Hallmarks of antigen experience and terminal exhaustion in T cells are absent in multiple myeloma patients from diagnosis through maintenance therapy

Code and data associated with Shasha et al., "Hallmarks of antigen experience and terminal exhaustion in T cells are absent in multiple myeloma patients from diagnosis through maintenance therapy". Description of files below:

scRNA-seq_code.tar: Python notebooks for analysis of scRNA-seq data, including import and figure generation

adata-rev.h5ad: processed CD8 T cell scRNA-seq data from all patients and samples combined

ics_tsv_repeat_dat.csv: ICS metadata

cytof_ics_repeat_data.tar: normalized ICS tsv and fcs files from all patients and samples

ics_repeat_analysis.R: R code for analysis of ICS data

cytof_data.tar: CyTOF fcs and txt files (bead normalized and compensated, gated to CD8 T cells)

本数据集配套Shasha等人发表的题为《T细胞的抗原暴露特征与终末耗竭表型在多发性骨髓瘤患者从确诊至维持治疗全程均不存在》的研究论文。以下为各配套文件的详细说明：
scRNA-seq_code.tar：用于单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）数据分析的Python Jupyter脚本包，涵盖数据导入与图表生成相关代码
adata-rev.h5ad：整合所有患者及样本的已处理CD8阳性T细胞单细胞RNA测序数据
ics_tsv_repeat_dat.csv：细胞内细胞因子染色（Intracellular Cytokine Staining, ICS）元数据
cytof_ics_repeat_data.tar：整合所有患者及样本的标准化细胞内细胞因子染色TSV与流式细胞术标准（Flow Cytometry Standard, FCS）文件
ics_repeat_analysis.R：用于细胞内细胞因子染色数据分析的R脚本
cytof_data.tar：经过磁珠标准化与补偿处理、并门控筛选出CD8阳性T细胞的质谱流式细胞术（Cytometry by Time-of-Flight, CyTOF）FCS与TXT文件