Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

CTTV020 epigenomes of cell lines PILOT RNA

ABSTRACT: These RNAseq experiments are carried out as part of the CTTV020 project to identify a gene expression signature of common immortalised cell lines / models. This signature / fingerprint will be used in combination with data from ChIPseq experiments from the same cell types to compare various human immortalised cell models against primary cells and tissues. The overall aims of the CTTV020 Cell Line Epigenome project are to establish a systematic approach for the determination of human biological & disease relevance through the generation of transciptomic and epigenomic data in cell types of interest \Integration of cell type mRNA expression and epigenome data with existing & newly generated reference data from human tissue and cell types to identify assay systems which will provide greater confidence in translating target biology and compound pharmacology to patients.\To provide a framework for the identification of optimal cell types for target identification/validation studies and drug discovery programs across multiple therapeutic areas. \Development of bioinformatics pipelines and CTTV components for analysis and provision of dataThis data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo Sapien

SUBMITTER:

PROVIDER: E-ERAD-386 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The activation of receptors displayed on the surface of cells typically initiates cytoplasmic signalling cascades that lead to changes in cellular transcriptional responses so that a cell expresses proteins that enable it to behave appropriately as a function of their position within an organism. Understanding these signals and learning how to either prevent or ectopically activate them could have many therapeutic benefits and applications. In some cases these signals are highly localised, being delivered by directly neighbouring cells that express ligands which specifically bind to and activate receptors; for example, stem cells display receptors for ligands provided by cells within their niche to both ensure continual production of cells, and that their cellular progeny are directed towards appropriate fates. While for some cell types we know something of these signals enabling the in vitro differentiation of stem cells towards certain cellular fates, the differentiation processes is often not complete and so immature cell types which are not fully functional are produced, implying that some important signals are missing. Here, we propose to systematically identify receptor-triggered signalling pathways by stimulating receptors on the surface of human stem cells by using a library of soluble recombinant oligomerised protein ligands and measuring the consequent transcriptional perturbations using RNA-seq. We propose to screen an existing library of ~50 oligomerised human ligands previously used in receptor protein interaction screens and first test them for their ability to bind to human stem cells to identify those ligands for which the stem cells express a cell surface receptor. For those ligands which interact with the stem cells (we estimate between 2 and 5), they will be added to stem cell cultures and their effects on transcription quantified. The budget requested is sufficient for us to include controls and test important parameters such different time points after addition of the proteins. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

Dataset Information

CTTV020 epigenomes of cell lines PILOT RNA

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