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IntScOmics SIGNED

A single-cell genomics approach integrating gene expression, lineage, and physical interactions

Total Cost €

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EC-Contrib. €

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Partnership

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Project "IntScOmics" data sheet

The following table provides information about the project.

Coordinator
KONINKLIJKE NEDERLANDSE AKADEMIE VAN WETENSCHAPPEN - KNAW 

Organization address
address: KLOVENIERSBURGWAL 29 HET TRIPPENHUIS
city: AMSTERDAM
postcode: 1011 JV
website: www.knaw.nl

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Netherlands [NL]
 Total cost 2˙500˙000 €
 EC max contribution 2˙500˙000 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2016-ADG
 Funding Scheme ERC-ADG
 Starting year 2018
 Duration (year-month-day) from 2018-01-01   to  2022-12-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    KONINKLIJKE NEDERLANDSE AKADEMIE VAN WETENSCHAPPEN - KNAW NL (AMSTERDAM) coordinator 2˙500˙000.00

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 Project objective

From populations of unicellular organisms to complex tissues, cell-to-cell variability in phenotypic traits seems to be universal. To study this heterogeneity and its biological consequences, researchers have used advanced microscopy-based approaches that provide exquisite spatial and temporal resolution, but these methods are typically limited to measuring a few properties in parallel. On the other hand, next generation sequencing technologies allow for massively parallel genome-wide approaches but have, until recently, relied on studying population averages obtained from pooling thousands to millions of cells, precluding genome-wide analysis of cell-to-cell variability. Very excitingly, in the last few years there has been a revolution in single-cell sequencing technologies allowing genome-wide quantification of mRNA and genomic DNA in thousands of individual cells leading to the convergence of genomics and single-cell biology. However, during this convergence the spatial and temporal information, easily accessed by microscopy-based approaches, is often lost in a single-cell sequencing experiment. The overarching goal of this proposal is to develop single-cell sequencing technology that retains important aspects of the spatial-temporal information. In particular I will focus on integrating single-cell transcriptome and epigenome measurements with the physical cell-to-cell interaction network (spatial information) and lineage information (temporal information). These tools will be utilized to (i) explore the division symmetry of intestinal stem cells in vivo; (ii) to reconstruct the cell lineage history during zebrafish regeneration; and (iii) to determine lineage relations and the physical cell-to-cell interaction network of progenitor cells in the murine bone marrow.

 Publications

year authors and title journal last update
List of publications.
2018 Anna Alemany, Maria Florescu, Chloé S. Baron, Josi Peterson-Maduro, Alexander van Oudenaarden
Whole-organism clone tracing using single-cell sequencing
published pages: 108-112, ISSN: 0028-0836, DOI: 10.1038/nature25969
Nature 556/7699 2019-09-09
2018 Jean-Charles Boisset, Judith Vivié, Dominic Grün, Mauro J. Muraro, Anna Lyubimova, Alexander van Oudenaarden
Mapping the physical network of cellular interactions
published pages: 547-553, ISSN: 1548-7091, DOI: 10.1038/s41592-018-0009-z
Nature Methods 15/7 2019-09-09
2018 Lennart Kester, Alexander van Oudenaarden
Single-Cell Transcriptomics Meets Lineage Tracing
published pages: 166-179, ISSN: 1934-5909, DOI: 10.1016/j.stem.2018.04.014
Cell Stem Cell 23/2 2019-09-09

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The information about "INTSCOMICS" are provided by the European Opendata Portal: CORDIS opendata.

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