November 30, 2022

A Single Cell Transcriptomics Platform

1st Call, Tech Trans

Short Summary

The goal of this proposal is to establish a state-of-the-art –omics platform that is specifically focused on enabling single cell transcriptomic experiments and analyses.

Goals

We envision that this primary Single Cell Transcriptomics Platform will consist of three layers: (1) establishment of already available and in-house validated scRNA-seq approaches such as Smart-seq2, Drop-seq, and 10X Genomics; (2) implementation of a state-of-the-art spatial transcriptomics workflow, as the resolution of cells not only in time but also in space has significant fundamental and clinical potential; and (3) provision of bioinformatic data analysis services and workflows centered around our principal software tool, ASAP (Gardeux et al., Bioinformatics, 2017).

Significance

The significance of establishing this platform is that, by enabling single cell transcriptomics for a wide biological community, we will be able to significantly increase our understanding of fundamental biological processes such as development as well as completely alter our approach toward drug design as well as patient-specific therapy.

Background

The recent development of single cell-targeting, high-throughput sequencing methods is revolutionizing our ability to tackle biological heterogeneity. One of these approaches is single cell RNA-seq (scRNA-seq), which has the capacity to assess the mRNA repertoire of hundreds to thousands of individual cells at a time. In the short period since its development, scRNA-seq has been truly transformative by uniquely enabling the identification and molecular characterization of healthy and pathological cells and the definition of cell type-specific signatures.

Publications

David, B. Deplancke$, V. Gardeux$. ASAP: an open, scalable and interactive web-based portal for (single-cell) omics analyses, Nucleic Acids Research, 48:W403-414, 2020.
Li*, J. Janssens*, M. De Waegeneer, S. Saroja Kolluru, K. Davie, V. Gardeux, W. Saelens, F. David, M. Brbić, J. Leskovec, C.N. McLaughlin, Q. Xie, R.C. Jones, K. Brueckner, J. Shim, S. Gopal Tattikota, F. Schnorrer, K. Rust, T.G. Nystul, Z. Carvalho-Santos, C. Ribeiro, S. Pal, T.M. Przytycka, A.M. Allen, S.F. Goodwin, C.W. Berry, M.T. Fuller, H. White-Cooper, E.L. Matunis, S. DiNardo, A. Galenza, L. Erin O’Brien, J.A.T. Dow, FCA Consortium, H. Jasper, B. Oliver, N. Perrimon#, B. Deplancke#, S.R. Quake#, L. Luo#, S. Aerts#. Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly, BioRxiv, 2021; Science, 2022.
Bues*, M. Biočanin*, J. Pezoldt, R. Dainese, A. Chrisnandy, S. Rezakhani, W. Saelens, V. Gardeux, R. Gupta, J. Russeil, Y. Saeys , E. Amstad, M. Claassen, M. Lutolf, B. Deplancke. Deterministic scRNA-seq of individual intestinal organoids reveals new subtypes and coexisting distinct stem cell pools, BioRxiv, 2020; Nature Methods, 2022.
Maier, M. Biočanin, J. Bues, F. Meyenhofer, C. Brunet Avalos, J.Y. Kwon, B. Deplancke, S.G. Sprecher. Multimodal and multisensory coding in the Drosophila larval peripheral gustatory center, BioRxiv, 2020.
Chen*, O. Guillaume-Gentil*, R. Dainese, P.Y. Rainer, M. Zachara, C.G. Gäbelein, J.A. Vorholt#, B. Deplancke#. Live cell transcriptome profiling using Live-seq, BioRxiv, 2021; Nature, 2022.