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CellTrack SIGNED

Cellular Position Tracking Using DNA Origami Barcodes

Total Cost €

0

EC-Contrib. €

0

Partnership

0

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 CellTrack project word cloud

Explore the words cloud of the CellTrack project. It provides you a very rough idea of what is the project "CellTrack" about.

newly    molecular    resolved    mouse    exact    types    opens    mrna    optical    barcodes    differentiated    nature    points    transcriptomics    collected    structures    technique    tissue    523    multiple    creation    hair    theme    stem    sequences    conjugated    samples    sequencing    deep    turning    transcriptome    previously    expression    cancers    al    stable    paths    cells    vivo    dimensional    cell    data    cloning    display    differentiation    441    developmental    made    scaffold    spatiotemporal    unknown    uncover    dependencies    regeneration    locations    expose    fluorophores    positions    small    perform    readable    crypt    physiological    2015    patterns    intestine    create    et    combinatorial    skin    gut    mapping    hybridization    combined    spatial    strategy    proliferating    nano    de    origami    progenitors    cancer    position    imaging    biology    salt    organs    time    origin    interdependencies    biological    effect    issue    dna    completely    benson    nucleotides    organ    procedure    resolution    single    follicle    folding   

Project "CellTrack" data sheet

The following table provides information about the project.

Coordinator
KAROLINSKA INSTITUTET 

Organization address
address: Nobels Vag 5
city: STOCKHOLM
postcode: 17177
website: www.ki.se

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 Sweden [SE]
 Total cost 1˙923˙262 €
 EC max contribution 1˙923˙262 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2016-COG
 Funding Scheme ERC-COG
 Starting year 2017
 Duration (year-month-day) from 2017-08-01   to  2022-07-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    KAROLINSKA INSTITUTET SE (STOCKHOLM) coordinator 1˙923˙262.00

Map

 Project objective

The research I propose here will provide an enabling technology; spatially resolved transcriptomics, to address important problems in cell- and developmental-biology, in particular: How are stem cells in the skin and gut proliferating without turning into cancers? How are differentiated cells related, in their transcriptome and spatial positions, to their progenitors?

To investigate these problems on a molecular level and open up paths to find completely new spatiotemporal interdependencies in complex biological systems, I propose to use our newly developed DNA-origami strategy (Benson et al, Nature, 523 p. 441 (2015) ), combined with a combinatorial cloning technique, to build a new method for deep mRNA sequencing of tissue with single-cell resolution. These new types of origami are stable in physiological salt conditions and opens up their use in in-vivo applications.

In DNA-origami we can control the exact spatial position of all nucleotides. By folding the scaffold to display sequences for hybridization of fluorophores conjugated to DNA, we can create optical nano-barcodes. By using structures made out of DNA, the patterns of the optical barcodes will be readable both by imaging and by sequencing, thus enabling the creation of a mapping between cell locations in an organ and the mRNA expression of those cells.

We will use the method to perform spatially resolved transcriptomics in small organs: the mouse hair follicle, and small intestine crypt, and also perform the procedure for multiple samples collected at different time points. This will enable a high-dimensional data analysis that most likely will expose previously unknown dependencies that would provide completely new knowledge about how these biological systems work. By studying these systems, we will uncover much more information on how stem cells contribute to regeneration, the issue of de-differentiation that is a common theme in these organs and the effect this might have on the origin of cancer.

 Publications

year authors and title journal last update
List of publications.
2018 Erik Benson, Abdulmelik Mohammed, Daniel Rayneau-Kirkhope, Andreas Gådin, Pekka Orponen, Björn Högberg
Effects of Design Choices on the Stiffness of Wireframe DNA Origami Structures
published pages: 9291-9299, ISSN: 1936-0851, DOI: 10.1021/acsnano.8b04148
ACS Nano 12/9 2019-08-30

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

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