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本仓库包含用于复现下述论文发表图表的Singularity镜像与数据集：Michael Rade、David Fandrei、Markus Kreuz等。论文标题为《针对多发性骨髓瘤中BCMA靶向CAR-T细胞治疗后的结局与毒性进行预测的纵向单细胞图谱》。 对应GitHub仓库：https://github.com/fraunhofer-izi/Rade_et_al_CAR_2025 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>># Content# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> seurat_objects.tar.gz： 用于论文制作的已处理Seurat对象："06_seurat_harmony_t_all.Rds"为"05_seurat_harmony_all.Rds"的子集（仅包含T细胞）。 "05_vdj_t.Rds"与"05_vdj_t.Rds"：为保护患者隐私，已移除克隆的核苷酸（nt）与氨基酸（aa）序列。本版本中，克隆的原始命名（原构成为基因名+核苷酸序列）已通过伪ID进行重命名。 cellranger_gex_adt.tar.gz： RNA与ADT数据的Cell Ranger输出结果。为保护患者隐私，已移除包含序列信息的T细胞受体（TCR）/B细胞受体（BCR）Cell Ranger输出文件。 souporcell.tar.gz： 用于对测序文库进行解多重（demultiplexing）的Souporcell输出结果。 featurer_reference_ADT_10x： 用于声明抗体捕获构建体及其关联条形码的Feature Reference CSV文件，此类文件为CellRanger运行所必需。 Table_multiplexing_info.xlsx： 包含各文库的多重测序信息，以及各样本在过滤步骤前后的细胞计数。 Table_cellranger_multi_omics.xlsx： 针对每一个10x文库的质控结果（Cell Ranger输出结果）。 Singularity镜像与R软件包： singularity-rstudio-4-3-2.sif：该Singularity镜像集成了R与Rstudio Server，用于生成本研究的全部结果。关于其使用方法，请参阅：https://github.com/fraunhofer-izi/Rade_et_al_CAR_2025/tree/main/singularity souporcell_latest.sif：该Singularity镜像集成了Souporcell工具（https://github.com/wheaton5/souporcell），用于执行测序文库解多重操作。Souporcell的输入文件为Cell Ranger输出的BAM文件。 4_3_2_R_packages.tar.gz：对应的R软件包集合。