Ontology highlight
ABSTRACT:
PROVIDER: PRJEB20505 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gene expression in the neonatal uterus and vagina from transformation related protein 63 (Trp63) conditional heterozygous and null mice was analyzed in order to identify upstream and downstream of Trp63 in the developing vagina. Differential gene expression between vaginal (Trp63 positive) and uterine (Trp63 negative) tissues should reflect both the upstream and downstream of Trp63 expression, whereas the comparison between conditional knockout and heterozygous vaginae should identify what is downstream of Trp63. Thus, the three-way comparison should identify what is upstream of Trp63. Total RNA was extracted from the Trp63 conditional heterozygous (Trp63 flox/wt ; Pax2-cre) uteri and vaginae, and Trp63 conditional knockout (Trp63 flox/floxt ; Pax2-cre) vaginae. Total 12 samples (3 different genotype/tissue groups x 4 independent samples each).
2013-03-14 | E-GEOD-44697 | biostudies-arrayexpress
Project description:Atopobium vaginae DSM 15829 genome sequencing
| PRJNA46677 | ENA
Project description:Bacterial vaginosis (BV), the most common vaginal infection among women worldwide, is characterized by an imbalance in the vaginal microbiota with a reduction of protective Lactobacillus species and overgrowth of facultative and strictly anaerobic bacteria. Although the development of a polymicrobial biofilm on the vaginal epithelium is a hallmark of BV, interactions between key BV-associated bacteria (BVAB) [i.e. Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia] present in the biofilm remain largely unexplored. In this study, we aimed to analyze the transcriptome of triple-species biofilms growing in a medium simulating vaginal tract secretions (mGTS) compared to a rich medium, New York City III (NYCIII). As such, triple-species biofilms formed by G. vaginalis, F. vaginae, and P. bivia were grown in either NYCIII or mGTS in anaerobic conditions. After that, RNA was extracted and cDNA libraries were constructed and sequenced. We first characterized the biofilm composition in both media by qPCR and observed that G. vaginalis was the most prevalent species in both conditions. RNA-sequencing data analysis revealed a total of 964, 596, and 656 differentially expressed genes in G. vaginalis, F. vaginae, and P. bivia, respectively, when comparing the transcriptome of biofilms in mGTS versus NYCIII. We identified 927 upregulated and 37 downregulated genes for G. vaginalis, 492 upregulated and 104 downregulated for F. vaginae, and 166 upregulated and 490 downregulated for P. bivia. Gene ontology enrichment showed that metabolic and biosynthetic processes were common within upregulated genes for G. vaginalis, while downregulated genes were associated with transmembrane transporters. For F. vaginae, transmembrane transporters were identified among upregulated genes, while downregulated genes were related to metabolism and cellular process, in which several KEGG pathways linked to metabolism were recognized. For P. bivia, upregulated genes were associated with transmembrane processes while downregulated genes were associated with metabolic processes; KEGG pathways were also identified. This work highlighted the adaptation of 3 key BVAB growing on a medium that simulates in vivo conditions and will contribute to a better understanding of bacterial interactions that are important in the pathogenesis of incident BV.
2025-04-16 | GSE279623 | GEO
Project description:Candidatus Lachnocurva vaginae Genome sequencing and assembly
| PRJNA562728 | ENA
Project description:Fannyhessea vaginae strain:44061 Genome sequencing and assembly
| PRJNA288564 | ENA
Project description:Bacterial vaginosis (BV) is the most common cause of vaginal discharge among women worldwide. BV is characterized by an imbalance in the vaginal microbiota with depletion of protective Lactobacillus species and overgrowth of facultative and strictly anaerobic bacteria. Although the development of a polymicrobial biofilm on the vaginal epithelium is a hallmark of BV, interactions between key BV-associated bacteria (BVAB) [i.e. Gardnerella vaginalis, Fannyhessea vaginae, and Prevotella bivia] present in the biofilm are still not completely understood. In this study, we aimed to analyse the transcriptome of single and triple-species biofilms growing in the rich medium, New York City III (NYCIII). A previous analysis of triple-species biofilms composition by qPCR showed that the biofilms were mainly composed of G. vaginalis, followed by F. vaginae and P. bivia. The transcriptomic analysis revealed a total of 431 (34 upregulated and 397 downregulated), 126 (36 upregulated and 90 downregulated), and 39 (31 upregulated and 8 downregulated) differentially expressed genes for G. vaginalis, F. vaginae, and P. bivia, respectively. Gene ontology only detected enrichment for the downregulated genes of G. vaginalis and 47 GO terms were associated with molecular functions, cellular components and biological processes, mainly metabolism. Hence, this work showed the adaptation of 3 BVAB when growing in a triple-species biofilm, with several genes being differentially expressed in all the species growing in a polymicrobial biofilm.
2024-09-25 | GSE268115 | GEO
Project description:Gene expression in the neonatal uterus and vagina from transformation related protein 63 (Trp63) conditional heterozygous and null mice was analyzed in order to identify upstream and downstream of Trp63 in the developing vagina. Differential gene expression between vaginal (Trp63 positive) and uterine (Trp63 negative) tissues should reflect both the upstream and downstream of Trp63 expression, whereas the comparison between conditional knockout and heterozygous vaginae should identify what is downstream of Trp63. Thus, the three-way comparison should identify what is upstream of Trp63.
2013-03-14 | GSE44697 | GEO
Project description:Interventions: Genomic test CANCERPLEX-JP OncoGuide NCC oncopanel system FndationONe CDx genome profile GUARDANT360 MSI Analysis System BRACAnalysis
Primary outcome(s): Development of genome database
Study Design: Single arm Non-randomized
| 2643590 | ecrin-mdr-crc