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RNA-seq analysis of cell-line models for monocyte to macrophage transformation: Project 3 of Open Targets - Epigenomes of Cell Lines

ABSTRACT: RNA-seq analysis of cell-line models for monocyte to macrophage transformation: Project 3 of Open Targets - Epigenomes of Cell Lines

PROVIDER: PRJEB16680 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1701140_1.fastq.gz	Fastqsanger.gz
	ERR1701140_2.fastq.gz	Fastqsanger.gz
	ERR1701141_1.fastq.gz	Fastqsanger.gz
	ERR1701141_2.fastq.gz	Fastqsanger.gz
	ERR1701142_1.fastq.gz	Fastqsanger.gz

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Project description:The goal of this experiment is to characterize the expression of two cell-line models of monocyte to macrophage transformation, U937 and THP-1. Either PMA (phorbol myristate acetate) and LPS (lipopolysaccharide) or VD3 (vitamin D3) and LPS were used as stimuli to induce differentiation. <br>The following protocol was used for both cell-lines: Cells from single replicates were cultured in parallel. At 0 hrs, cells were split into 6 aliquots with two aliquots in each of three treatment conditions; no treatment, 2 nM PMA or 66 nM Vitamin D3. At 24 hrs, one aliquot of cells from each treatment condition was stimulated with a spike-in of LPS to a final concentration of 100 ng/mL or given an equal amount of medium as a control. 18 hrs after LPS stimulation cells were harvested. <br>This RNA-seq experiment is being carried out as part of the Open Targets project to identify a gene expression signature of common immortalized cell lines/models. This signature will be used in combination with data from ChIP-seq experiments from the same cell lines against primary cells and tissues. The overall aim of the Open Targets Cell Line Epigenome project is to establish a systematic approach for the determination of human biological and disease relevance through the generation of transcriptomic and epigenomic data in cell lines of interest. Comparison of cell line mRNA expression and epigenome data with existing and newly generated reference data from human tissue and cell types will identify assay systems that will provide greater confidence in translating target biology and compound pharmacology to patients.

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