Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Global gene expression profiles during differentiation of mouse embryonic stem cells to macrophages

ABSTRACT: 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/We established protocols to generate monocytes and macrophages from murine embryonic stem cell (129 background) in vitro. Briefly, murine embryonic stem cells were grown in bacteriological dishes in the presence of differentiation medium supplement ed with 15% L929 and 1ng/ml IL-3 for 8 days to generate embryoid bodies (EBs). Subsequently, EBs were transferred to gelatinized tissue culture dish. Supernatants containing macrophage progenitors were collected, spun down and plated onto bacteriological dishes to differentiate into macrophages. Four biological replicates of murine embryonic stem cells, macrophage progenitors and macrophages were collected and their RNA were isolated via the Qiagen RNA Isolation Kit. The RNA were treated with RNAse free DNase and eluted in RNase-free water. THe RNA concentration was assessed using a NanoDrop spectrophotometer, while RNA integrity (RIN >8) were obtained for all samples by Agilent 2100 Bioanalyzer. We aim to sequence 5GBp per replicate and 4 replicates per lane on an Illumina platform.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER:

PROVIDER: E-ERAD-132 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Conditional-ready mouse embryonic stem cell derived macrophages enable the study of essential genes in macrophage function.

Yeung A T Y AT Hale C C Xia J J Tate P H PH Goulding D D Keane J A JA Mukhopadhyay S S Forrester L L Billker O O Skarnes W C WC Hancock R E W RE Dougan G G

Scientific reports 20150310

The ability to differentiate genetically modified mouse embryonic stem (ES) cells into functional macrophages provides a potentially attractive resource to study host-pathogen interactions without the need for animal experimentation. This is particularly useful in instances where the gene of interest is essential and a knockout mouse is not available. Here we differentiated mouse ES cells into macrophages in vitro and showed, through a combination of flow cytometry, microscopic imaging, and RNA- ...[more]

PMID: 25752829

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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/

Dataset Information

Global gene expression profiles during differentiation of mouse embryonic stem cells to macrophages

Publications

Conditional-ready mouse embryonic stem cell derived macrophages enable the study of essential genes in macrophage function.

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