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Transcriptome profiling of THP-1 cells treated with chemicals

ABSTRACT: Transcriptome profiling of THP-1 cells treated with chemicals

PROVIDER: PRJNA787325 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17174300.fastq.gz	Fastqsanger.gz
	SRR17174301.fastq.gz	Fastqsanger.gz
	SRR17174302.fastq.gz	Fastqsanger.gz
	SRR17174303.fastq.gz	Fastqsanger.gz
	SRR17174304.fastq.gz	Fastqsanger.gz

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Transcriptome profiling of THP-1 cells treated with chemicals

Project description:We profiled the transcriptome of Dexamethasone-, Tofacitinib-, Tacrolimus-, Prednisolone-, sodium lauryl sulfate (SLS)-, Aciclovir-, Benzoic acid-, Genistein-, Ribavirin-, Mercuric chloride-, Cyclosporine- and LPS-treated monocytes and without chemical-treated (basal, vehicle) monocytes. A Bioconductor software package in R called edgeR was used to conduct the differential expression analysis. Lowly expressed genes were filtered out by keeping only genes with worthwhile counts in a minimum number of samples. The default normalization method in edgeR, trimmed mean of M-values (TMM) normalization was performed, and dispersion estimates (common and tagwise dispersions) were obtained to proceed with differential expression determination. Differentially expressed genes were determined by conducting pairwise comparisons between each type of immunosuppressor or non-immunosuppressor and vehicle or control by applying fold-change and p-value cutoffs (|fold-change| > 1.5 and p-value < 0.05). Each immunosuppressor, excluding sodium lauryl sulfate, was compared with the vehicle group. Immunosuppressor sodium lauryl sulfate and non-immunosuppressor lipopolysaccharide were compared with the basal group. Non-immunosuppressors genistein and ribavirin were compared with the vehicle group.

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Gene expression of LY6E-silent THP-1 cells and control THP-1 cells

Project description:Expression profiling of LY6E-silent THP-1 cells (THP-1-shLY6E) and control cells (THP-1-shCtrl). Results provide evidence that LY6E is effectively knocked down in THP-1shLY6E, compared to THP-1-shCtrl, and show the different expressed genes following LY6E silence in THP-1 cells.

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Project description:THP-1 macrophages were treated with EVs and stimulated with LPS, and then total RNA was extracted from cells. Extracted total RNAs were investigated by microarray analysis. Increase and decrease of mRNA expression were investigated between EV-treated and non-treated THP-1 macrophages.

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