Multiplexed imaging mass cytometry reveals distinct tumor-immune microenvironments linked to immunotherapy responses in melanoma

- melanoma_IMC_data.zip The zip file contains the raw IMC images (in the raw_tiff folder) and corresponding single cell masks (in the mask folder) associated with the paper "Multiplexed imaging mass cytometry reveals distinct tumor-immune microenvironments linked to immunotherapy responses in melanoma". The MCD files by CyTOF IMC were exported to a multi-channel TIFF file including 41 channels, and the order of the channel was provided in the Melanoma_panel.csv. - Melanoma_code_data.zip The zip file contains the 4 folders described as follows: Folder ”data“: the processed data for the result shown in paper - Folder "input": - sc_data.csv: the single cell protein expression data; - Folder "abundance": the cell type abundance files; - Folder "clidata": the response and survival data for 4 melanoma datasets used in the paper; - Folder "hc_result": TME archetypes annotation for each sample/ROI from hierarchical clustering; - Folder "ICB": data for ICB analysis (presented in FigS3); - Folder "meta": panel file for clustering; - Folder "RNAseq_data": the RNAseq data for 4 melanoma datasets used in the paper; - Folder "RNAseq_deconv": the result of cell type deconvolution from bulk RNAseq; - Folder "spatial": data for neighbourhood analysis (presented in Fig3, FigS4). - Folder "output": intermediate result for analysis. Folder "Rscript": R scripts for reproducing results in the paper. - generate_Figs.Rmd: ploting figures presented in the paper; - functions.R: functions used for analysis; - Clustering.Rmd: determining cell types based on marker intensities; - Spatial_analysis.Rmd: neighbourhood analysis to get significant interction/avoidance cell relationships. Folder "Figs": figures presented in paper. Folder "HE_figs": the H&E image and the ROIs distribution for each sample.- melanoma_IMC_data.zip：该压缩包包含与论文《Multiplexed imaging mass cytometry reveals distinct tumor-immune microenvironments linked to immunotherapy responses in melanoma》相关的原始成像质谱流式细胞术(Imaging Mass Cytometry, IMC)成像文件（存放于raw_tiff文件夹）及对应单细胞掩码文件（存放于mask文件夹）。其中，通过CyTOF生成的MCD(Mass Cytometry Data)文件被导出为包含41个通道的多通道TIFF(Tagged Image File Format)文件，通道顺序详见Melanoma_panel.csv。 - Melanoma_code_data.zip：该压缩包包含如下内容： 文件夹"data"：用于复现论文结果的已预处理数据 文件夹"input"： - sc_data.csv：单细胞蛋白表达数据； - 子文件夹"abundance"：细胞类型丰度文件； - 子文件夹"clidata"：论文中使用的4个黑色素瘤数据集的免疫治疗应答与生存数据； - 子文件夹"hc_result"：通过层级聚类得到的每个样本/区域兴趣点(Region of Interest, ROI)的肿瘤微环境(Tumor Microenvironment, TME)原型注释结果； - 子文件夹"ICB"：免疫检查点阻断(Immune Checkpoint Blockade, ICB)分析所用数据（对应补充图FigS3）； - 子文件夹"meta"：用于细胞聚类的标记物面板文件； - 子文件夹"RNAseq_data"：论文中使用的4个黑色素瘤数据集的转录组测序(RNA Sequencing, RNAseq)数据； - 子文件夹"RNAseq_deconv"：基于批量转录组测序数据的细胞类型反卷积结果； - 子文件夹"spatial"：邻域分析所用数据（对应主图Fig3、补充图FigS4）； 文件夹"output"：分析流程产生的中间结果文件； 文件夹"Rscript"：用于复现论文结果的R脚本： - generate_Figs.Rmd：用于绘制论文中展示的统计图的脚本； - functions.R：分析流程中使用的自定义工具函数； - Clustering.Rmd：基于标记物表达强度鉴定细胞类型的分析脚本； - Spatial_analysis.Rmd：用于识别具有显著相互作用/排斥关系的细胞邻域的分析脚本； 文件夹"Figs"：论文中展示的正式统计图； 文件夹"HE_figs"：每个样本的苏木精-伊红(HE)染色图像及对应区域兴趣点(ROI)的分布情况。