Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia: scRNA-seq and CyTOF processed datasets

This data was generated as part of the Tumor Profiler study. If you use it in your research, please cite: Wegmann, R., Bonilla, X., Casanova, R. et al. Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia. Nat Commun 15, 9402 (2024). https://doi.org/10.1038/s41467-024-53535-4 Derived data - scRNA-seq This is an R data set (.RDS) containing a SingleCellExperiment object with the following slots: Assays: counts: raw counts colData: Cell-level metadata barcodes: The cell barcode fractionMT: Fraction mitochondrial genes per cell n_umi: Total number of UMIs per cell n_gene: Total number of genes per cell log_umi: log10 total number of UMIs per cell g2m_score: Cell cycle phase score for G2M s_score: Cell cycle phase score for S cycle_phase: predicted cell cycle phase celltype_major_full_ct_name: Major cell type full name celltype_major: Major cell type short name celltype_final_full_ct_name: Cell subtype full name celltype_final: Cell subtype short name sample_id rowData: Gene-level metadata gene_ids gene_names Derived data - CyTOF This is an R data set (.RDS) containing a SingleCellExperiment object with the following slots: Assays: counts_raw: signal intensity based on CyTOF dual counts exprs_raw: arcsinh transformed raw counts (cofactor 5) counts: batch corrected raw counts (linear scaling based on a quantile) exprs: arcsin transformed counts (cofactor 5) scaled: 0-1 normalized exprs (clipped to the 99.95th percentile) colData (cell metadata) bc_id: barcode of the sample during staining run: CyTOF experiment batch, named after the first sample of the batch type: Sample type (blood or bone marrow) sample_id: TuPro sample ID pred_id: Predicted cell type [char] pred_n: Predicted cell type [integer] rowData (marker metadata) channel_name: Name and isotopic mass of the metal ion corresponding to this marker marker_name: Protein name channel_group, channel_group_integer: Biological processes the channel identifies, e.g. specific cell type, signalling, cell death tsne_channel: Logical - use this channel for dimensionality reduction? channel_order: Define the order of channels for plotting cluster_channel: Logical - use this channel for clustering?本数据集源自肿瘤分析器（Tumor Profiler）研究项目。若将其用于学术研究，请引用以下文献： Wegmann R、Bonilla X、Casanova R等. 急性髓系白血病中先天性与获得性耐药的单细胞图谱. 自然-通讯（Nat Commun）, 2024, 15: 9402. https://doi.org/10.1038/s41467-024-53535-4 ### 衍生数据集——单细胞RNA测序（scRNA-seq） 本R语言数据集（.RDS格式）包含一个SingleCellExperiment对象，其包含以下插槽： #### 检测矩阵（Assays）： counts：原始计数矩阵 #### colData：细胞级元数据 barcodes：细胞条形码 fractionMT：每个细胞的线粒体基因占比 n_umi：每个细胞的UMI（唯一分子标识符）总数量 n_gene：每个细胞的检测基因总数量 log_umi：每个细胞UMI总数量的以10为底的对数值 g2m_score：G2/M期细胞周期评分 s_score：S期细胞周期评分 cycle_phase：预测得到的细胞周期时相 celltype_major_full_ct_name：主要细胞类型完整名称 celltype_major：主要细胞类型简称 celltype_final_full_ct_name：细胞亚型完整名称 celltype_final：细胞亚型简称 sample_id：样本ID #### rowData：基因级元数据 gene_ids：基因序列标识符 gene_names：基因名称 ### 衍生数据集——质谱流式细胞术（CyTOF） 本R语言数据集（.RDS格式）包含一个SingleCellExperiment对象，其包含以下插槽： #### 检测矩阵（Assays）： counts_raw：基于CyTOF双计数的信号强度 exprs_raw：经过反正双曲正弦变换的原始计数（辅因子为5） counts：经过批次校正的原始计数（基于分位数的线性缩放） exprs：经过反正双曲正弦变换的校正后计数（辅因子为5） scaled：经0-1归一化的exprs值（截断至99.95百分位数） #### colData（细胞元数据） bc_id：染色阶段的样本条形码 run：CyTOF实验批次，以该批次的首个样本命名 type：样本类型（血液或骨髓） sample_id：TuPro样本ID pred_id：预测的细胞类型（字符型） pred_n：预测的细胞类型（整数型） #### rowData（标记物元数据） channel_name：对应该标记物的金属离子名称与同位素质量 marker_name：蛋白质名称 channel_group、channel_group_integer：该通道所识别的生物学过程，例如特定细胞类型、信号通路、细胞死亡相关 tsne_channel：逻辑值——是否将该通道用于降维分析？ channel_order：定义绘图时的通道顺序 cluster_channel：逻辑值——是否将该通道用于聚类分析？