CITE-seq data from Staphylococcus aureus induce drug resistance in cancer T cells in Sézary Syndrome

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 Romidepsin
• stimulation - 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 pool
• sum - number of Unique Molecular Identifiers (UMIs) assigned to the cell
• detected - number of genes detected in the cell
• subsets_Mito_percent - proportion of UMIs stemming from mitochondrial genes
• sizeFactor - calculated sizeFactor for normalization
• TRA_top5 - assignment of TCRalpha chain clonotype to one of the top5 clonotypes detected based on CDR3 amino acid sequence
• TRB_top5 - assignment of TCRbeta chain clonotype to one of the top5 clonotypes detected based on CDR3 amino acid sequence
• cc_phase - inferred cell cycle phase
• cc_score_s - inferred cell cycle S-phase score
• cc_score_G2M - inferred cell cycle G2M-phase score
• leiden_totalVI - leiden clustering assignment from lantent space of totalVI run
• cell_type - Cell type assignment of the cell

SCE object contains three alternative experiment objects:

1. ADT - Antibody derived tag (ADT) UMI counts from surface protein modality
2. VI_ADT - Antibody derived tag (ADT) UMI counts from surface protein modality denoised and normalized by totalVI
3. TF - Transcription factor activation scores (from DoRothEA) for each cell calculated using decoupleR

SCE object contains three dimension reductions:

1. PCA - principal component analysis calculated based on highly variable genes
2. totalVI - latent space loadings from totalVI analysis
3. umap - Uniform Manifold Approximation and Projection calculated based on latent space from totalVI

Code used in the analysis of this data is available on GitHub