Opendata, web and dolomites


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

Total Cost €


EC-Contrib. €






 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.

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

Project "ThDEFINE" data sheet

The following table provides information about the project.


Organization address
city: LONDON
postcode: NW1 2BE

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


Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    GENOME RESEARCH LIMITED UK (LONDON) coordinator 1˙778˙456.00


 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.


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 ( 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.)

EAST (2020)

Using Evolutionary Algorithms to Understand and Secure Web/Enterprise Systems

Read More  

BactRNA (2019)

Bacterial small RNAs networks unravelling novel features of transcription and translation

Read More  


Gaining insights into human evolution and disease prevention from adaptive natural selection driven by lethal epidemics

Read More