European gradient
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB45259 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR5962170.fastq.gz | Fastqsanger.gz | |||
| ERR5962180.fastq.gz | Fastqsanger.gz | |||
| ERR5962180_1.fastq.gz | Fastqsanger.gz | |||
| ERR5962180_2.fastq.gz | Fastqsanger.gz | |||
| ERR5962190.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 227 |
Similar Datasets
Project description:Response pattern of soil prokaryotic community under an artificial moisture gradient
| PRJEB19528 | ENA
Project description:Soil pH dominance over livestock management in determining bacterial assemblages through a latitudinal gradient of European meadows and pastures
| PRJEB56444 | ENA
Project description:The purpose of this study was to compare changes in translation (using Gradient Encoding, described below) to changes in mRNA abundance. Lysates of wildtype v-Abl transformed pre-B cells harvested before and after 12 hours of treatment either with 2.5 uM imatinib, a v-Abl kinase inhibitor, or 10ng/mL (10.9 nM) rapamycin, an mTOR inhibitor, were fractionated by sedimentation through linear sucrose gradients. Gradient fractions were encoded such that the mRNA from successive fractions was labeled with increasing ratios of Cy5 to Cy3. mRNAs derived from fractions in the lighter portion of the gradient therefore have a lower Cy5 to Cy3 ratio, whereas those deeper in the gradient have a higher Cy5 to Cy3 ratio. The ratio of Cy5 to Cy3 for each mRNA therefore reflects its average position within the gradient. We thus encoded the sedimentation rate of each mRNA across the entire gradient. The resulting ratios were quantitatively measured for each mRNA species by hybridization to DNA microarrays, and related to the 260 nm absorbance peaks representing different numbers of ribosomes bound per mRNA Compound Based Treatment: wildtype v-Abl transformed pre-B cells were treated with imatinib mesylate (IMA), rapamycin (RAP) or nothing (NONE)
2013-01-10 | GSE35039 | GEO
Project description:A custom 8x60 k expression microarray for larvae of European fire salamander (Salamandra salamandra) was designed based on transcriptome sequencing. It is known the fact, that oligonucleotide probes differ in the binding behavior towards their target sequences. Therefore, we performed a calibration of our microarray where we assessed the binding behavior of the individual probes empirically. This information was used to normalize gene expression data measurements with the same microarray in another experiment. Please refer to the accompanying publication (Czypionka et al. 2015." Ecological transcriptomics – a non-lethal sampling approach for endangered fire salamanders" Methods in Ecology and Evolution) for more information.
2015-06-20 | GSE70055 | GEO
Project description:Understanding and quantifying the effects of environmental factors influencing the variation of abundance and diversity of microbial communities was a key theme of ecology. For microbial communities, there were two factors proposed in explaining the variation in current theory, which were contemporary environmental heterogeneity and historical events. Here, we report a study to profile soil microbial structure, which infers functional roles of microbial communities, along the latitudinal gradient from the north to the south in China mainland, aiming to explore potential microbial responses to external condition, especially for global climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 5.0, we showed that microbial communities were distinct for most but not all of the sites. Using substantial statistical analyses, exploring the dominant factor in influencing the soil microbial communities along the latitudinal gradient. Substantial variations were apparent in nutrient cycling genes, but they were in line with the functional roles of these genes. 300 samples were collected from 30 sites along the latitudinal gradient, with 10 replicates in every site
2015-05-23 | E-GEOD-69171 | biostudies-arrayexpress
Project description:Understanding and quantifying the effects of environmental factors influencing the variation of abundance and diversity of microbial communities was a key theme of ecology. For microbial communities, there were two factors proposed in explaining the variation in current theory, which were contemporary environmental heterogeneity and historical events. Here, we report a study to profile soil microbial structure, which infers functional roles of microbial communities, along the latitudinal gradient from the north to the south in China mainland, aiming to explore potential microbial responses to external condition, especially for global climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 5.0, we showed that microbial communities were distinct for most but not all of the sites. Using substantial statistical analyses, exploring the dominant factor in influencing the soil microbial communities along the latitudinal gradient. Substantial variations were apparent in nutrient cycling genes, but they were in line with the functional roles of these genes.
2015-05-23 | GSE69171 | GEO
Project description:Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming induced environmental changes is critical to evaluating their influence on soil biogeochemical cycles. In this study, a functional gene array (i.e. GeoChip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. Varied thaw history was reported to be the main driver of soil and plant differences across a gradient of minimally, moderately and extensively thawed sites. Compared with the minimally thawed site, the number of detected functional gene probes across the 15-65 cm depth profile at the moderately and extensively thawed sites decreased by 25 % and 5 %, while the community functional gene beta-diversity increased by 34% and 45%, respectively, revealing decreased functional gene richness but increased community heterogeneity along the thaw progression. Particularly, the moderately thawed site contained microbial communities with the highest abundances of many genes involved in prokaryotic C degradation, ammonification, and nitrification processes, but lower abundances of fungal C decomposition and anaerobic-related genes. Significant correlations were observed between functional gene abundance and vascular plant primary productivity, suggesting that plant growth and species composition could be co-evolving traits together with microbial community composition. Altogether, this study reveals the complex responses of microbial functional potentials to thaw related soil and plant changes, and provides information on potential microbially mediated biogeochemical cycles in tundra ecosystems.
2019-06-03 | GSE97107 | GEO
Project description:The purpose of this study was to compare changes in translation (using Gradient Encoding, described below) to changes in mRNA abundance. Lysates of wildtype v-Abl transformed pre-B cells harvested before and after 12 hours of treatment either with 2.5 uM imatinib, a v-Abl kinase inhibitor, or 10ng/mL (10.9 nM) rapamycin, an mTOR inhibitor, were fractionated by sedimentation through linear sucrose gradients. Gradient fractions were encoded such that the mRNA from successive fractions was labeled with increasing ratios of Cy5 to Cy3. mRNAs derived from fractions in the lighter portion of the gradient therefore have a lower Cy5 to Cy3 ratio, whereas those deeper in the gradient have a higher Cy5 to Cy3 ratio. The ratio of Cy5 to Cy3 for each mRNA therefore reflects its average position within the gradient. We thus encoded the sedimentation rate of each mRNA across the entire gradient. The resulting ratios were quantitatively measured for each mRNA species by hybridization to DNA microarrays, and related to the 260 nm absorbance peaks representing different numbers of ribosomes bound per mRNA Compound Based Treatment: wildtype v-Abl transformed pre-B cells were treated with imatinib mesylate (IMA), rapamycin (RAP) or nothing (NONE) compound_treatment_design
2013-01-10 | E-GEOD-35039 | biostudies-arrayexpress
Project description:Connecting genes to phenotypic traits in bacteria is often challenging because of a lack of environmental cues in laboratory settings. However, laboratory-based model ecosystems offer a means to better account for natural conditions compared to standard planktonic cultures, aiding in the linking of genotypes and phenotypes. Here, we present a simple, cost-effective, laboratory-based model ecosystem to study aerobic methane-oxidizing bacteria (methanotrophs). This system, referred to as the gradient syringe, is made by inoculating bacteria into semi-solid agarose held within a disposable syringe. Empty space at one end of the syringe is flushed with methane gas, while the other end is open to the atmosphere through a sterile filter. We show this system replicates the methane-oxygen counter gradient typically found in the natural soil environment of methanotrophs. Culturing the methanotroph Methylomonas sp. strain LW13 in this system produced a distinct horizontal band at the intersection of the counter gradient, which we discovered was due not to increased cell growth at this location but instead to an increased amount of extracellular polymeric substances (EPS). We also discovered that different methanotrophic taxa formed EPS bands with distinct locations and morphologies when grown in the methane-oxygen counter gradient. By comparing transcriptomic data from LW13 growing within and surrounding this EPS band, we identified genes implicated in cell growth and EPS formation within the gradient syringe, and validated the involvement of these genes with knockout strains. This work highlights the use of a laboratory-based model ecosystem that more closely mimics the natural environment to uncover methanotroph phenotypes missing from standard planktonic cultures, and link these phenotypes their genetic determinants.
2023-10-05 | GSE243827 | GEO