This repository contains the code used for analysis and to generate the figures for the following article:
Chella Krishna Vadivel, Andreas Willerslev-Olsen, Martin Rich Javadi Namini, Ziao Zeng, Lang Yan, Maria Danielsen, Maria Gluud, Emil Marek Heymans Pallesen, Karolina Wojewoda, Amra Osmancevic, Signe Hedebo, Yun-Tsan Chang, Lise M. Lindahl, Sergei B. Koralov, Larisa J Geskin, Susan E Bates, Lars Iversen, Thomas Litman, Rikke Bech, Marion Wobser, Emmanuella Guenova, Maria R. Kamstrup, Niels Odum*, Terkild B. Buus*; Staphylococcus aureus induce drug resistance in cancer T cells in Sézary Syndrome. Blood 2024; blood.2023021671. DOI: https://doi.org/10.1182/blood.2023021671
CITE-seq data generated in this study has been deposited to FigShare under DOI: http://doi.org/10.6084/m9.figshare.23649780. CITE-seq data used in reanalysis of previously published cohort (Herrera & Cheng et al) is deposited at GEO under GSE171811.
Notebooks
- Figure 2 and Supplementary Figure 2 - CITE-seq analysis
- Figure 5B - CITE-seq cytokine expression
- Supplementary Figure 3 - Skin vs Blood
- Supplementary Figure 4 - Romidepsin resistance geneset analysis
We have also included a notebook showing how the multisce object used in the above notebooks can be converted and saved as a normal SingleCellExperiment object here