Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Facilitates Quantitative Analysis of P. gingivalis and HUVEC Transcriptomes

ABSTRACT: 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. Non-adherent bacteria were removed by washing with PBS, and the cell-adherent bacteria were killed using gentamicin (300 μg/mL) and metronidazole (200 μg/mL) for 1 h at 37 °C in 5% CO2.Total RNA was isolated from the samples using TRIzol® reagent.cDNA libraries for Illumina® sequencing were generated using the KC-DigitalTM Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA). The library products corresponding to 200–250 bps were then enriched, quantified, and sequenced using a Nova-seq 6000 sequencer (Illumina, San Diego, CA, USA). Results: Using an optimized data analysis workflow, intracellular P. gingivalis showed a total of 573 DEGs compared with the control bacteria, and of these DEGs, 304 and 269 were upregulated and downregulated, respectively. A total of 838 DEGs were detected in P. gingivalis-infected HUVECs compared with their uninfected counterparts, and of these, 297 and 541 genes were upregulated and downregulated, respectively. Conclusions: This study firstly provides the transcriptional landscape of intracellular P. gingivalis as well as that of endothelial cells infected by this bacteria based on dual RNA sequencing.

ORGANISM(S): Porphyromonas gingivalis ATCC 33277 Homo sapiens

PROVIDER: GSE184085 | GEO | 2021/09/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:San Diego Seagrass

| PRJNA483963 | ENA

Signaling of Neisseria meningitidis MC58 mutants to primary human umbilical vein endothelial cells (HUVEC)

Project description:We examined the adherence-mediated signaling of meningococci to human cells by comparing gene expression profiles of primary human umbilical vein endothelial cells (HUVEC) infected by piliated and adherent wild-type (WT), frpC/frpA-deficient mutant, or the non-adherent (ΔpilD) N. meningitidis MC58 bacteria defective in production of the type IV pilus, respectively. Surprisingly, no significant difference was found between the transcriptomes of HUVECs infected by bacteria producing, or not the RTX FrpC and FrpA proteins, thus failing to provide any hints on their biological activity. In contrast, pili-mediated adhesion of meningococci resulted in alterations of expression levels of human genes known to regulate apoptosis, cell proliferation, inflammatory response or adhesion. In particular, genes for signaling pathway proteins involved in early embryonic development, such as transforming growth factor-β (TGF-β)/Smad, Wnt/β-catenin, and Notch/Jagged were found to be upregulated upon adhesion of N. meningitidis together with genes for a number of transcription factors. This reveals that adhering piliated meningocci manipulate signaling pathways controlling human cell proliferation, survival and defense mechanisms, while establishing a commensal relationship with the host. Keywords: time course, infection response, genetic modification

2006-09-01 | GSE4646 | GEO

RNA-seq of coding RNA of Staphylococcus aureus wild type strain before and after 30 min of exposure to 13 mM itaconic acid stress reveals adaption to the immunometabolite itaconate by inducing acid and oxidative stress responses

Project description:S. aureus COL was cultivated in RPMI medium in 3 biological replicates and harvested at an OD500 of 0.5 before (as control) and at 30 min after exposure to 13 mM itaconic acid stress. Cells were disrupted in 3 mM EDTA/ 200 mM NaCl lysis buffer with a Precellys24 ribolyzer followed by RNA isolation using the acid phenol extraction protocol as described. The RNA quality was approved by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6000 kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, USA) was applied to prepare the cDNA libraries. The cDNAs were sequenced paired end on an Illumina HiSeq 1500 (San Diego, CA, USA) using 70 and 75 bp read length and a minimum sequencing depth of 10 million reads per library.

2023-09-10 | E-MTAB-13287 | biostudies-arrayexpress

RNA-seq of coding RNA of Streptococcus pneumoniae D39 wild type strain before and after 30 min of exposure to sub-lethal doses of 800 µM HOCl stress during the log phase of microaerophilic grown bacteria

Project description:RNA-seq of coding RNA of Streptococcus pneumoniae D39 wild type strain before and after 30 min of exposure to sub-lethal doses of 800 µM HOCl stress during the log phase of microaerophilic grown bacteria. The S. pneumoniae D39 wild type strain was cultivated in RPMI medium and treated with thiol-reactive compound NaOCl, which dissociates in aqueous solution to hypochlorous acid (HOCl) and hypochlorite (OCl−) - the concentration of HOCl was determined by absorbance measurements - here 800 µM HOC, at an OD600 of 0.4 for 30 min. Bacteria were harvested before and after treatment in ice-cold killing buffer (50 mM Tris pH 7.5, 5 mM MgCl2, 20 mM NaN3), centrifuged at 4,750 rpm for 10 min at 4°C. The pellets were immediately frozen in liquid nitrogen and stored at -80°C. RNA isolation was performed using the acidic phenol-chloroform extraction protocol. After DNase-I treatment (Zymo Research, Germany), the RNA quality was checked by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6,000 kit using an Agilent 2,100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). For RNA-seq transcriptomics, Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, United States) was applied to prepare the cDNA libraries. The cDNAs were sequenced paired end on an Illumina HiSeq 1,500 (San Diego, CA, United States) using 70 bp read length and a minimum sequencing depth of 10 million reads per library.

2022-12-06 | E-MTAB-11968 | biostudies-arrayexpress

RNA-Seq analysis of Bacillus methanolicus MGA3 grown with and without 5-aminovalerate to investigate the transcriptional response of Bacillus methanolicus to 5-aminovalerate.

Project description:Bacillus methanolicus MGA3, which has a low tolerance for 5-aminovalerate. To investigate the transcriptional response of Bacillus methanolicus to 5-aminovalerate transcriptomic analysis by differential RNA-Seq in the presence and absence of 5AVA was perfromed. In detail: B. methanolicus cultures were grown in MVcM or MVcMY media containing 200 mM methanol supplemented with and without 50 mM 5AVA, respectively. Cells were harvested in the mid log phase at an OD600 of 0.6 and isolation of total RNA isolation was performed individually for each cultivation condition. Isolated RNA samples from B. methanolicus MGA3 were used in biological triplicates for the cDNA library preparation prior to sequencing. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was checked by Agilent RNA Pico 6000 kit on Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). RNA was free of detectable rRNA. Preparation of cDNA libraries were performed according to the manufacturer’s instructions of TruSeq stranded mRNA Kit (Illumina, San Diego, USA). Subsequently, each cDNA library was sequenced on a HiSeq1500 (2 x 75nt PE rapid v2) Sequencer system (Illumina, San Diego, USA).

2021-02-25 | E-MTAB-10101 | biostudies-arrayexpress

RNA-seq of coding RNA of Streptococcus pneumoniae D39 after FCS addition

Project description:Streptococcus pneumoniae (S.p.) is the most common causative agent of community-acquired pneumonia worldwide. A key pathogenic mechanism that exacerbates severity of disease is the disruption of the alveolo-capillary barrier. However, the specific virulence mechanisms responsible for this in the human lung are not yet fully understood. RNA sequencing of Streptococcus pneumoniae transcriptome under infection media conditions, but without the presence of lung tissue, representing anon-host-infection scenario FCS+/- was analyzed,. RNA isolation was performed using an acidic phenol-chloroform extraction protocol (Wetzstein et al., 1992). After DNase-I treatment (Zymo Research, Germany), the RNA quality was checked by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6000 kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). For RNA-seq transcriptomics, Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, United States) was applied to prepare the cDNA libraries. The cDNAs were sequenced paired end on an Illumina HiSeq 1500 (San Diego, CA, United States) using 70 and 75 bp read length and a minimum sequencing depth of 10 million reads per library.

2023-11-30 | E-MTAB-13533 | biostudies-arrayexpress

Project description:San Diego VIM containing Pseudomonas aeruginosa

| PRJNA531714 | ENA

RNAseq analysis of global gene expression patterns in Corynebacterium glutamicum Adaptive Laboratory Evolution (ALE) strains GluA T5 and GluA T7 with accelerated growth and glutarate production.

Project description:The Adaptive Laboratory Evolution (ALE) experiment allowed to select Corynebacterium glutamicum strain GluA T5, which grew faster and produced more glutarate than the parent strain GluA T0, and strain GluA T7 that grew as fast as GluA T5, but produced more 5AVA than GluA T5. To explore differences in the gene expression in the evolved strains, C. glutamicum GluA T0, GluA T5 and GluA T7 biological triplicates were grown in CGXII minimal medium with 4% (w/v) glucose supplemented with 1 mM IPTG. Exponentially growing cells were harvested by centrifugation (14000 × g, 1 min) and kept at -80°C. RNA isolation, purification and quality control was performed as described [82] and the high quality RNA (RNA integrity number > 9.0) was kept at -80°C until further use. Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the ribosomal RNA molecules from the isolated total RNA. Preparation of cDNA libraries were performed according to the manufacturer’s instructions of TruSeq stranded mRNA Kit (Illumina, San Diego, USA). Subsequently, each cDNA library was sequenced on a HiSeq1500 (2 x 70nt PE rapid v2) and NextSeq 500 (2 x 75nt PE mid output v2.5) Sequencer system (Illumina, San Diego, USA).

2021-01-31 | E-MTAB-10025 | biostudies-arrayexpress

microRNA changes during pDC activation

Project description:To identify microRNA changes during plasmacytoid dendritic cell (PDC) activation, we stimulated human primary PDCs with 10ug/ml R837 (Invivogen, San Diego, CA, USA) for 4 hours.

2013-03-25 | GSE21160 | GEO

Porphyromonas gingivalis triggers microglia activation and neurodegenerative processes through NOX4

Project description:Periodontitis and infections with periodontal bacteria have been highlighted as risk factors for dementia. In recent years attention has been drawn to the role of microglia cells in neurodegenerative diseases. However, there is limited knowledge of the influence of periodontal bacteria on microglia cells. The aim of the present study was to investigate the interactions between the periodontal bacteria P. gingivalis and microglia cells, and to unravel if these interactions could contribute to Alzheimer’s pathology. Periodontitis and infections with periodontal bacteria have been highlighted as risk factors for dementia. In recent years attention has been drawn to the role of microglia cells in neurodegenerative diseases. However, there is limited knowledge of the influence of periodontal bacteria on microglia cells. The aim of the present study was to investigate the interactions between the periodontal bacteria P. gingivalis and microglia cells, and to unravel if these interactions could contribute to Alzheimer’s pathology. We found, through microarray analysis, that stimulation of microglia cells with P. gingivalis resulted in upregulation of several Alzheimer´s disease associated genes, including NOX4. We also showed that P. gingivalis LPS mediated ROS production and IL-6 and IL-8 induction via NOX4 in microglia. The viability of neurons was shown to be reduced by conditioned media from microglia cells stimulated with P. gingivalis LPS, and that the reduction was NOX4 dependent. The levels of total and phosphorylated Tau in neurons were increased by conditioned media from microglia cells stimulated with P. gingivalis or LPS. This increase was NOX4 dependent. In summary our findings give us a potential mechanistic explanation of how the periodontal pathogen P. gingivalis could trigger or exacerbate AD pathogenesis.

2024-10-18 | GSE274532 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data