txid851[Organism:exp] - GEO DataSets

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Select item 2001715611.

Metformin treatment on Fusobacterium nucleatum

(Submitter supplied) High throughput RNA sequencing For RNA sequencing, F. nucleatum was incubated with 1 mM or 5 mM metformin for 7 hours, when the bacterium were under logarithmic phase. Total RNA of F. nucleatum was stabilized with RNA protect Bacteria Reagent (QIAGEN, Germany) and extracted using a QIAGEN RNeasy kit (QIAGEN, Germany) following the manufacturer’s instructions.

Organism:: Fusobacterium nucleatum subsp. nucleatum ATCC 25586

Type:: Expression profiling by high throughput sequencing

Platform:: GPL29979
9 Samples

Download data: TXT

Series

Accession:: GSE171561

ID:: 200171561

SRA Run Selector

Select item 2002499552.

Transcriptome fine-mapping reveals FoxJ, a σE-dependent small RNA with unusual mRNA activation activity in Fusobacterium nucleatum

(Submitter supplied) The oral commensal Fusobacterium nucleatum can spread to extra-oral sites where it is associated with pathologies as diverse as pre-term birth or cancer. Due to the evolutionary distance of F. nucleatum to other model bacteria, we lack a deeper understanding of RNA regulatory networks that allow this bacterium to adapt to different environmental niches. As a first step in that direction, we recently showed that F. more...

Organism:: Fusobacterium nucleatum subsp. nucleatum ATCC 23726

Type:: Expression profiling by high throughput sequencing

Platform:: GPL33873
15 Samples

Download data: WIG

Series

Accession:: GSE249955

ID:: 200249955

PubMed Full text in PMC Similar studies

Select item 2002463963.

A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum

(Submitter supplied) The common oral microbe Fusobacterium nucleatum has recently gained attention when it was found to colonize tumors throughout the human body. Fusobacteria are also interesting in regard to bacterial RNA biology as these early-branching species encode many small noncoding RNAs (sRNAs) but lack homologs of the common RNA-binding proteins (RBPs) CsrA, Hfq and ProQ. Here, to search for alternate sRNA-associated RBPs in F. more...

Organism:: Fusobacterium nucleatum subsp. nucleatum ATCC 23726

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL33873
26 Samples

Download data: WIG

Series

Accession:: GSE246396

ID:: 200246396

PubMed Full text in PMC Similar studies

Select item 2001923394.

Expanding the genetic tool kit helps dissect a global stress response in the early-branching species Fusobacterium nucleatum

(Submitter supplied) We elucidated the global regulatory network of sigma E in Fusobacterium nucleatum. For this, we developed new genetic tools for the anaerobic bacterium. This uncovered a conserved regulon of the sigma factor including a noncoding arm of the sRNA FoxI. In this process, FoxI serves as a negative regulator of sigma E to downregulate several outer membrane proteins as well as the putative galactose transporter mglBAC.

Organism:: Fusobacterium nucleatum subsp. nucleatum ATCC 23726

Type:: Expression profiling by high throughput sequencing

Platform:: GPL31122
33 Samples

Download data: WIG

Series

Accession:: GSE192339

ID:: 200192339

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001743205.

The fused methionine sulfoxide reductase MsrAB promotes oxidative stress defense and bacterial virulence in Fusobacterium nucleatum

(Submitter supplied) Recognizably associated with oral infections, adverse pregnancy outcomes, and colorectal cancer, the Gram-negative oral bacterium Fusobacterium nucleatum is known to colonize many extraoral sites including placenta and colon. How this anaerobe copes with oxidative stress imposed by the host immune response in various tissues is unknown. Here, we revealed that F. nucleatum harbors a gene locus coding for a single, fused methionine sulfoxide reductase (MsrAB), a two-component transduction system (ModRS), thioredoxin (Trx)- and cytochrome c (CcdA)-like proteins. more...

Organism:: Fusobacterium nucleatum subsp. nucleatum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL29799
12 Samples

Download data: XLSX

Series

Accession:: GSE174320

ID:: 200174320

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001680516.

Genetic and molecular determinants of polymicrobial interactions in Fusobacterium nucleatum

(Submitter supplied) A gram-negative colonizer of the oral cavity, Fusobacterium nucleatum not only interacts with many pathogens in the oral microbiome but also has the ability to spread to extraoral sites including placenta and amniotic fluid, promoting preterm birth. To date, however, the molecular mechanism of interspecies interactions –termed coaggregation–by F. nucleatum and how coaggregation affects bacterial virulence remain poorly defined. more...

Organism:: Fusobacterium nucleatum subsp. nucleatum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL29799
6 Samples

Download data: XLSX

Series

Accession:: GSE168051

ID:: 200168051

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001613607.

RNA landscape of the emerging cancer-bug Fusobacterium nucleatum

(Submitter supplied) Fusobacterium nucleatum, long known as a constituent of the oral microflora, has recently garnered much attention for its newly discovered prevalence in colorectal and breast cancer tissue. The growing interest in this emerging cancer-associated bacterium sharply contrasts with a paucity of knowledge about its basic gene expression features and physiological responses. Post-transcriptional networks are also unknown, for fusobacteria lack all established small RNA-associated proteins. more...

Organism:: Fusobacterium polymorphum ATCC 10953; Fusobacterium animalis 7_1; Fusobacterium vincentii 3_1_36A2; Fusobacterium nucleatum subsp. nucleatum ATCC 25586; Fusobacterium periodonticum 2_1_31

Type:: Expression profiling by high throughput sequencing

5 related Platforms
90 Samples

Download data: WIG

Series

Accession:: GSE161360

ID:: 200161360

PubMed Similar studies SRA Run Selector

Select item 2001307148.

A survey of Fusobacterium nuceatum genes modulated by host cell infection

(Submitter supplied) Here we report comprehensive transcriptomic profiles from Fusobacterium nucleatum (Fn) under conditions that mimic the first stages of bacterial infection in a highly-differentiated adenocarcinoma epithelial cell line. Our transcriptomic in vitro adenocarcinoma approach allows us to measure the expression dynamics and regulation of bacterial virulence and response factors in real time and is a novel strategy for clarifying the role of Fn infection in CRC progression. more...

Organism:: Fusobacterium nucleatum

Type:: Expression profiling by high throughput sequencing

Platform:: GPL26625
9 Samples

Download data: TXT

Series

Accession:: GSE130714

ID:: 200130714

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001250859.

Method for absolute quantification of microbial communities by using both microarrays and competitive PCR

(Submitter supplied) We investigated an improved method that combines competitive PCR and microarray techniques. This approach allowed us to quantify specific bacterial groups mounted on DNA chips with accuracy close to that of real-time PCR, despite a measurement at the end point of PCR, and also to estimate the bacterial DNA content in sample DNA.

Organism:: Bacteria; Acinetobacter baumannii; Escherichia coli; Staphylococcus aureus; Staphylococcus epidermidis; Bacillus cereus; Schaalia odontolytica; Fusobacterium nucleatum subsp. nucleatum; Treponema denticola; Cereibacter sphaeroides; Streptococcus gordonii; Streptococcus agalactiae; Enterococcus faecalis; Bifidobacterium adolescentis; Homo sapiens; Prevotella intermedia; Prevotella nigrescens; Campylobacter rectus; Helicobacter pylori; Pseudomonas aeruginosa; Aggregatibacter actinomycetemcomitans; Phocaeicola vulgatus; Capnocytophaga gingivalis; Deinococcus radiodurans; Streptococcus mutans; Streptococcus intermedius; Cutibacterium acnes; Neisseria meningitidis; Porphyromonas gingivalis; Fusobacterium nucleatum; Clostridium beijerinckii; Lactobacillus gasseri; Tannerella forsythia

Type:: Other

Platform:: GPL25612
178 Samples

Download data: CSV

Series

Accession:: GSE125085

ID:: 200125085

Select item 20003641010.

The effect of blood on Fusobacterium nucleatum

(Submitter supplied) 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. more...

Organism:: Fusobacterium nucleatum; Fusobacterium nucleatum subsp. nucleatum ATCC 25586

Type:: Expression profiling by array

Platform:: GPL9447
3 Samples

Download data: CEL

Series

Accession:: GSE36410

ID:: 200036410

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20002884111.

A five-species transcriptome array for oral mixed-biofilm studies

(Submitter supplied) Investigation of whole genome gene expression levels of P. gingivalis W83, F. nucleatum DSMZ 25586, S. sanguinis SK36, A. actinomycetemcomitans HK1651, S. mutans UA159 in an 24 h old culture. Additionally, whole genome gene expression level changes of S. mutans UA159 biofilm cells after co-cultivation with S. mitis ATCC 11843 were compared to its single species biofilm growth after 24 h. Aim: Demonstration of the usefulness of a five-species gene expression array. more...

Organism:: Streptococcus mitis; Streptococcus sanguinis SK36; Streptococcus mutans UA159; Porphyromonas gingivalis W83; Fusobacterium nucleatum; Aggregatibacter actinomycetemcomitans HK1651

Type:: Expression profiling by array

Platforms:: GPL13444 GPL10873
12 Samples

Download data: CALLS, PAIR, TXT

Series

Accession:: GSE28841

ID:: 200028841

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20001855412.

Characterization of the autoaggregation response of Fusobacterium nucleatum

(Submitter supplied) 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. more...