Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12201326.fastq.gz | Fastqsanger.gz | |||
| SRR12201326_1.fastq.gz | Fastqsanger.gz | |||
| SRR12201326_2.fastq.gz | Fastqsanger.gz | |||
| SRR12201327.fastq.gz | Fastqsanger.gz | |||
| SRR12201327_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 114 |
Similar Datasets
Project description:In the present study, genomic binding sites of glucocorticoid receptors (GR) were identified in vivo in the rat hippocampus applying chromatin immunoprecipitation followed by next-generation sequencing. We identified 2470 significant GR-binding sites (GBS) and were able to confirm GR binding to a random selection of these GBS covering a wide range of P values. Analysis of the genomic distribution of the significant GBS revealed a high prevalence of intragenic GBS. Gene ontology clusters involved in neuronal plasticity and other essential neuronal processes were overrepresented among the genes harboring a GBS or located in the vicinity of a GBS. Male adrenalectomized rats were challenged with increasing doses of the GR agonist corticosterone (CORT) ranging from 3 to 3000 μg/kg, resulting in clear differences in the GR-binding profile to individual GBS. Two groups of GBS could be distinguished: a low-CORT group that displayed GR binding across the full range of CORT concentrations, and a second high-CORT group that displayed significant GR binding only after administering the highest concentration of CORT. All validated GBS, in both the low-CORT and high-CORT groups, displayed mineralocorticoid receptor binding, which remained relatively constant from 30 μg/kg CORT upward. Motif analysis revealed that almost all GBS contained a glucocorticoid response element resembling the consensus motif in literature. In addition, motifs corresponding with new potential GR-interacting proteins were identified, such as zinc finger and BTB domain containing 3 (Zbtb3) and CUP (CG11181 gene product from transcript CG11181-RB), which may be involved in GR-dependent transactivation and transrepression, respectively. In conclusion, our results highlight the existence of 2 populations of GBS in the rat hippocampal genome. - See more at: http://press.endocrine.org/doi/10.1210/en.2012-2187?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%3dpubmed#sthash.LqK088DP.dpuf
2016-07-09 | GSE84202 | GEO
Project description:Group B Streptococcus (GBS) is a pervasive perinatal pathogen, yet factors driving GBS dissemination in utero are poorly defined. Gestational diabetes mellitus (GDM), a complication marked by dysregulated immunity and maternal microbial dysbiosis, increases risk for GBS perinatal disease. We interrogated host-pathogen dynamics in a novel murine GDM model of GBS colonization and perinatal transmission. GDM mice had greater GBS in utero dissemination and subsequently worse neonatal outcomes. Dual-RNA sequencing revealed differential GBS adaptation to the GDM reproductive tract, including a putative glycosyltransferase (yfhO), and altered host responses. GDM disruption of immunity included reduced uterine natural killer cell activation, impaired recruitment to placentae, and altered vaginal cytokines. Lastly, we observed distinct vaginal microbial taxa associated with GDM status and GBS invasive disease status. Our translational model of GBS perinatal transmission in GDM hosts recapitulates several clinical aspects and enables discovery of host and bacterial drivers of GBS perinatal disease.
2023-07-05 | GSE236335 | GEO
Project description:Purpose: Analysis of the effect of different fats and amonut of cDDGS in the feedstuff on miRNA expression in porcine backfat Methods: miRNA-seq analysis was performed on backfat samples collected from 24 male and female crossbred fatteners originating from sows (Polish Landrace × White Large Polish) mated with a boar (Duroc × Pietrain) divided into four dietary groups: 7-cDDGS+rapeseed oil (group I), n=6 (+cDDGS+rapeseed oil -group II), n= 6 (+cDDGS+beeftallow -group III),n=5 (+cDDGS+coconut oil -group IV). The miRNA libraries were constructed from total RNA using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer protocol. The quantification of the obtained libraries was performed on a Qubit 2.0 spectrophotometer (Invitrogen, Life Technologies), while a quality control on a TapeStation 2200 instrument (D1000 ScreenTape; Agilent). 100 single-end cycle sequencing was performed on the HiScanSQ platform (Illumina) with the use of TruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). MicroRNA differentially expressed between dietary groups were identified with the DESeq2 software. Results: The comparison of miRNA profiles between dietary groups showed The highest number of miRNAs with altered expression was identified in the comparison of animals fed the diet containing cDDGS and coconut oil (group IV) with animals from the –cDDGS + rapeseed oil (group I) (37 miRNA, p adjusted <0.01). Moreover, in comparison between the group IV and groups III and II , 29 (12 upregulated and 17 downregulated in +cDDGS+coconut oil group) and 28 (10 upregulated and 18 downregulated in +cDDGS+coconut oil group) miRNAs were identified, respectively (p adjusted <0.1) Conclusions: Obtained results suggest that coconut oil induces changes in miRNA profile of backfat in pigs.
2021-09-17 | GSE184177 | GEO
Project description:The CiaRH and LiaFSR two-component regulatory systems in Streptococcus agalactiae (Group B Streptococcus, GBS) are essential mediators of the organism s response to biologically important sources of environmental stress, and positive regulators of GBS virulence. Transcriptional profiling of CiaR mutant GBS and LiaR mutant GBS reveals that LiaR is positively-regulated by CiaR, and the individual mutant transcriptomes share a number of commonly-regulated genes. To determine the GBS response to loss of both of these key regulatory systems, we constructed a GBS mutant strain with non-polar deletions in both ciaR and liaR, and performed transcriptional profiling using DNA microarray analysis, comparing wild-type GBS to CiaR/LiaR double mutant GBS under non-stressed conditions.
2012-11-18 | GSE14572 | GEO
Project description:Diabetic wound infections have poor healing outcomes due to the presence of numerous pathogens in addition to an impaired immune response. Group B Streptococcus (GBS) is one of the most commonly isolated bacteria from diabetic wound infections, but virulence mechanisms GBS uses during these infections have not been investigated. Here, we developed a new murine model of GBS diabetic wound infection to determine how GBS establishes infection and persists in the wound environment. Using dual RNA sequencing, we demonstrate that GBS infection of diabetic wounds triggers an inflammatory response, leading to increased transcript levels of inflammatory cytokines and chemokines as well as markers of neutrophil degranulation such as myeloperoxidase, calprotectin, and elastase. We then confirm that diabetic wounds infected with GBS have significantly higher abundance of Il-1b, KC (CXCL1), myeloperoxidase, calprotectin and elastase in wound tissues than uninfected controls . When examining how GBS adapts to this hyper-inflammatory environment we find that GBS upregulates numerous virulence factors including the surface plasminogen-binding protein pbsP, the nuclease nucA, the cyl operon which is responsible for hemolysin production and pigmentation as well as numerous effectors of type VII secretion. In addition, we recovered multiple hyper-pigmented/hemolytic GBS colonies from the murine diabetic wound environment which encode mutations in the two-component system covRS. We then go on to demonstrate that a mutant in cylE, which is repressed by CovR, is attenuated in diabetic wound infection. Finally, we examine the most highly upregulated gene pbsP in diabetic wound infection and find that PbsP is necessary for diabetic wound infection via adherence to the skin and promotion of inflammation.
2022-09-30 | GSE201342 | GEO
Project description:Streptococcus agalactiae (Group B Streptococcus, GBS) is a leading cause of early-onset neonatal bacterial infection. Evasion of innate immune defenses is critical to neonatal GBS disease pathogenesis. Effectors of the innate immune system such as antimicrobial peptides, as well as numerous antibiotics, target the peptidoglycan layer of the gram positive bacterial cell wall. The intramembrane-sensing histidine kinase class of two-component regulatory systems has recently been identified as important to the gram-positive response to cell wall stress. We identified and characterized the GBS homolog of LiaR, the response regulator component of the LiaFSR system and constructed site-directed, non-polar deletion mutations in the regulator gene liaR. GBS LiaR deletion mutant strains are more susceptible to cell wall active antibiotics (vancomycin and bacitracin) as well as antimicrobial peptides (colistin, nisin and the human cathelicidin LL-37) compared to isogenic wild-type GBS. LiaR mutant GBS are significantly attenuated in mouse models of both GBS sepsis and GBS pneumonia. To determine the genes regulated by LiaR that account for these defects, transcriptional profiling was performed using DNA microarray analysis, comparing wild-type GBS to LiaR mutant GBS under non-stressed conditions.
2012-11-18 | GSE14571 | GEO
Project description:Group B Streptococcus (GBS) is a leading cause of infant sepsis worldwide. Colonization of the gastrointestinal tract is a critical precursor to late-onset disease in exposed newborns. Neonatal susceptibility to GBS intestinal translocation stems from intestinal immaturity; however, the mechanisms by which GBS exploits the immature host remain unclear. β-hemolysin/cytolysin (βH/C) is a highly conserved toxin produced by GBS capable of disrupting epithelial barriers. However, its role in the pathogenesis of late-onset GBS disease is unknown. Our aim was to determine the contribution of βH/C to intestinal colonization and translocation to extraintestinal tissues. Using our established mouse model of late-onset GBS disease, we exposed animals to GBS COH-1 (WT), a βH/C-deficient mutant (KO), or vehicle control (PBS) via gavage. Blood, spleen, brain, and intestines were harvested 4 days post-exposure for determination of bacterial burden and isolation of intestinal epithelial cells. We used RNA-sequencing to examine the transcriptomes and performed gene ontology enrichment and KEGG pathway analysis. A separate cohort of animals were followed longitudinally to compare colonization kinetics and mortality between WT and KO groups. We demonstrate that disseminated to extraintestinal tissues occurred only in the WT exposed animals. We observed major transcriptomic changes in the colon of colonized animals, but not in the small intestine. We noted differential expression of genes among WT and KO exposed mice indicating that βH/C contributes to alterations in epithelial barrier structure and immune response signaling. Overall, our results demonstrate an important role for βH/C in the pathogenesis of late-onset GBS disease.
2023-05-31 | GSE230856 | GEO
Project description:Regulation of gene expression in response to variable and often adverse environmental conditions is an essential component of microbial pathogenesis. We identified the two-component regulatory system CiaRH in a screen for genes essential for the survival of Streptococcus agalactiae (Group B Streptococcus, GBS) on exposure to in vitro models of environmental stress. We constructed site-directed, non-polar deletion mutations in the regulator gene ciaR and compared the growth of CiaR mutant GBS to wild-type GBS under stressed conditions. CiaR mutant GBS are more sensitive than wild-type GBS to elevated temperature, low pH, chemical mutagens and ultraviolet light; the mutants are also more sensitive to cell-wall active antibiotics and antimicrobial peptides. CiaR mutant strains are markedly attenuated in a mouse model of GBS sepsis. To determine the genes regulated by CiaR that account for these defects, transcriptional profiling was performed using DNA microarray analysis, comparing wild-type GBS to CiaR mutant GBS under non-stressed conditions.
2012-11-18 | GSE14569 | GEO
Project description:The underlying change of gene network expression of Guillain-Barre syndrome (GBS) remains elusive. We sought to identify GBS-associated gene networks and signalling pathways by analyzing the transcriptional profile of leukocytes in the patients with GBS.
2011-07-28 | GSE31014 | GEO
Project description:Genome wide expression profiling was used to identify signifnificantly changed genes in fetal membranes after GBS treatment Genome-wide expression profiles in GBS-inoculated human extraplacental membranes in vitro were used to identify transcriptomic pathways altered by GBS . Using bioinformatics analysis of these expression profiles we aimed to test our hypothesis that GBS activates pathways related to inflammation and premature birth in human extraplacental membranes.
2018-01-18 | GSE96557 | GEO