A longitudinal single-cell atlas to predict outcome and toxicity after BCMA-directed CAR T cell therapy in multiple myeloma

This repository contains singularity images and datasets to reproduce the publication figures in: Michael Rade, David Fandrei, Markus Kreuz et al. A longitudinal single-cell atlas to predict outcome and toxicity after BCMA-directed CAR T cell therapy in multiple myeloma Corresponding github repo: https://github.com/fraunhofer-izi/Rade_et_al_CAR_2025 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>># Content# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>seurat_objects.tar.gz: Processed Seurat objects used for publication:06_seurat_harmony_t_all.Rds” is a subset (only T cells) of “05_seurat_harmony_all.Rds”. 05_vdj_t.Rds and 05_vdj_t.Rds: To protect patient privacy, nt and aa sequences of the clones were removed. The names of the clones (originally gene + nt sequence) were renamed using pseudo IDs in this fishare version cellranger_gex_adt.tar.gz:Cell ranger output for RNA and ADT data. To protect patient privacy, TCR/BCR Cell ranger output (which contains sequences) has been removed. souporcell.tar.gz:Sourporcell output used for demultiplexing the libraries. featurer_reference_ADT_10xFeature reference CSV files in which antibody capture constructs and associated barcodes are declared. These files are required for CellRanger. Table_multiplexing_info.xlsxMultiplexing information for each library and numbers of cells for each sample before and after the filtering steps Table_cellranger_multi_omics.xlsxQuality control for each 10x library (cellranger output) Singularity Images and R packages singularity-rstudio-4-3-2.sif:Singularity image contains R and Rstudio Server. This image was used to produce the results.For a description of how to use it, see: https://github.com/fraunhofer-izi/Rade_et_al_CAR_2025/tree/main/singularity souporcell_latest.sif:Singularity contain the image souporcell (https://github.com/wheaton5/souporcell) and was used for demultiplexing. Input for souporcell are BAM files (cellranger output). 4_3_2_R_packages.tar.gz:Corresponding R packages