Opendata, web and dolomites

ThDEFINE SIGNED

Re(defining) CD4+ T Cell Identities One Cell at a Time

Total Cost €

0

EC-Contrib. €

0

Partnership

0

Views

0

 ThDEFINE project word cloud

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

deal    cytokines    regulatory    tissues    principles    dynamics    immunity    compartment    revealed    individual    sorting    autoimmunity    limitation    revealing    communicate    basic    central    population    quantitative    en    masse    rna    massively    marker    transcription    infections    map    markers    initiates    regulation    seq    vitro    single    unexplored    networks    adoptive    bulk    immune    active    continuum    thousands    transcriptomes    types    signalling    gene    crispr    entire    transcriptional    throughput    mouse    patterns    computational    predictions    consists    cas    unbiased    reveal    surface    variation    combines    overcome    decoding    functional    confirm    enabled    heterogeneity    chemokines    assays    landscape    chart    white    mammalian    profiling    cells    dissect    interactions    modules    transfer    blood    genetic    performing    parallel    sequencing    adaptive    screen    heterogeneous    validate    operate    engineering    homeostasis    powerful    predict    cancer    vivo    exists    cell    populations    knockout    conventional    bioinformatics    masked    molecules    cd4   

Project "ThDEFINE" data sheet

The following table provides information about the project.

Coordinator
GENOME RESEARCH LIMITED 

Organization address
address: THE GIBBS BUILDING, EUSTON ROAD 215
city: LONDON
postcode: NW1 2BE
website: http://www.sanger.ac.uk

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 United Kingdom [UK]
 Total cost 1˙980˙685 €
 EC max contribution 1˙980˙685 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2014-CoG
 Funding Scheme ERC-COG
 Starting year 2016
 Duration (year-month-day) from 2016-01-01   to  2020-12-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    GENOME RESEARCH LIMITED UK (LONDON) coordinator 1˙778˙456.00
2    EUROPEAN MOLECULAR BIOLOGY LABORATORY DE (HEIDELBERG) participant 202˙228.00

Map

 Project objective

The immune system consists of a complex continuum of cell types that communicate with each other and non-immune tissues in homeostasis, and during infections, autoimmunity and cancer. Conventional transcriptional and functional profiling enabled by cell surface marker sorting has revealed a great deal about how specific cell types operate en masse, yet important transcriptional heterogeneity that exists within cell populations remains unexplored. High-throughput single cell RNA-seq can overcome this limitation by profiling entire transcriptomes of thousands of individual cells, revealing cell-to-cell variation by decoding patterns within populations masked in bulk transcriptomes. We will exploit this to dissect the mouse CD4 T cell compartment, a heterogeneous white blood cell population that initiates adaptive immune responses. In AIM 1, we will chart the dynamics of in vivo CD4 cell states in mouse before, during and after immune response challenges. By sequencing thousands of single cell transcriptomes, we will map the landscape of CD4 T cell states in an unbiased, quantitative and comprehensive way. In AIM 2, we will predict key transcription factors, cell surface markers, and signalling molecules, including cytokines/chemokines in each cell state through novel computational approaches. Furthermore, our analyses will establish regulatory modules and networks of gene-gene interactions active in immune responses. In AIM 3, we will (a) confirm the in vivo impact of new cell states by performing adoptive cell transfer assays; and (b) validate our predictions of regulatory molecules and interactions using a massively parallel CRISPR/Cas knockout screen in vitro. This powerful integrated approach combines single cell RNA-sequencing, bioinformatics and genetic engineering to dissect CD4 T cell states, a central compartment of mammalian adaptive immunity, and reveal basic principles of gene regulation.

 Publications

year authors and title journal last update
List of publications.
2017 Tapio Lönnberg, Valentine Svensson, Kylie R. James, Daniel Fernandez-Ruiz, Ismail Sebina, Ruddy Montandon, Megan S. F. Soon, Lily G. Fogg, Arya Sheela Nair, Urijah N. Liligeto, Michael J. T. Stubbington, Lam-Ha Ly, Frederik Otzen Bagger, Max Zwiessele, Neil D. Lawrence, Fernando Souza-Fonseca-Guimaraes, Patrick T. Bunn, Christian R. Engwerda, William R. Heath, Oliver Billker, Oliver Stegle, Ashraful Haque, Sarah A. Teichmann
Single-cell RNA-seq and computational analysis using temporal mixture modeling resolves T H 1/T FH fate bifurcation in malaria
published pages: eaal2192, ISSN: 2470-9468, DOI: 10.1126/sciimmunol.aal2192
Science Immunology 2/9 2019-04-09
2018 Ida Lindeman, Guy Emerton, Lira Mamanova, Omri Snir, Krzysztof Polanski, Shuo-Wang Qiao, Ludvig M. Sollid, Sarah A. Teichmann, Michael J. T. Stubbington
BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq
published pages: 563-565, ISSN: 1548-7091, DOI: 10.1038/s41592-018-0082-3
Nature Methods 15/8 2019-04-09
2016 Michael J T Stubbington, Tapio Lönnberg, Valentina Proserpio, Simon Clare, Anneliese O Speak, Gordon Dougan, Sarah A Teichmann
T cell fate and clonality inference from single-cell transcriptomes
published pages: 329-332, ISSN: 1548-7091, DOI: 10.1038/nmeth.3800
Nature Methods 13/4 2019-05-30

Are you the coordinator (or a participant) of this project? Plaese send me more information about the "THDEFINE" project.

For instance: the website url (it has not provided by EU-opendata yet), the logo, a more detailed description of the project (in plain text as a rtf file or a word file), some pictures (as picture files, not embedded into any word file), twitter account, linkedin page, etc.

Send me an  email (fabio@fabiodisconzi.com) and I put them in your project's page as son as possible.

Thanks. And then put a link of this page into your project's website.

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

More projects from the same programme (H2020-EU.1.1.)

LO-KMOF (2019)

Vapour-deposited metal-organic frameworks as high-performance gap-filling dielectrics for nanoelectronics

Read More  

TRUST (2018)

Truth and Semantics

Read More  

PLAT_ACE (2019)

A new platform technology for the on-demand access to large acenes

Read More