Soil nematode
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA690214 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Soil nematode raw sequence reads on Mt. Halla
| PRJNA691425 | ENA
Project description:The toxicity and toxicogenomics of selected anatase and rutile nanoparticles (NP) and bulk titanium dioxide (TiO2) particles were evaluated in the soil nematode Caenorhabditis elegans. Results indicated that bulk or nano-TiO2 particles were slightly toxic to soil nematode C. elegans, as measured by reproduction EC50 values ranging from 4 to 32 mg/L. Whole-genome microarray results indicated that the regulation of glutathione-S-transferase gst-3, cytochrome P450 cypp33-c11, stress resistance regulator scl-1, oxidoreductase wah-1, and embryonic development pod-2 genes were significantly affected by nano-sized and bulk TiO2 particles. More specifically, it was determined that anatase particles exerted a greater effect on metabolic pathways, whereas rutile particles had a greater effect on developmental processes. The up-regulation of the pod-2 gene corroborated the phenotypic effect observed in the reproduction test. Our results demonstrated that C. elegans is a good genomic model for nano-TiO2 toxicity assessment.
2014-07-17 | GSE59470 | GEO
Project description:Nematode attached microbes Raw sequence reads
| PRJNA752946 | ENA
Project description:Marine nematode metagenome Raw sequence reads
| PRJNA422296 | ENA
Project description:Purpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia. Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either 1) xylose, 2) n-acetylglucosamine, 3) glucose and gentamycin, 4) xylan, or 5) pectin were generated by sequencing using an Illumina platform (GENEWIZ performed sequencing). Sequence reads that passed quality filters were aligned to a soil metagenome using Burrows Wheeler Aligner. Resulting SAM files were converted to raw reads using HTSeq, and annotated using Uniref90 or EGGNOG databases. Results: To reduce the size of the RNA-Seq counts table and increase its computational tractability, transcripts containing a minimum of 75 total counts, but no more than 3 zero counts, across the 15 samples were removed. The subsequent dataset was normalized using DESeq2, resulting in a dataset consisting of 6947 unique transcripts across the 15 samples, and 185,920,068 reads. We identified gene categories that were enriched in a sample type relative to the overall dataset using Fisher’s exact test. Conclusions: our dataset confirms that the functional module consortia generated from targeted enrichments of a starting soil inoculum had distinct functional trends by enrichment type.
2020-01-14 | GSE143587 | GEO
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 | iProX
Project description:We report both raw and processed scRNA-seq profiling reveals how root tissues adapt to soil conditions and compaction stress
2024-02-01 | GSE251706 | GEO
Project description:Background: Earthworms are essential for a healthy soil ecosystem, performing key functions such as bioturbation. The soil ecosystem can be challenged by natural toxins such as isothiocyanates (ITC), secondary metabolites produced by many commercial crops. This study investigated the effects of the natural toxin, 2-phenylethyl isothiocyanate on the earthworm Eisenia andrei using an ecotoxicogenomics approach that combined standardised ecotoxicological testing with gene expression analyses. Results and discussion: Exposure to 2-Phenylethyl ITC reduced both survival and reproduction of E. andrei in a dose-dependent manner, with an EC50 (reproduction) value of 556 nmol/g soil. Cross-species comparative genomic hybridisation validated the applicability of an existing 4x44k E. fetida microarray to E. andrei. Gene expression profiles revealed the importance of metallothionein (mt) as an early warning signal when E. andrei is exposed to low concentrations of 2-phenylethyl ITC. Allignment of these mt genes with the mt-2 gene of Lumbricus rubellus showed that there must at least have 2 mt genes in the Eisenia sp. genome. At high exposure concentrations of 2-phenylethyl ITC gene expression was mainly affected by inhibiting chitinase activities, inducing an oxidative stress response, and stimulating energy metabolism. KEGG pathway analysis, furthermore, implied that the high concentration may cause impaired light sensitivity, angiogenesis (e.g. wound healing), olfactory perception (olfaction), learning and memory. Conclusions: Increased levels of isothiocyanates may be found in the field in the near future. Risks of such compounds should be carefully investigated before allowing them to enter the soil on a large scale. This is the first study to investigate the effects of an isothiocyanate on an earthworm both on the ecotoxicological and genomic level.
2013-08-11 | GSE43600 | GEO