GEO DataSets

(Submitter supplied) Oal anaerobic bacteria have to face constant oxidative stress in order to survive in the inflammatory environment of the periodontal pocket. In this study, we analyzed the transcriptome profiles of P. gingivalis and Filifactor in monoculture as compared to P. gingivalis+F.alocis coculture under H2O2 stress condtions, to analyze the genes responsible for enhanced survival of P. gingivalis in presence of F. more...

Organism:

Porphyromonas gingivalis W83; Filifactor alocis ATCC 35896

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24003 GPL33710 GPL33711

9 Samples

Download data: CSV

(Submitter supplied) Wild type Porphyromonas gingivalis strain ATCC33277 (V3176) and PG1626 - deficient mutant (V3177) were grown in iron replete conditions was used to compare to Porphyromonas gingivalis strains grown in iron chelated conditions.

Organism:

Porphyromonas gingivalis ATCC 33277

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30130

16 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Haemophilus influenzae; Porphyromonas gingivalis W83; Porphyromonas gingivalis

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL33075 GPL18755

24 Samples

Download data

(Submitter supplied) To understand the role of CdhR and its adjacent gene PG1236 in nitric oxide (NO) stress resistance, isogenic mutants P. gingivalis FLL457 (ΔPG1237::ermF), FLL458 (ΔPG1236::ermF) and FLL459 (ΔPG1236-37::ermF) were made by allelic exchange mutagenesis and their gene expression was studied under control and NO stress conditions. DNA microarray analysis of FLL457 showed that approximately 2% of the genes were up regulated and over 1% of the genes down regulated. more...

Organism:

Porphyromonas gingivalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33075

12 Samples

Download data: XLSX

(Submitter supplied) To understand the role of CdhR and its adjacent gene PG1236 in nitric oxide (NO) stress resistance, isogenic mutants P. gingivalis FLL457 (ΔPG1237::ermF), FLL458 (ΔPG1236::ermF) and FLL459 (ΔPG1236-37::ermF) were made by allelic exchange mutagenesis and their gene expression was studied under control and NO stress conditions. DNA microarray analysis of FLL457 showed that approximately 2% of the genes were up regulated and over 1% of the genes down regulated. more...

Organism:

Porphyromonas gingivalis W83; Haemophilus influenzae

Type:

Expression profiling by array

Platform:

GPL18755

12 Samples

Download data: XLS

(Submitter supplied) We use high through put RNA sequenceing technology to study the genome-wide expression profile of a unknown-function gene PG0686 mutant, designated as FLL361, in key-stone oral pathogen Porphyromonas gingivalis under anaerobic conditions and oxidative stress conditions.

Organism:

Porphyromonas gingivalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32620

12 Samples

Download data: CSV

(Submitter supplied) To investigate the comprehensive function of trkA in Porphyromonas gingivalis W83, we established isogenic trkA deletion strain via homologous recombination and compared the transcriptional alteration between mutant and wild type group through RNA sequencing.

Organism:

Porphyromonas gingivalis W83

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32551

6 Samples

Download data: TXT

(Submitter supplied) Role of RNA-binding protein, Pgr, in Porphyromonas gingivalis.

Organism:

Porphyromonas gingivalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25359

16 Samples

Download data: XLSX

(Submitter supplied) Tn-Seq was used to identify P. gingivalis genes that confer fitness during cooperative growth with S. gordonii or F. nucleatum in a murine abscess model.

Organism:

Porphyromonas gingivalis

Type:

Other

Platform:

GPL28580

20 Samples

Download data: TXT

(Submitter supplied) Transcriptomics profiling of P. gingivalis W50 wild type compared to a FeoB mutant.

Organism:

Porphyromonas gingivalis; Porphyromonas gingivalis W50; Porphyromonas gingivalis W83

Type:

Expression profiling by array

Platform:

GPL15412

12 Samples

Download data: GPR

(Submitter supplied) The aim of the study was to identify the role of flavodoxin gene in the virulence of P. gingivalis W83.The mRNA profiles of P. gingivalis W83 and flavodoxin mutant strain were generated by deep sequencing, in triplicate, using Illumina sequencing platform. Differential expression analysis of two groups (Three biological replicates per group) was performed using the DESeq R package. In total, 376 genes met the DEGs criteria (194 upregulated genes and 182 down-regulated genes). more...

Organism:

Porphyromonas gingivalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24653

6 Samples

Download data: TXT

(Submitter supplied) Purpose: This study provides the transcriptional landscape of intracellular P. gingivalis as well as that of endothelial cells infected by this bacteria based on dual RNA sequencing. Methods: HUVECs were seeded in 6-well plates and cultured to 80% confluence. After washing with phosphate-buffered saline (PBS), cell were infected with P. gingivalis at a multiplicity of infection (MOI) of 100 for 2 h at 37 °C in 5% CO2, unless otherwise stated. more...

Organism:

Homo sapiens; Porphyromonas gingivalis ATCC 33277

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18306 GPL11154

12 Samples

Download data: TXT

(Submitter supplied) Porphyromonas gingivalis expresses a limited number of two-component systems, including RprY, an orphan response regulator that lacks a cognate sensor kinase. In this study, we examimed the regulon controlled by RprY and found that RprY can control the expression of genes encoding the type IX secretion system (T9SS) machinery and virulence factors secreted through the T9SS, including the gingipain proteases and peptidylarginine deiminase (PPAD).

Organism:

Porphyromonas gingivalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28580

10 Samples

Download data: TXT

(Submitter supplied) Our results show that compared to wild type, a deletion mutant of the cas3 gene, an essential nuclease part of the class 1 type I CRISPR-Cas system, increases the virulence of P gingivalis.

Organism:

Porphyromonas gingivalis; Galleria mellonella

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24653 GPL25944

46 Samples

Download data: CSV

(Submitter supplied) The genomes of P. gingivalis strains 33277 and 381 are highly related phylogenetically. However, 33277 displays a reduced capacity to stimulate HEK cell TLR2-dependent signaling and THP-1 cell-dependent IL-1β production compared to 381, suggesting strain-specific differences in the expression of one or more bacterial immune-modulatory cell surface molecules. Genomic sequencing identified a single nucleotide polymorphism in the 33277 fimB allele (A>T), encoding a truncated FimB protein, relative to the 381 fimB allele. more...

Organism:

Porphyromonas gingivalis ATCC 33277; Porphyromonas gingivalis 381

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26349 GPL25781

6 Samples

Download data: XLSX

(Submitter supplied) The aim of the present study to compare the transcriptomic profile of P.gingivalis when growing within an in vitro multispecies biofilm or in a planktonic state, using microarray technology.

Organism:

Porphyromonas gingivalis ATCC 33277; Porphyromonas gingivalis

Type:

Expression profiling by array

Platform:

GPL26732

6 Samples

Download data: TXT

(Submitter supplied) The P. gingivalis 33277 transposon mutant J5-c5, isolated in this study, was demonstrated to exhibit a lipid A deacylase phenotype. The mutant is unable to deacylate lipid A, which confers to it, in stark contrast to wild-type, an inability to evade the powerful TLR4 innate immune response. The mutant was shown to contain five transposons. In order to determine the affected gene responsible for this phenotype, we took the approach of comparing gene expression between wild-type and J5-c5 transposon mutant. more...

Organism:

Porphyromonas gingivalis ATCC 33277

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25781

6 Samples

Download data: TAB

(Submitter supplied) Porphyromonas gingivalis (P. gingivalis) 381 and W83 growing in motility condition (i.e. stabbed in soft agar culture) and on surface of solid agar culture (Biofilm) were prepared. Applied medium was BAPHK supplemented with hemin and menadione . The cultures were then permitted to grow anaerobically at 37°C for 24 hours, which corresponds to initial stages of surface translocation by P. gingivalis. At this point, RNA extraction was performed using the cultures, and these samples were processed and submitted for RNA sequencing using an Illumina platform. Significant changes in gene expression were observed in cells growing in motility and biofilm modes , and the majority of changes were associated with cell surface proteins, membrane proteins, biosynthesis of folates and bioenergetic pathways.

Organism:

Porphyromonas gingivalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21491

12 Samples

Download data: XLSX

(Submitter supplied) HcpR has been shown to be required for growth of Porphyromonas gingivalis in the presence of nitrite (Infect Immun. 2012 Sep;80(9):3319-31. doi: 10.1128/IAI.00561-12. Epub 2012 Jul 9). It also has been shown to regulate the expression of hcp. To define the entire regulon of HcpR RNAseq examination of the wild type and mutant (deficient in HcpR) strains have been used to define the regulon in response to nitrite exposure in bacteria grown in the presence and absence of nitrite. more...

Organism:

Porphyromonas gingivalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25359

16 Samples

Download data: XLS

(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:

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; Treponema denticola; Cereibacter sphaeroides; Streptococcus gordonii; Streptococcus agalactiae; Enterococcus faecalis; Bifidobacterium adolescentis; Homo sapiens; Prevotella intermedia; Prevotella nigrescens; Bacteria; Acinetobacter baumannii; Escherichia coli; Staphylococcus aureus; Staphylococcus epidermidis; Bacillus cereus; Schaalia odontolytica; Fusobacterium nucleatum subsp. nucleatum

Type:

Other

Platform:

GPL25612

178 Samples

Download data: CSV