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Exploring differentially expressed genes of staphylococcus aureus exposed to human tonsillar cells using RNA sequencing

ABSTRACT: Exploring differentially expressed genes of staphylococcus aureus exposed to human tonsillar cells using RNA sequencing

PROVIDER: PRJNA939634 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23648671_1.fastq.gz	Fastqsanger.gz
	SRR23648671_2.fastq.gz	Fastqsanger.gz
	SRR23648672_1.fastq.gz	Fastqsanger.gz
	SRR23648672_2.fastq.gz	Fastqsanger.gz
	SRR23648673_1.fastq.gz	Fastqsanger.gz

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Exploring differentially expressed genes of staphylococcus aureus exposed to human tonsillar cells using RNA sequencing

Project description:Nasal colonization is well described; however, we have limited knowledge about S. aureus throat colonization. The main objective of this project was to explore differentially expressed genes (DEGs) in S. aureus throat isolate TR145 exposed for 1 or 3 hours (h) to human tonsil epithelial cells (HTEpiC) by using RNA sequencing (RNA-seq) and pathway analysis. We have shown the suitability of using HTEpiC as an in vitro model for investigating key determinants in S. aureus during co-incubation with the HTEpiC cells. Among the DEGs were genes encoding proteins involved in adhesion and immune evasion, as well as iron acquisition and transport. As their expression is induced upon meeting with the HTEpiC, they might be explored further for future targets for intervention to prevent either colonization or infection in the throat region.

2023-03-30 | GSE226317 | GEO

Exploring differentially expressed genes of Staphylococcus aureus exposed to human tonsillar cells using RNA sequencing.

Project description:BackgroundThe nose and the throat are the most predominant colonizing sites of Staphylococcus aureus, and colonization is a risk factor for infection. Nasal colonization is well described; however, we have limited knowledge about S. aureus throat colonization. The main objective of this study was to explore differentially expressed genes (DEGs) in S. aureus throat isolate TR145 exposed to human tonsil epithelial cells (HTEpiC) by using RNA sequencing (RNA-seq) and pathway analysis. DEGs in S. aureus at 1 or 3 hours (h) interaction with its host were explored.ResultsS. aureus was co-cultured in absence and presence of tonsillar cells at 1 or 3 h. Over the 3 h time frame, the bacteria multiplied, but still caused only minor cytotoxicity. Upon exposure to tonsillar cell line, S. aureus changed its transcriptomic profile. A total of 508 DEGs were identified including unique (1 h, 160 DEGs and 3 h, 78 DEGs) and commonly shared genes (1 and 3 h, 270 DEGs). Among the DEGs, were genes encoding proteins involved in adhesion and immune evasion, as well as iron acquisition and transport. Reverse transcription qPCR was done on selected genes, and the results correlated with the RNA-seq data.ConclusionWe have shown the suitability of using HTEpiC as an in vitro model for investigating key determinants in S. aureus during co-incubation with host cells. Several DEGs were unique after 1 or 3 h exposure to host cells, while others were commonly expressed at both time points. As their expression is induced upon meeting with the host, they might be explored further for future targets for intervention to prevent either colonization or infection in the throat.

| S-EPMC10337072 | biostudies-literature

Exploring differentially expressed miRNAs (DEmiRNAs) in plasma sample between lung adenocarcinoma patients and healthy people

Project description:Exploring differentially expressed miRNAs (DEmiRNAs) in plasma sample between lung adenocarcinoma patients and healthy people using a small RNA (sRNA) sequencing,results showed that we could used these DEmiRNAs identified could discriminate healthy peoples from lung adenocarcinoma patients. In present study, we applied an RNA sequencing (RNA-seq) approach to explore the differentially expressed miRNAs (DEmiRNAs) in plasma sample between 6 lung adenocarcinoma patients and 4 healthy people.

2021-03-09 | GSE151963 | GEO

Transcriptomic analysis of differential expressed genes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection

Project description:Purpose: The goals of this study are to understand the transcriptional changes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection and determine the differential expressed genes Methods: Transcriptional profiles of human tonsillar epithelial cells UT-SCC-60B and human tonsillar epithelial cells infected with EV71 were generated by next generation sequencing, in triplicate, using Illumina X-ten/NovaSeq. The sequence reads that passed quality filters were analyzed abundance of mRNA using StringTie, the FPKM values of genes and transcripts were calculated by Ballgown of R software, alternative splicing events were determined by rMATS Results: Using an optimized data analysis workflow, we mapped more than 36 million sequence reads per sample. Total 11137 gene counts and 26860 transcript counts were identified in human tonsillar epithelial cells, 11347 gene counts and 27994 transcript counts were identified in EV71-infected human tonsillar epithelial cells. Total 96 genes and 499 transcripts were down-regulated, 105 genes and 550 transcripts were up-regulated according the criteria that fold changes are more than 1.5, p value less is than 0.05 and mean of FPKM value is more than 0.5 to defined as the differential expressed genes or differential expressed transcripts. Total 11563 novel genes and 14927 novel transcripts were identified and 3266 novel transcripts had the potential coding probabilities. Finally, total 5742 genes occurred alternative splicing events. Conclusions: Our study represents the first detailed analysis of the transcriptional changes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection, this results will provide novel insight into the interaction between human tonsillar epithelial cells and EV71

2019-08-31 | GSE136668 | GEO

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RNAseq analysis of genes differentially expressed in C. elegans exposed to the mold Penicillium brevicompactum

Project description:RNAseq analysis of genes differentially expressed in C. elegans exposed to the mold Penicillium brevicompactum

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Exploring differentially expressed genes related to metabolism by RNA-Seq in porcine embryonic fibroblast after insulin treatment

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