Project Introduction
- Welcome to immgenT, the meta world of mouse T cells!
- Our goal is to coordinate wide community participation around a project of deceptively simple definition: to profile every T cell, in every body location of the mouse, and in every state that immunologic challenges push T cells into. Profiling will be performed at the single-cell level, with the combined determination of mRNA, surface protein (CITE-seq/TotalSeq), and TCR-V sequence (two chains). As all ImmGen arms, the intent is to create a very broad and homogenous set of data, to serve as a general reference, and to enable integrative computational analyses. The OpenSource format is highly suited for a program of this ambition, to allow input and participation from a large community. We aim for an extensive matrix of body locations (lymphoid and parenchymal organs, different stages of development), of challenged states (bacterial, fungal, viral and parasitic infections, autoimmune and inflammatory lesions, tumors, pharmacological intervention), with time, sex and specific genetic mutations as additional variables.
- The interactive table below gives an idea of the project's present and future experiments. As of January 2023, we have sequenced 309,723 QC-passing, non-spleen-ctrl T cells across 31 samples, across tissues, age, sex, and models of autoimmunity, infection, and cancer.
- This dataset represents a unique opportunity for a meta-analysis of T cells, with complex bioinformatic questions to resolve. It is very much a work-in-progress, and by no means definitive at this stage, but meant to incite further suggestions.
- How to participate?
- First and most simply, by making suggestions on the moderated discussion forum to the immgenT project landscape (Forum). Which location/challenge is the project missing? Other suggestions as to experimental groups?
- Secondly and more organically, if you have an idea, specific know-how, a model of T cell function/challenge that you feel is in scope, and whose workup and analysis you would like to be actively involved in, please consider participating by submitting a short proposal and justification (proposal template) to ImmGen.
- Thirdly, if you are interested in some aspects of analyzing this data(multimodal analysis, visualization, cell annotation, transcriptional programs, etc.), please reach out and consider participating by submitting a short proposal and justification (proposal template) to ImmGen.
- Current participants
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A Cassano, A Chervonsky, A Goldrath, A Lebron-Figueroa, A Malik, A Schietinger, AM Globig, B Jabri, C Benoist, C Thefane, D Bangs, D Kaplan, D Mallah, D Sinclair, D Zemmour, E Chang, E Ferraj, E Lucas, E Weiss, G Bee, G Galleti, I Iliev, I Magill, J Altman, J Choi, J Huh, J Kang, J Merkschlager, J Park, J Voisine, K Block, K Cadwell, K Hogquist, K Osum, L Brossay, L Gapin, L Garcia-Rivera, L Yang, M Alegre, M Croze, M Jenkins, M Kronenberg, M Pepper, M Starnbach, M Vacchio, N Abdollahi, N Morris, N Siwapornchai, N van Panhuys, O Barreiro del Rio, P Thomas, R Bosselut, R Lai, S Andrea, S Behar, S Borys, S Candéias, S Gaffen, S H Hart, S Jameson, S Kaech, S Kossida, S Muljo, S Quon, S Reilly, S Schattgen, S Zhang, T Kusakabe, T Shinkawa, U von Andrian, V Giuducelli, V Kuchroo, V Piekarsa, W Lin, X Gong.
- Read the Nature Immunology Correspondence here.
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