene expression could contribute to some of the observed differences in susceptibility to common diseases and responses to drug treatments. We characterize gene expression in the full set of HapMap lymphoblastoid cell lines derived from individuals of European and African ancestry for 9,156 transcript clusters (gene-level) evaluated using the Affymetrix GeneChip® Human Exon 1.0 ST Array. Gene expression was found to differ significantly between these samples for 383 transcript clusters. Biological processes including ribosome biogenesis and antimicrobial humoral response were found to be enriched in these differential genes, suggesting their possible roles in contributing to the population differences at a higher level than mRNA expression and the population differences in response to environmental information. Genome-wide association studies for local or distant genetic variants that correlate with the differentially expressed genes enabled identification of significant associations with one or more single nucleotide polymorphisms (SNPs), consistent with the hypothesis that genetic factors and not simply population identity or other characteristics (age of cell lines, length of culture etc.) contribute to differences in gene expression in these samples. Our results provided a comprehensive view of the genes differentially expressed between populations and the enriched biological processes involved in these genes. We also provided an evaluation of the contribution of genetic variation and non-genetic factors to the population differences in gene expression. Keywords: exon array
2008-05-08 | GSE7851 | GEO
Project description:The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid (SA) and jasmonic acid (JA), have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Differences in the level of gene expression, or expression level polymorphisms (ELPs), can be mapped in a segregating population to identify regulatory quantitative trait loci (expression QTLs, e-QTLs) affecting host resistance responses. We assessed Arabidopsis accessions Bayreuth-0 (Bay-0) and Shahdara (Sha) for natural variation in the response to JA. We treated vegetatively grown plants with either JA or a control solution (Silwet), and harvested the plants 4, 28, or 52 hours after chemical treatment. We present Affymetrix GeneChip microarray expression data for 2 biological replications of the control (Silwet) samples for Bay-0 and Sha. These GeneChips were used to generate genetic markers which allowed the development of high-density haplotype maps of a Bay-0 x Sha RIL population.
2006-11-14 | E-TABM-60 | biostudies-arrayexpress
Project description:The study of natural genetic variation for plant disease resistance responses is a complementary approach to utilizing mutants to elucidate genetic pathways. While some key genes involved in pathways controlling disease resistance, and signaling intermediates such as salicylic acid (SA) and jasmonic acid (JA), have been identified through mutational analyses, the use of genetic variation in natural populations permits the identification of change-of-function alleles, which likely act in a quantitative manner. Whole genome microarrays, such as Affymetrix GeneChips, allow for molecular characterization of the disease response at a genomics level and characterization of differences in gene expression due to natural variation. Differences in the level of gene expression, or expression level polymorphisms (ELPs), can be mapped in a segregating population to identify regulatory quantitative trait loci (expression QTLs, e-QTLs) affecting host resistance responses. We assessed Arabidopsis accessions Bayreuth-0 (Bay-0) and Shahdara (Sha) for natural variation in the response to SA. We treated vegetatively grown plants with either SA or a control solution (Silwet), and harvested the plants 4, 28, or 52 hours after chemical treatment. We present Affymetrix GeneChip microarray expression data for 2 biological replications of the control (Silwet) samples for Bay-0 and Sha. These GeneChips were used to generate genetic markers which allowed the development of high-density haplotype maps of a Bay-0 x Sha RIL population.
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