Microbiome Composition and Metabolic Pathways in Shallow and Deep Periodontal Pockets
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB87865 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR14801400_1.fastq.gz | Fastqsanger.gz | |||
| ERR14801400_2.fastq.gz | Fastqsanger.gz | |||
| ERR14801500_1.fastq.gz | Fastqsanger.gz | |||
| ERR14801500_2.fastq.gz | Fastqsanger.gz | |||
| ERR14801600_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 3266 |
Similar Datasets
Project description:Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.
2024-11-24 | GSE263620 | GEO
Project description:The goal was to obtain the differential transcriptome in the deep cones between shallow and deep wounds and between the Yorkshire and Duroc breeds over time. We made shallow and deep wounds on the backs of 3 Yorkshire and 3 Duroc pigs, biopsied the wounds at 1 2 3 12 and 20 weeks, extracted and amplified the RNA from the deep cones, and hybridized the Affymetrix GeneChip®. We compared wound depth by breed over time; the system included 3 factors (depth, breed and time). The system also included repeated measures since the same pigs were used at each time. It also included paired data since the shallow and deep wounds compared were located on the same pig.
2011-12-31 | E-GEOD-26095 | biostudies-arrayexpress
Project description:Periodontitis can impair the osteogenic differentiation of human periodontal mesenchymal stem cells, but the underlying molecular mechanisms are still poorly understood. Long noncoding RNAs (lncRNAs) have been demonstrated to play significant roles under both physiologic and pathological conditions. We performed comprehensive lncRNAs profiling by lncRNA microarray to identify differentially expressed long noncoding RNA expression between Periodontal ligament stem cells from healthy Periodontal tissue and periodontal ligament stem cells from inflammatory periodontal tissue. Our analysis identified 233 lncRNAs and 423 mRNAs that were differently expressed (fold change >2.0, p-value < 0.05) between the two groups of cells. The GO analysis revealed that the significantly down-regulated biological processes included multicellular organismal process, developmental process and multicellular organismal development and the significantly up-regulated biological processes included cellular process, biological regulation and response to stimulus in periodontal ligament stem cells from inflammatory periodontal tissue. The Pathway analysis revealed that the differentially expressed mRNAs may involved in Focal adhesion, ECM-receptor interaction, Bacterial invasion of epithelial cells, Long-term depression, Circadian entrainment and HIF-1 signaling pathway. Two-condition experiment, periodontal ligament stem cells from healthy periodontal tissue (hPDLSCs) vs. periodontal ligament stem cells from inflammatory periodontal tissue (pPDLSCs), Biological replicates: 3 control replicates (hPDLSCs), 3 testing replicates (pPDLSCs).
2016-02-19 | E-GEOD-78074 | biostudies-arrayexpress
Project description:The goal was to obtain the differential transcriptome in the deep cones between shallow and deep wounds and between the Yorkshire and Duroc breeds over time.
2011-12-31 | GSE26095 | GEO
Project description:Periodontitis can impair the osteogenic differentiation of human periodontal mesenchymal stem cells, but the underlying molecular mechanisms are still poorly understood. Long noncoding RNAs (lncRNAs) have been demonstrated to play significant roles under both physiologic and pathological conditions. We performed comprehensive lncRNAs profiling by lncRNA microarray to identify differentially expressed long noncoding RNA expression between Periodontal ligament stem cells from healthy Periodontal tissue and periodontal ligament stem cells from inflammatory periodontal tissue. Our analysis identified 233 lncRNAs and 423 mRNAs that were differently expressed (fold change >2.0, p-value < 0.05) between the two groups of cells. The GO analysis revealed that the significantly down-regulated biological processes included multicellular organismal process, developmental process and multicellular organismal development and the significantly up-regulated biological processes included cellular process, biological regulation and response to stimulus in periodontal ligament stem cells from inflammatory periodontal tissue. The Pathway analysis revealed that the differentially expressed mRNAs may involved in Focal adhesion, ECM-receptor interaction, Bacterial invasion of epithelial cells, Long-term depression, Circadian entrainment and HIF-1 signaling pathway.
2016-02-19 | GSE78074 | GEO
Project description:Oral Microbiome of Deep and Shallow Dental Pockets In Chronic Periodontitis
| PRJNA182936 | ENA
Project description:We used microarrays to detect the differences in gene-expression of the periontal ligament between patients with healthy periodontal ligament and patients with periodontitis RNA was extracted directly from the middle third of the human periodontal ligament
2011-03-17 | E-GEOD-27993 | biostudies-arrayexpress
Project description:Periodontal tissue supports teeth in the alveolar bone socket via fibrous attachment of the periodontal ligament (PDL). The PDL contains many stromal cell types, including osteoblasts, cementoblasts, periodontal fibroblasts, and stem/progenitor cells. However, the characteristics and lineage hierarchy of each cell type remain poorly defined. Here we present a single-cell atlas of PDL, highlighting diverse cell populations in PDL.
2022-09-28 | GSE197828 | GEO
Project description:Periodontal infections have been associated with systemic inflammation and risk for atherosclerosis and vascular disease. We investigated the effects of comprehensive periodontal therapy on gene expression of peripheral blood monocytes. Approximately 1/3 of the patients showed substantial changes in expression in genes relevant to innate immunity, apoptosis, and cell signaling. We concluded that periodontal therapy may alter monocytic gene expression in a manner consistent with a systemic anti-inflammatory effect. Experiment Overall Design: Fifteen patients with periodontitis contributed with blood samples at four time points: 1 week prior to periodontal treatment (#1), at treatment initiation (baseline, #2), 6 weeks (#3) and 10 weeks post-baseline (#4). At baseline and 10 weeks, periodontal status was recorded and subgingival plaque samples were collected and processed by checkerboard DNA-DNA hybridization. Periodontal therapy, including periodontal surgery and extractions but no adjunctive antibiotics, was completed within 6 weeks. At each of the four time points, serum concentrations of 19 biomarkers were determined using multiplex assays for Luminex technology. Peripheral blood monocytes were purified, RNA was extracted, reverse-transcribed, labeled, and hybridized with Affymetrix U133 Plus 2.0 chips. Expression profiles were analyzed using linear random effects models. Further analysis of Gene Ontology (GO) terms summarized the expression patterns into biologically relevant categories. Treatment resulted in substantial improvement in clinical periodontal status and reduction in levels of several periodontal pathogens. Expression profiling over time revealed more than 11,000 probes sets differentially expressed at a false discovery rate of <0.05.
2008-06-15 | E-GEOD-6751 | biostudies-arrayexpress