Profiling heterogeneity in Human derived IPSC neurons
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PROVIDER: EGAS00001002885 | EGA |
REPOSITORIES: EGA
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1) 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 please see http://www.sanger.ac.uk/datasharing/
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This dataset contains all the data available for this study on 2020-05-18.
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Project description:The goal of this project is to understand the etiology and pathology of host-pathogen interaction using high-throughput cellular phenotyping. By combining the expertise in pathogen biology, informatics and stem cell biology across the institute, this project will use targeted genetic modification in mouse embryonic stem cells to identify functions of host genes in innate immunity. We will also explore the biology of mouse embryonic stem cells and their differentiation into immune competent cells. To this end we will generate homozygous and inducible knockout lines in mouse embryonic stem cells, which will be differentiated into immune competent cells, such as macrophages or dendritic cells. These will be subjected to a panel of immune challenge and stimulation assays to characterise the functions of the disrupted genes. To identify new functions for mammalian genes in innate immunity we will:\Generate a panel of homozygous inducible gene knockout mouse ES cell lines working from a list of ca. 80 candidate genes (MGP phenotyping and GWAS hits). \Scale up differentiation protocols for immune challenge and stimulation assays.\Benchmark in vitro differentiated ES cell models against primary immune cells from selected MGP mouse lines and eventually against human iPS cells.\Screen a panel of 30 genetically modified cell lines in immunological challenge and stimulation assays, defining phenotypes at the cellular level by high content imaging, biochemically by assaying cytokine production, and at the molecular level by transcriptome analysis.\Define novel gene functions in innate immunity through network analysis of gene expression data from all challenged cell lines.\In the longer term scale up the production and phenotyping of genetically modified cell lines (mouse or human as appropriate).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/
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2019-09-20 | E-MTAB-5965 | biostudies-arrayexpress
Project description:Tissue-specific methylation patterns suggest a role for CpG island methylation in differentiation and cell-type-specific gene regulation. We have profiled CpG island methylation in different cells of the immune cell lineage to investigate this role. MBD-affinity purification combined with next generation sequencing was used to analyse CpG island methylation in dendritic cells, B cells, Th1, Th2 and naïve T cells. ChIP-seq was carried out to determine RNA polymerase II binding sites in these cell types and this was compared to the methylation profiles obtained. 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/ Abstract: We have profiled CpG island methylation in various immune system cell types and related this to gene expression in these cells.
2011-11-10 | E-ERAD-27 | biostudies-arrayexpress
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2015-06-09 | E-ERAD-363 | biostudies-arrayexpress
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2015-09-15 | E-ERAD-385 | biostudies-arrayexpress
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/
2015-04-21 | E-ERAD-351 | biostudies-arrayexpress
Project description:n order to progress human induced pluripotent stem cells (hiPSCs) towards the clinic, several outstanding questions must be addressed. It is possible to reprogram different somatic cell types into hiPSCs and from studies in the mouse, it appears that an epigenetic memory of the starting cell type is carried over to hiPSCs. However a comprehensive comparative study of the characteristics of these hiPSCs has been missing from the literature. Importantly studies which aimed to address these aspects of hiPSCs have used cells from different patients. In order to avoid this important confounding variable and to keep the genetic background constant, tissue samples were procured from the patients and reprogrammed to iPS cells. The methylation status of these iPS cells will be compared.Protocol:Primary cell cultures were generated and reprogrammed to iPS cells. DNA was extracted and immunoprecipitated using anti-methyl cytosine and anti-hydroxymethyl cytosine antibodies.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/
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2016-10-25 | E-MTAB-3952 | biostudies-arrayexpress
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