A multiplex single-cell RNA-Seq pharmacotranscriptomics pipeline for drug discovery

This work was supported by the University of Oulu and funded by the Research Council of Finland (Profi6 336449, 333583, 288475 and 271845 to D.U. and 349787 to J.R.), Sigrid Juselius Foundation (to D.U.) and Finnish Cancer Foundation (to D.U.).

Raw (only for JHOS2) and processed scRNA-Seq data from this manuscript were deposited to the National Center for Biotechnology Information Genome Expression Omnibus under accession number GSE274905. The Leiden cluster markers, the subsample pseudobulk DGE analysis results, the patient-derived bulk RNA-Seq processed data and the interactive 3D UMAPs are available from Mendeley Data (https://doi.org/10.17632/j9j4mdm9yr.1). The raw FASTQ files used to generate results for the patient-derived models will be provided for scientific research upon reasonable request to fulfill privacy and ethical concerns. Source data are provided with this paper. All relevant code is available from GitHub (https://github.com/ungureanulab/pharmacotranscriptomics).

Imaging was performed at the Biomedicum Imaging Unit, University of Helsinki, with the support of the Helsinki Institute of Life Science (HiLIFE) and Biocenter Finland.