GEO DataSets

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

Organism:

Porphyromonas gingivalis; Haemophilus influenzae; Porphyromonas gingivalis W83

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) 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) 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) 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 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; Porphyromonas gingivalis ATCC 33277

Type:

Expression profiling by array

Platform:

GPL26732

6 Samples

Download data: TXT

(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:

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; Neisseria meningitidis; Porphyromonas gingivalis; Fusobacterium nucleatum; Clostridium beijerinckii; Lactobacillus gasseri; Tannerella forsythia; Campylobacter rectus; Helicobacter pylori; Pseudomonas aeruginosa; Aggregatibacter actinomycetemcomitans; Phocaeicola vulgatus; Capnocytophaga gingivalis; Deinococcus radiodurans; Streptococcus mutans; Streptococcus intermedius; Cutibacterium acnes

Type:

Other

Platform:

GPL25612

178 Samples

Download data: CSV

(Submitter supplied) We examine the transcriptome of both P. gingivalis and A. baumannii in monotypic communities compared to heterotypic communities with both organisms. We identify a number of genes responsible for enhanced biofilm development as well as metabolic synergy.

Organism:

Acinetobacter baumannii; Porphyromonas gingivalis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24653 GPL24655 GPL24654

16 Samples

Download data: TXT

(Submitter supplied) In this in vitro study, using DNA microarray we investigate the differential gene expression of Porphyromonas gingicalis ATCC 33277 when growing in the presence or in absence of its own monospecies biofilm.

Organism:

Porphyromonas gingivalis; Porphyromonas gingivalis ATCC 33277

Type:

Expression profiling by array

Platform:

GPL23193

6 Samples

Download data: TXT

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

Organism:

Porphyromonas gingivalis; Porphyromonas gingivalis W83

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL6533 GPL24003

24 Samples

Download data: PAIR

(Submitter supplied) To study the expression profile of ECF sigma factor PG1660 mutant under anaerobic conditions and hydrogen peroxide stress conditions compared to the wild-type W83 by using DNA-microarray. The role of ECF sigma factor PG1660 involved in oxidative stress was published Yuetan Dou, Devon Osbourne, Rachelle McKenzie, Hansel M Fletcher. (2010) Involvement of extracytoplasmic function sigma factors in virulence regulation in Porphyromonas gingivalis W83. more...

Organism:

Porphyromonas gingivalis; Porphyromonas gingivalis W83

Type:

Expression profiling by array

Platform:

GPL6533

18 Samples

Download data: PAIR, XLSX

(Submitter supplied) The aim of the present study was to compare the genome-wide transcription activities of P.gingivalis under both states, as biofilm and as planktonic growth, using microarray technology.

Organism:

Porphyromonas gingivalis

Type:

Expression profiling by array

Platform:

GPL23193

6 Samples

Download data: TXT

(Submitter supplied) We report the results of high throughput sequencing on P. gingivalis cells in the presence or absence of 4 aminobenzoate/para-amino benzoic acid (pABA)

Organism:

Porphyromonas gingivalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21491

4 Samples

Download data: TXT

(Submitter supplied) The aim of this study is to determine the effects of different concentration Nal-P-113 in biofilm formation. Besides, we performed gene expression profiling in Nal-P-113-treated P. gingivalis W83 to delineate the underlying molecular mechanism of Nal-P-113-inhibited biofilm formation.

Organism:

Porphyromonas gingivalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22953

4 Samples

Download data: TXT