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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.

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

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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