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RNAseq of human epithelial nasopharyngeal carcinoma cell line Detroit 562, following infection with strains of Streptococcus pneumoniae

ABSTRACT: RNAseq of human epithelial nasopharyngeal carcinoma cell line Detroit 562, following infection with strains of Streptococcus pneumoniae

PROVIDER: PRJEB32013 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3262080_1.fastq.gz	Fastqsanger.gz
	ERR3262080_2.fastq.gz	Fastqsanger.gz
	ERR3262090_1.fastq.gz	Fastqsanger.gz
	ERR3262090_2.fastq.gz	Fastqsanger.gz
	ERR3262100_1.fastq.gz	Fastqsanger.gz

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Project description:A total of 432 genes were found to be differentially expressed in M1SF370 bacterial population internalized in Detroit 562 human pharyngeal cells when compared with the same strain incubated in the absence of Detroit 562 cells. While most of them (349/432 i.e. 80.8%) were up regulated, 83 genes were down regulated contributing to 19.2% of the total differentiated genes. The major contributor of the latter category was phage-related genes (35 genes). Almost ¼ of these genes (106) belonged to a category of Unknown or possible predicted function. Most notably, up-regulated genes belonged to amino acid transport , cell division, cell envelope biogenesis, DNA replication correlated well with up-regulated 67 genes belonged to translation and ribosomal structure. Further, up-regulation of 12/15 virulence-related genes indicated that human host cell internalized bacteria are highly virulent as compared to laboratory grown culture in test-tubes. S. pyogenes strain type M1 SF370 (wild-type) was procured from ATCC (ATCC 700294). Detroit 562 pharyngeal cells were obtained from ATCC and maintained in MEM with 10% FBS in humidified CO2-incubator. Purified cDNA preparations from the Detroit cells-internalized bacteria and that were cultured without Detroit cells, were labeled with either Alexafluor-555 or Alexafluor-647 depending on the experimental design ( i.e. dye swap experiment). Differentially labeled probes were then combined and purified. Using four independently isolated RNA preparations (biological replicates), a total of 8 experiments (incorporating 4 dye swaps) were performed. Accordingly eight hybridization measurements for this mutant were obtained. Exp-1 and -2 (GSM687276, GSM687310-dye swap) are the technical replicates of the biological sample-1, Exp-3 and -4 (GSM687311, GSM687312-dye swap) are technical replicates of biological sample-2, Exp-5 and -6, (GSM687313,GSM687319-dye swap,) are technical replicates of the biological sample-3, and finally Exp-7 and -8, (GSM687320,GSM687321-dye swap) are technical replicates of the biological sample-4. .

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RNAseq of human epithelial nasopharyngeal carcinoma cell line Detroit 562, following infection with strains of Streptococcus pneumoniae

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