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ABSTRACT:
PROVIDER: PRJEB85243 | ENA |
REPOSITORIES: ENA
Similar Datasets
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Project description:We sampled skin and blubber from 6 fin whale (Balenoptera physalus) individuals living in the northern Mediterranean Sea. Blubber was analyzed for Organochlorines levels while genomic DNA extracted from the skin of the animals with the lowest (mean value = 19 µg/g lipid basis, l.b.) (group 1, n=3) and the highest (mean value = 53 µg/g l.b.) (group 2, n=3) levels of contaminants were used for DNAm profiling through reduced representation bisulfite sequencing (RRBS).
2022-01-01 | GSE153525 | GEO
Project description:DNA methylation is an important regulator of genome function in the eukaryotes, but it is currently unclear if the same is true in prokaryotes. While regulatory functions have been demonstrated for a small number of bacteria, there have been no large-scale studies of prokaryotic methylomes and the full repertoire of targets and biological functions of DNA methylation remains unclear. Here we applied single-molecule, real-time sequencing to directly study the methylomes of 232 phylogenetically diverse prokaryotes. Collectively, we identified 834 methylated motifs, enabling the specific annotation of 415 DNA methyltransferases (MTases), and adding substantially to existing databases of MTase specificities. While the majority of MTases function as components of restriction-modification systems, 139 MTases have no cognate restriction enzyme in the genome, suggesting some other functional role. Several of these âorphanâ MTases are conserved across species and exhibit patterns of DNA methylation consistent with known regulatory MTases. Based on these patterns of methylation, we identify candidate novel regulators of gene expression in several phyla of bacteria, and candidate regulators of DNA replication in Haloarchaea. Together these data substantially advance our knowledge of DNA restriction-modification systems, and hint at a wider role for methylation in prokaryotic genome regulation. Single-molecule, real-time sequencing of DNA modifications across 232 diverse prokaryotic genomes.
2016-01-20 | E-GEOD-69872 | biostudies-arrayexpress
Project description:Our aim was to study the immune system of a Mediterranean sea urchin Paracentrotus lividus. Using a label free quantitative mass spectrometry approach we analyzed how bacterial lipopolysaccharide (LPS) is able to modulate the coelomocytes proteome and effect its cellular pathways such as cytoskeleton reorganization, stress and energetic homeostasis.
2020-01-30 | PXD008439 | Pride
Project description:The goal of this study was to identify the key functions of the six main symbionts that are hosted in gills of the marine bivalve, Idas modiolaeformis, which lives at deep-sea hydrocarbon seeps and wood falls in the Eastern Atlantic Ocean and the Mediterranean Sea. These symbionts include the main autotrophic methane- and sulfur-oxidizing lineages (Methyloprofundus, Thioglobus, Thiodubillierella), as well as a Methylophagaceae methylotrophic autotroph, a flavobacterial degrader of complex polysaccharides Urechidicola and a Nitrincolaceae heterotroph that specializes in degradation of nitrogen-rich compounds such as peptides and nucleosides. Four I. modiolaeformis individuals were preserved in RNAlater following retrieval from a brine pool habitat in the Eastern Mediterranean at 1,150 m water depth (32° 13.4' N 34° 10.7' E), using a remotely-operated vehicle. RNAlater was discarded after 24 hours, and the specimens were kept at -80°C until DNA/RNA/protein co-extraction using the AllPrep DNA/RNA/Protein Mini Kit (Cat. No. 80004, Qiagen).
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2022-10-14 | PXD034541 | Pride