Transcriptomic analysis of Fusobacterium nucleatum-stimulated Human gingival fibroblasts
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ABSTRACT:
PROVIDER: PRJNA486466 | ENA |
REPOSITORIES: ENA
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Project description:Neutrophils are known to be stimulated by different periodontal bacteria to produce reactive oxygen species and cytokines. It is inportant to investigate the gene changes made by bacteria of importance, of which, for periodontal disease, fusobaterium nucleatum is one. we used microarrays to investigate gene experssion changes in peripheral blood neutrophils werwhich e stimulated with or with out Fusobacterium Nucleatum (10953). Neutrophils from periodonatlly healthy individuals (n=4) were isolated and stimulated for 3hrs with or without fusobaterium nucleatum (10953). RNA was then extracted from these and pooled before hybridization on Affymetrix microarrays
2010-07-20 | E-GEOD-20151 | biostudies-arrayexpress
Project description:Neutrophils are known to be stimulated by different periodontal bacteria to produce reactive oxygen species and cytokines. It is inportant to investigate the gene changes made by bacteria of importance, of which, for periodontal disease, fusobaterium nucleatum is one. we used microarrays to investigate gene experssion changes in peripheral blood neutrophils werwhich e stimulated with or with out Fusobacterium Nucleatum (10953).
2010-07-20 | GSE20151 | GEO
Project description:Fusobacterium nucleatum is a Gram-negative oral bacterial species associated with periodontal disease progression. As periodontal disease progresses, it is known F. nucleatum coaggregated with blood is frequently detected in the gingival crevice. However, it is largely unknown whether these interactions between F. nucleatum and blood induce a particular genetic response. We tested the cultures of F. nucleatum ATCC 25586 with or without blood in a semi-defined growth medium by microarray analysis and found 14 genes that were affected after only about 4hr. of adhered blood. Then, we selected 7 genes that changed significantly and tested these genes via real-time RT-PCR to confirm the validity of the microarray results. As a result, one amino sugar-binding protein on the membrane of F. nucleatum was especially expressed high via both microarray and real-time RT-PCR. Based upon these data, it appears that the protein on the F. nucleatum membrane binds and transfers the amino sugar only under blood conditions. This study aims to determine the effect of blood on the gene expression profiling of F. nucreatum. The study contains 2 separate experiments that both measure the cultures without or with blood. The samples with blood contain 9% and 33% blood.
2012-09-01 | E-GEOD-36410 | biostudies-arrayexpress
Project description:To better understand the global responses of GFs to F. nucleatum infection along the time sequence, we performed a genome-wide transcriptome analysis by RNA-sequencing technology to determine the global changes on gene expression level
2019-09-12 | GSE118691 | GEO
Project description:Transcriptomic analysis of Fusobacterium nucleatum-stimulated Human gingival-derived mesenchymal stem cells
| PRJNA523396 | ENA
Project description:Fusobacterium nucleatum is a Gram-negative oral bacterial species associated with periodontal disease progression. As periodontal disease progresses, it is known F. nucleatum coaggregated with blood is frequently detected in the gingival crevice. However, it is largely unknown whether these interactions between F. nucleatum and blood induce a particular genetic response. We tested the cultures of F. nucleatum ATCC 25586 with or without blood in a semi-defined growth medium by microarray analysis and found 14 genes that were affected after only about 4hr. of adhered blood. Then, we selected 7 genes that changed significantly and tested these genes via real-time RT-PCR to confirm the validity of the microarray results. As a result, one amino sugar-binding protein on the membrane of F. nucleatum was especially expressed high via both microarray and real-time RT-PCR. Based upon these data, it appears that the protein on the F. nucleatum membrane binds and transfers the amino sugar only under blood conditions.
2012-09-01 | GSE36410 | GEO
Project description:Fusobacterium nucleatum-treated LoVo cells reported an increased promoting CRC metastasis effect compared with PBS control. To understand the underlying mechanisms of Fusobacterium nucleatum-induced metastasis ability of CRC cells, we performed RNA-sequencing in LoVo cells s with or without Fusobacterium nucleatum treatment with three independent biological replicates.
2021-10-19 | GSE173549 | GEO
Project description:To investigate the role of Fusobacterium nucleatum-mediated m6A modification, we performed m6A-sequencing to map the m6A modification in control or Fusobacterium nucleatum-treated HCT116 cells.
2022-02-07 | GSE150308 | GEO
Project description:To investigate the effect of the Zn ionophore, PBT2, on the transcriptomic response of Fusobacterium nucleatum ATCC 25586, RNA was extracted from bacterial samples which had been treated as follows: Untreated (0.006% DMSO v/v), DMSO-Zn treated (0.006% DMSO v/v + 200 uM ZnSO4), or PBT2-Zn treated (0.125 ug/mL PBT2 + 200 uM ZnSO4) (DMSO was the vehicle control). RNA samples were collected at 0h, 0.5h, and 1h post challenge in biological triplicate and sequenced using Illumina HiSeq platform. We mapped sequences to the reference genome F. nucleatum subsp. nucleatum ATCC 25586 and performed DEseq2 analysis to determine differentially expressed genes across time and treatment.
2021-07-15 | E-MTAB-8681 | biostudies-arrayexpress
Project description:Fusobacterium nucleatum is a Gram negative oral bacterial species associated with periodontal disease progression. This species is perhaps best known for its ability to adhere to a vast array of other bacteria and eukaryotic cells. Numerous studies of F. nucleatum have examined various coaggregation partners and inhibitors, but it is largely unknown whether these interactions induce a particular genetic response. We tested coaggregation between F. nucleatum ATCC strain 25586 and various species of Streptococcus in the presence of a semi-defined growth medium containing saliva. We found that this condition could support efficient coaggregation, but surprisingly also stimulated a similar degree of autoaggregation. We further characterized the autoaggregation response, since few reports have examined this in F. nucleatum. After screening several common coaggregation inhibitors, we identified L-lysine as a competitive inhibitor of autoaggregation. We performed a microarray analysis of the planktonic vs. autoaggregated cells and found nearly 100 genes that were affected after only about 60 min. of aggregation. We tested a subset of these genes via real-time RT-PCR and confirmed the validity of the microarray results. Some of these genes were also found to be inducible in cell pellets created by centrifugation. Based upon these data, it appears that autoaggregation activates a genetic program that may be utilized for growth in a high cell density environment, such as the oral biofilm. The study aims to determine the effect of autoaggregation upon the transcriptome. The study contains 2 separate experiments that both measure dispersed (i.e. non-aggregated) vs. aggregated cells and each experiment was performed in duplicate. Samples with no added components other than medium were dispersed, samples containing 25% saliva were aggregated, and samples containing 25% saliva + 50mM L-lysine remained dispersed.
2009-10-15 | E-GEOD-18554 | biostudies-arrayexpress