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E-MTAB-4101

ABSTRACT: RNA-seq analysis of six cell line models for haematopoiesis: Project 1 of Open Targets - Epigenomes of Cell Lines

PROVIDER: E-MTAB-4101 | ExpressionAtlas | 2019-07-05

REPOSITORIES: ExpressionAtlas

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			Action	DRS
	E-MTAB-4101-analysis-methods.tsv	Tabular
	E-MTAB-4101-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-4101-coexpressions.tsv.gz	Tabular
	E-MTAB-4101-configuration.xml	Xml
	E-MTAB-4101-factors.xml	Xml

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RNA-seq analysis of six cell line models for haematopoiesis: Project 1 of Open Targets - Epigenomes of Cell Lines

Project description:This experiment captures the baseline expression of 6 cell lines (K562, KU812, MEG01, HEL9217, F36-P, UT7) selected for Project 1, Open Targets 020. These cell lines are all possible cell models for haematopoiesis.<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.

2016-01-27 | E-MTAB-4101 | biostudies-arrayexpress

RNA-seq analysis of 2 cell line models of lung disease (A549 and BEAS-2B) and primary bronchial epithelial cells in Project 3 of Open Targets 020 - Epigenomes of Cell Lines

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2017-07-04 | E-MTAB-4729 | biostudies-arrayexpress

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Project description:The aim of this experiment was to characterize the gene expression of several immortalized B cell lines (Namalwa, Daudi, Ramos, Raji, Toledo, ARH-77). Two independent cultures were carried out for each of the cell lines. Cell lines were grown using supplier recommended culture methods and harvested sub-confluence in exponential growth phase. This RNA-seq experiment is being carried out as part of the Open Targets project to identify a gene expression signature of common immortalised 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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Project description:RNA-seq analysis of two cell line models of lung diseases in Project 3 of Open Targets - Epigenomes of Cell Lines

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2019-05-14 | E-MTAB-6870 | ExpressionAtlas

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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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RNA-seq analysis of several in vitro models of hepatocyte function: Project 4 of Open Targets - Epigenomes of Cell Lines

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E-MTAB-4729

Project description:RNA-seq analysis of 2 cell line models of lung disease (A549 and BEAS-2B) and primary bronchial epithelial cells in Project 3 of Open Targets 020 - Epigenomes of Cell Lines

2019-05-15 | E-MTAB-4729 | ExpressionAtlas

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