Ontology highlight
ABSTRACT:
PROVIDER: PRJNA476618 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7359890_1.fastq.gz | Fastqsanger.gz | |||
| SRR7359890_2.fastq.gz | Fastqsanger.gz | |||
| SRR7359891_1.fastq.gz | Fastqsanger.gz | |||
| SRR7359891_2.fastq.gz | Fastqsanger.gz | |||
| SRR7359892_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 20 |
Similar Datasets
Project description:To investigate the effect of cholic acid sulfate to MAIT cells, PBMCs were stimulated with each antigen (5-OP-RU, cholic acid sulfates; CA3S and CA7S) and scRNA sequencing was performed. the homeostatic related genes expressed in cholic acid sulfate stimulation, while the inflammatory related gene expressed in 5-OP-RU stimulation. This analysis showed that cholic acid sulfate contributes to maintenance of MAIT cells.
2024-06-12 | GSE203394 | GEO
Project description:The success of Enterococcus faecium and E. faecalis evolving as multi-resistant nosocomial pathogens is associated with their ability to acquire and share adaptive traits, including mobile genetic elements (MGE) encoding antimicrobial resistance. Here, we define the mobilome in representative successful hospital associated genetic lineages, E. faecium ST17 (n=10) and ST78 (n=10), E. faecalis ST6 (n=10) and ST40 (n=10) using DNA microarray analyses. The hybridization patterns of 272 targets representing plasmid backbones (n=85), transposable elements (n=85), resistance determinants (n=67), prophages (n=29), and CRISPR-cas sequences (n=6) separated the strains according to species, and for E. faecalis also according to STs. Although plasmids belonging to the RCR-, Rep_3-, RepA_N- and Inc18-families were well represented with no significant differences in prevalence, the presence of specific replicon classes differed highly between the species; E. faecium was dominated by rep17/pRUM, rep2/pRE25, rep14/EFNP1 and rep20/pLG1 and E. faecalis by rep9/pCF10, rep2/pRE25 and rep7. Tn916-elements conferring tetracycline resistance (tetM) were found in all E. faecalis strains, but only in two E. faecium strains. A significant higher prevalence of IS256-, IS3-, ISL3-, IS200/IS605-, IS110-, IS982-, and IS4-transposases were detected in E. faecium, and of IS110-, IS982- and IS1182-transposases in E. faecalis ST6 compared to ST40. Notably, the transposases of IS981, ISEfm1 and IS1678 which have only been reported in few enterococcal isolates, were well represented in the E. faecium strains. E. faecalis ST40 strains harboured possible functional CRISPR-Cas systems, and still resistance and prophage sequences were generally well represented. Gene targets defined as the enterococcal mobilome, including plasmids, IS elements and transposons, resistance determinants, prophage sequences and CRISPR-Cas systems were highly prevalent, underlining their potential importance in the evolution of hospital associated STs. An association between axe-txe to the RepA_N-family and ω-ε-ζ to the Inc18-family, implicates the contribution of TA-systems in stable plasmid maintenance carrying virulence and resistance determinants in enterococci. The concurrent presence of defined MGE and their associated resistance markers was generally confirmed and illustrates the importance of horizontal gene transfer in the development of multidrug resistant enterococci.
2014-07-08 | GSE59190 | GEO
Project description:Enterococcus faecalis is a common commensal organism and a prolific nosocomial pathogen that causes biofilm-associated infections. Numerous E. faecalis OG1RF genes required for biofilm formation have been identified, but few studies have compared genetic determinants of biofilm formation and biofilm morphology across multiple conditions. Here, we cultured transposon (Tn) libraries in CDC biofilm reactors in two different media and used Tn sequencing (TnSeq) to identify core and accessory biofilm determinants, including many genes that are poorly characterized or annotated as hypothetical. Multiple secondary assays (96-well plates, submerged Aclar, and MultiRep biofilm reactors) were used to validate phenotypes of new biofilm determinants.
2021-04-03 | GSE171419 | GEO
Project description:The success of Enterococcus faecium and E. faecalis evolving as multi-resistant nosocomial pathogens is associated with their ability to acquire and share adaptive traits, including mobile genetic elements (MGE) encoding antimicrobial resistance. Here, we define the mobilome in representative successful hospital associated genetic lineages, E. faecium ST17 (n=10) and ST78 (n=10), E. faecalis ST6 (n=10) and ST40 (n=10) using DNA microarray analyses. The hybridization patterns of 272 targets representing plasmid backbones (n=85), transposable elements (n=85), resistance determinants (n=67), prophages (n=29), and CRISPR-cas sequences (n=6) separated the strains according to species, and for E. faecalis also according to STs. Although plasmids belonging to the RCR-, Rep_3-, RepA_N- and Inc18-families were well represented with no significant differences in prevalence, the presence of specific replicon classes differed highly between the species; E. faecium was dominated by rep17/pRUM, rep2/pRE25, rep14/EFNP1 and rep20/pLG1 and E. faecalis by rep9/pCF10, rep2/pRE25 and rep7. Tn916-elements conferring tetracycline resistance (tetM) were found in all E. faecalis strains, but only in two E. faecium strains. A significant higher prevalence of IS256-, IS3-, ISL3-, IS200/IS605-, IS110-, IS982-, and IS4-transposases were detected in E. faecium, and of IS110-, IS982- and IS1182-transposases in E. faecalis ST6 compared to ST40. Notably, the transposases of IS981, ISEfm1 and IS1678 which have only been reported in few enterococcal isolates, were well represented in the E. faecium strains. E. faecalis ST40 strains harboured possible functional CRISPR-Cas systems, and still resistance and prophage sequences were generally well represented. Gene targets defined as the enterococcal mobilome, including plasmids, IS elements and transposons, resistance determinants, prophage sequences and CRISPR-Cas systems were highly prevalent, underlining their potential importance in the evolution of hospital associated STs. An association between axe-txe to the RepA_N-family and M-OM-^I-M-NM-5-M-NM-6 to the Inc18-family, implicates the contribution of TA-systems in stable plasmid maintenance carrying virulence and resistance determinants in enterococci. The concurrent presence of defined MGE and their associated resistance markers was generally confirmed and illustrates the importance of horizontal gene transfer in the development of multidrug resistant enterococci. All together 272 DNA targets representing mobile genetic elements and antimicrobial resistance determinants associated with enterococci were spotted on a CustomArray 4x2K microarray from CustomArray Inc. Each fourplex microarray slide contain four identical sectors that were stripped and re-hybridized up to six times. Each target was represented by 1-5 probes each. The total of 1250 probes were Tm balanced by altering their lenght between 35 and 40 nucleotides. Total DNA of 41 samples were hybridized and a control strain, the fully sequenced E. faecalis V585, was included in one of the four sectors on each slide in each set of hybridization to monitor the overall array and hybridization quality.
2014-07-08 | E-GEOD-59190 | biostudies-arrayexpress
Project description:To investigate the effect of cholic acid sulfate to MAIT cells, PBMCs were stimulated with 5-OP-RU and CA7S and scRNA sequencing was performed. Inflammatory genes were induced by 5-OP-RU, while wound healing related genes were inducesed by CA7S. This analysis showed that cholic acid sulfate may contributes to maintenance of MAIT cells.
2024-06-12 | GSE228498 | GEO
Project description:Two cultures, one grown on cholic acid and the other on pyruvate.
2011-03-29 | GSE28048 | GEO
Project description:To investigate the contribution of novel antigen for MAIT cells; Cholic acid sulfate, we established Sult2a KO mice lacking antigen-producing the enzyme. We performed scRNA sequencing of whole thymocyte and liver cells from these and wild type mice. Sult2a was deficient in hepatocytes, whereas there was no change in other genes or cell proportions, suggesting that deficient of Sult2a did not affect to other genes. The analysis of thymocye implied that cholic acid sulfate may have affected the MAIT subsets.
2024-06-12 | GSE204917 | GEO
Project description:Genome-wide changes in hepatic gene expression in wild-type mice on a diet supplemented with cholic acid, a naturally occurring bile acid
2009-05-08 | E-MEXP-2109 | biostudies-arrayexpress
Project description:Two cultures, one grown on cholic acid and the other on pyruvate. 3x dual-channel slides.
2011-03-29 | E-GEOD-28048 | biostudies-arrayexpress
Project description:Transcriptional profiling of changes in global hepatic gene expression in mice lacking Foxa2 in the liver (Foxa2loxP/loxP;Alfp.Cre) on a diet supplemented with cholic acid, a naturally occurring bile acid
2009-05-08 | E-MEXP-2107 | biostudies-arrayexpress