Illumina sequencing of library 8947268, constructed from sample accession ERS370596 for study accession ERP004375.  This is part of an Illumina multiplexed sequencing run (11765_1).  This submission includes reads tagged with the sequence ATCACG.

Illumina HiSeq 2000 paired end sequencing

Pilot Study 1 Wild type Embryonic Stem Cell Derived Macrophages stimulated with Tri-Dap (Toll-like receptor agonist) + LPS 1ng/ml

Mus musculus

High-throughput cellular phenotyping to understand the etiology and pathology of host-pathogen interaction.

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/

Cellular_phenotyping_of_host_pathogen_interactions

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