reSeArCH Letter
Acknowledgements We thank J. Vogel and S. Gorski for comments on the
manuscript and T. Walzthoeni (Bioinformatics Core Facility, Institute of
Computational Biology,Helmholtz Zentrum München) for bioinformatics
support. The work was funded by the European Research Council (ERC-2016-
CoG 721016-HERPES and ERC-2018-PoC-DL3 832409 T-GRAND-SLAM)
and Infect-ERA grant eDEVILLI (031L0005B) to L.D. The Helmholtz Institute
for RNA-based Infection Research (HIRI) supported this work with a seed
grant through funds from the Bavarian Ministry of Economic Affairs and
Media, Energy and Technology (grant allocation no. 0703/68674/5/2017
and 0703/89374/3/2017). F.J.T. and M.L. acknowledge financial support by
the Graduate School QBM (GSC 1006); F.J.T. was supported by BMBF grants
01IS18036A and 01IS18053A, the German Research Foundation (DFG)
within the Collaborative Research Centre 1243, Subproject A17, the Helmholtz
Association (Incubator grant sparse2big, ZT-I-0007) and the Chan Zuckerberg
Initiative DAF (advised fund of Silicon Valley Community Foundation, 182835).
M.L. and P.A. acknowledge financial support from the Joachim Herz Stiftung and
IZKF, respectively.
Author contributions Conceptualization: F.E., A.-E.S. and L.D.; computational
methodology: M.L., C.S.J. and F.E.; investigation: F.E., M.A.P.B., T.K., T.H., M.L.,
P.A., F.J.T. and A.-E.S.; infection experiments: M.A.P.B. and T.H.; establishment
of scSLAM-seq: M.A.P.B., T.K., P.A., A.-E.S. and L.D; writing: F.E., A.-E.S. and L.D.;
funding acquisition: A.-E.S., F.E. and L.D.; supervision: F.J.T., A.-E.S., F.E. and L.D.Competing interests A patent (EP 18 17 9371) has been filed on the GRAND-
SLAM approach to analyse the relative contribution of transcriptional activity
based on U-to-C conversions. The authors declare no other competing interests.Additional information
Supplementary information is available for this paper at https://doi.org/
10.1038/s41586-019-1369-y.
Correspondence and requests for materials should be addressed to F.E. or
A.-E.S. or L.D.
Reprints and permissions information is available at http://www.nature.com/
reprints.