Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1049878 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27135516_1.fastq.gz | Fastqsanger.gz | |||
| SRR27135516_2.fastq.gz | Fastqsanger.gz | |||
| SRR27135517_1.fastq.gz | Fastqsanger.gz | |||
| SRR27135517_2.fastq.gz | Fastqsanger.gz | |||
| SRR27135518_1.fastq.gz | Fastqsanger.gz |
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Project description:Little progress has been made in studying the toxicity of realistic 'non-pristine' forms of nanoparticles that presents in real soil environment. It is presently unkown whether the transformed nanoparticles in realistic environment exerts an adverse effect to rhizobium-legume symbiosis on molecular level. We used microarray to investigate the toxicogenomic responses of the model legume Medicago truncatula following 30 days exposure to three different types of biosolids (control biosolids (control BS), a mixture of Ag, ZnO and TiO2 manufactured nanomaterials added biosolids (Nano BS) and a corresponding bulk metals added biosolids (Bulk BS) ) amended soil that were aged for 6 months prior to exposure in pot experiment.
2015-07-01 | GSE64788 | GEO
Project description:Little progress has been made in studying the toxicity of realistic 'non-pristine' forms of nanoparticles that presents in real soil environment. It is presently unkown whether the transformed nanoparticles in realistic environment exerts an adverse effect to rhizobium-legume symbiosis on molecular level. We used microarray to investigate the toxicogenomic responses of the model legume Medicago truncatula following 30 days exposure to three different types of biosolids (control biosolids (control BS), a mixture of Ag, ZnO and TiO2 manufactured nanomaterials added biosolids (Nano BS) and a corresponding bulk metals added biosolids (Bulk BS) ) amended soil that were aged for 6 months prior to exposure in pot experiment. Our Genechip® Medicago Genome Array is designed specially to monitor gene expression in Medicago truncatula, Medicago sativa, and the symbiotic organism Sinorhizobium meliloti. For our study, RNA were extracted from shoots and roots of Medicago truncatula that exposure to control, Bulk and Nano BS treatments for 30 days, and used for all hybridization on Affymetrix microarray. The objective of our study is to investigate the molecular mechanisms of toxicity of Nano BS in comparison with their counterpart Bulk BS treatment, using a commercial Medicago truncatula microarrays.
2015-07-01 | E-GEOD-64788 | biostudies-arrayexpress
Project description:Genome-wide microarray analysis was performed using RNA extracted from soil cultures of Streptomyces coelicolor A3(2) in the presence or absence of chitin. The vast majority of genes in chitin and amino sugar metabolism, as well as many other genes for carbon and energy, nitrogen and sulfur metabolism, were differentially expressed in response to addition of chitin. Moreover, the gene expressions of eight gene clusters for secondary metabolites were also significantly up-regulated in the chitin amended soil. To reveal the role of a pleiotropic transcriptional regulator, DasR, which has been reported to be involved in regulation of chitin metabolism, antibiotic production and morphological differentiation, the gene expression patterns of wild type and dasR mutant in soil amended with chitin were compared by microarray analysis. The dasR mutation resulted in up-regulation of four antibiotic gene clusters and down-regulation of chitin metabolism.
2012-11-07 | GSE39164 | GEO
Project description:Genome-wide microarray analysis was performed using RNA extracted from soil cultures of Streptomyces coelicolor A3(2) in the presence or absence of chitin. The vast majority of genes in chitin and amino sugar metabolism, as well as many other genes for carbon and energy, nitrogen and sulfur metabolism, were differentially expressed in response to addition of chitin. Moreover, the gene expressions of eight gene clusters for secondary metabolites were also significantly up-regulated in the chitin amended soil. To reveal the role of a pleiotropic transcriptional regulator, DasR, which has been reported to be involved in regulation of chitin metabolism, antibiotic production and morphological differentiation, the gene expression patterns of wild type and dasR mutant in soil amended with chitin were compared by microarray analysis. The dasR mutation resulted in up-regulation of four antibiotic gene clusters and down-regulation of chitin metabolism. A study using total RNA extracted from soil cultures of Streptomyces ceolicolor A3(2). A whole genome microarray of S. coelicolor (NimbleGen Custom Prokaryotic Gene Expression 72K 4-plex Arrays) was designed and manufactured by Roche (Roche NimbleGen, Madison, WI). Each array contained four sets of 8 sequence-specific 60-mer probes per gene corresponding to 7825 genes from the S. coelicolor A3(2) genome.
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Project description:characterization of soil communities amended with 13C-methanol using proteomic SIP
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Project description:This study began with 72 male 4-week-old BALB/c mice. The mice were split evenly into one of four cohorts: Control, River, Pine, and Road. The control mice were raised with standard corn cob bedding whereas the remaining mice were raised with clean bedding amended with 300 mL of one of three different types of soil. The soil exposure continued throughout the experiment, with 300 mL of new soil added with bi-weekly cage changes. The soils used to amend the cage bedding were previously characterized as having high (Pine), medium (River), and low (Road) diversity. The River and Pine soil were collected from Duke Forest and the Road soil was collected adjacent to Highway 15-501 in Chapel Hill, North Carolina. All mice were given a standard diet and the cages were distributed reverse osmosis treated water through a centralized Lixit® system that was fed to each cage in parallel. After 32 days of standard rearing with amended soils, the mice were exposed via oropharyngeal aspiration to either live influenza A (PR8) virus or heat inactivated (HI) virus.
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Project description:Humans are chronically exposed to a mixture of environmental chemicals (ECs), many with endocrine disrupting potential, contributing to the development of non-communicable diseases. The adverse health effects of exposure to single ECs have been extensively studied but less is known about the impact of chronic exposure to low levels of a mixture of ECs, which is the real-life exposure scenario. Biosolids, derived from human wastewater treatment, closely reflects the human exposome in both the array and concentration of ECs and is a novel, real-life model to investigate the health risks posed by developmental exposure to mixtures of ECs. Previous studies using the prenatal biosolids exposure model found an increased accumulation of the endocrine disrupting chemical diethylhexylphthalate in the fetal liver and metabolic perturbations including increased thyroid gland weight in the male fetus and reduced bodyweight in prepubertal male lambs. To understand the basis of this sexually dimorphic metabolic phenotype we investigated the transcriptome of liver, the primary metabolic organ, in lambs of both sexes. Since many liver genes show sexual dimorphism, with sex-biased genes playing a pivotal role in lipid and drug metabolism, sex-differences in liver gene expression and the impact of prenatal biosolids exposure on it was examined. We hypothesized that maternal preconceptional and gestational exposure of sheep to biosolids programs sex-specific transcriptional changes in the offspring liver. Ewes (F0) were grazed on either inorganic fertilizer (Control) or biosolids-treated pastures (Biosolids) from 1 month before mating till parturition. All lambs (F1) were raised on control pastures after lambing until euthanasia at 9.5 weeks of age. RNA from liver from Control male (n=7), Control female (n=8), BTP male (n=7) and BTP female (n=8) lambs were subjected to next generation sequencing and DESeq2 R package was used to identify differentially expressed genes due to prenatal biosolids exposure and sex-differentially expressed genes .
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