Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Single cell mRNA -sequencing reveals cell-to-cell variation in three mouse ES cell culture conditions

ABSTRACT: We sequence mRNA from single mESCs from three culture conditions: serum + LIF, 2i + LIF and alternative 2i + LIF. We extensively analysed population and single cell gene expression to identify differences and similarities between conditions. This is a subset of data from ArrayExpress accession E-ERAD-186 (ENA: ERP003293)

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: Aleksandra Kolodziejczyk

PROVIDER: E-MTAB-2600 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

Kim Jong Kyoung JK Kolodziejczyk Aleksandra A AA Ilicic Tomislav T Teichmann Sarah A SA Marioni John C JC

Nature communications 20151022

Single-cell RNA-sequencing (scRNA-seq) facilitates identification of new cell types and gene regulatory networks as well as dissection of the kinetics of gene expression and patterns of allele-specific expression. However, to facilitate such analyses, separating biological variability from the high level of technical noise that affects scRNA-seq protocols is vital. Here we describe and validate a generative statistical model that accurately quantifies technical noise with the help of external RN ...[more]

PMID: 26489834

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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

Single cell mRNA -sequencing reveals cell-to-cell variation in three mouse ES cell culture conditions

Publications

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

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