CITE-seq data from <b><i>Staphylococcus aureus</i></b><b> induce drug resistance in cancer T cells in Sézary Syndrome</b>

CITE-seq dataset of cells from a Sézary Syndrome patient cultured in the presence or absence of Romidepsin and/or S. aureus enterotoxins (SE) used in 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 SS17.rds is contains R Data Serialization (RDS) file of a SingleCellExperiment (SCE) R object containing integrated single-cell CITE-seq data from four samples (PBS, Romidepsin, SE and Romidepsin+SE treatment) after 36 hours of in vitro culture. The column data (colData) of the SCE object contains the following information from each cell: treatment - whether cell was cultured in the presence (Romidepsin) or absence (DMSO) of Romidepsinstimulation - whether cell was cultured in the presence (SE) or absence (PBS) of S. aureus enterotoxins (SE)group - cell sample condition origin (a combination of stimulation and treatment columns)lane - whether cell was included in lane1 or lane2 of the two 10X Chromium lanes run in parallel from the same cell suspension poolsum - number of Unique Molecular Identifiers (UMIs) assigned to the celldetected - number of genes detected in the cellsubsets_Mito_percent - proportion of UMIs stemming from mitochondrial genessizeFactor - calculated sizeFactor for normalizationTRA_top5 - assignment of TCRalpha chain clonotype to one of the top5 clonotypes detected based on CDR3 amino acid sequenceTRB_top5 - assignment of TCRbeta chain clonotype to one of the top5 clonotypes detected based on CDR3 amino acid sequencecc_phase - inferred cell cycle phasecc_score_s - inferred cell cycle S-phase scorecc_score_G2M - inferred cell cycle G2M-phase scoreleiden_totalVI - leiden clustering assignment from lantent space of totalVI runcell_type - Cell type assignment of the cellSCE object contains three alternative experiment objects: ADT - Antibody derived tag (ADT) UMI counts from surface protein modalityVI_ADT - Antibody derived tag (ADT) UMI counts from surface protein modality denoised and normalized by totalVITF - Transcription factor activation scores (from DoRothEA) for each cell calculated using decoupleRSCE object contains three dimension reductions: PCA - principal component analysis calculated based on highly variable genestotalVI - latent space loadings from totalVI analysisumap - Uniform Manifold Approximation and Projection calculated based on latent space from totalVICode used in the analysis of this data is available on GitHub