Similar Datasets
Project description:Picea schrenkiana topsoil Raw sequence reads_soil prokaryotes and fungi
| PRJNA667810 | ENA
Project description:Exposure to less hygienic conditions during early childhood has been associated with stimulation and development of the immune system. A recent study indicated exposure of piglets to soil-borne microbes during lactation was related with modulation of gut microbiota and immune function. To identify potential molecular mechanisms and pathways impacted by early life topsoil exposure, we analyzed gene expression (mRNA and miRNA) in peripheral blood mononuclear cells (PBMC) from these piglets. Total RNA was extracted from PBMC of piglets exposed to topsoil only from d 4-d 21 of life (mRNA n=6; miRNA n=5) or unexposed control pigs (mRNA n=6; miRNA n=8) at 11, 20, and 56 days of age. Small RNA and mRNA were sequenced with 50-bp single-end reads using Illumina chemistry. Differential expression (DE) analysis was performed using PROC Glimmix of SAS to evaluate changes in expression due to topsoil exposure over time with genes declared DE at a false discovery rate (FDR) of q<0.10. A total of 138 mRNA and 21 miRNAs were identified as DE for the treatment by age interaction. Ontology enrichment analysis of DE mRNA revealed GO terms directly involved in the connection between T-cell and antigen-presenting cells that are associated with T-cell activation. Key regulatory genes identified include PTPRJ, ITGB3, TRBV30, CD3D, mir-143, mir-29, and mir-148a. While these results require validation, this study provides data supporting the hypothesis that less hygienic environments during early life may contribute to the development of the immune system
2022-07-31 | GSE205321 | GEO
Project description:A topsoil sample obtained from a highly industrialized area was tested on CALUX® cell line and exposed cells processed with proteomic and bioinformatics analyses. GC-MS/MS analysis of topsoil extracts was also performed to confirm PCDD, PCDF and dl-PCBs presence. CALUX® and GC-MS/MS data confirmed the presence of PCDD/Fs and dl-PCBs in the topsoil extract. Proteomic analysis of the cells exposed to the soil extracts identified 43 differential proteins. Enrichment analysis highlights biological processes such as cellular response to chemical stimulus, to stress, response to inorganic substance, regulation of translation, regulation of apoptotic process as well as response to organonitrogen compounds in light of particular drugs and compounds, extrapolated by bioinformatics and linked to the identified proteins modifications. These results confirm the complex epidemiological situation occurring among Taranto inhabitants and underline the need to further investigate the presence and sources of inferred chemicals in Taranto soils. The combined analysis reveals a more complex scenarios of chemicals able to affect cellular pathways and leading to toxicities rather than those identified by the bioassay. The approach to couple proteomic to CALUX® is a promising tool and deserves further investigation to be applied in soil pollution monitoring and risk assessment.
2022-02-17 | PXD027074 | Pride
Project description:Transcript profiles of H. annosum from different tissues and mycelium grown on different substrates and under different stresses were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) H. irregulare genome sequence version 1. One aim of this study was to compare gene expression profiles of H. annosum during saprotrophic growth on topsoil from mineral soil, drained and undrained peatland.
2015-10-01 | GSE55290 | GEO
Project description:Estonian forest and grassland topsoil samples
| PRJEB24121 | ENA