Data for Patient-derived model capturing hypoxia and extracellular matrix remodelling of immunologically cold high-grade serous tumours

This dataset contains the fsc files obtained by flow cytometry and the images obtained by second harmonic generation microscopy, immunohistochemistry or immunofluorescence used for the preparation of the manuscript. These datasets were used to asses the role of physiologically relevant oxygen levels in stroma-driven extracellular matrix remodelling and its influence in immune infiltration and immune-stroma-tumour interactions in high-grade serous carcinoma. The data is divided into two main folders, namely flow cytometry and images. Each of the folders contains subfolders named as the FigureID_Brief Experimental Description Flow cytometry folders contain the raw fsc files obtained by flow cytometry that are named as Date_cell type_oxygen_treatment_PatientID or sampleID Date indicates the date when the experiment was run by flow cytometry or when the images were taken. Cell type can indicate: TME stands for tumor microenvironment when dissociated patient tumors were used MNC stands for mononuclear cells when immune cells were included in the culture Kura stands for KURAMOCHI cell line CAF(s)stands for cancer-associated fibroblasts When co-cultures or multi-cultures were used, all cell types are listed in the file name, separated by underscore Oxygen condition: indicates either "Physo" that stands for cells cultured in physoxia or "Hypo" for cells cultured in hypoxia Treatment: indicates either NT that stands for not treated or control conditions treated with a vehicle or Gal that stands for galunisertib treated samples. In the absence of any denomination the samples were not treated. PatientID: is indicated with "Pn" where n is a randomly assigned number for deidentification of the patient material on the day of the experiment. No patient material was reused on different days of analysis SampleID indicates biological replicates Image folders contain the images acquired by second harmonic generation microscopy (SHG), immunohistochemistry (IHC) or immunofluorescence (IF). The subfolders for IHC are named with the date of the imaging (mm/dd/yy).The files are named as Oxygen_Cell type_treatment_PatientID or sampleID_protein detected Oxygen condition: indicates either "Physo" that stands for cells cultured in physoxia or "Hypo" for cells cultured in hypoxia Cell type can indicate: HGSC stands for high-grade serous carcinoma when dissociated patient tumors were used MNC stands for mononuclear cells when immune cells were included in the culture Kura stands for KURAMOCHI cell line CAF(s)stands for cancer-associated fibroblasts Treatment: indicates either NT that stands for not treated or control conditions treated with a vehicle or Gal that stands for galunisertib treated samples. In the absence of any denomination the samples were not treated. PatientID: is indicated with "Pn" where n is a randomly assigned number for deidentification of the patient material on the day of the experiment. No patient material was reused on different days of analysis SampleID indicates biological replicates ROI: indicates region of interest Protein detected: COL1: collagen I HIF1a: hypoxia-inducible factor 1a aSMA: alpha-smooth muscle actin FN: fibronectin HE: hematoxylin and eosin staining TC: Masson's trichrome staining CD8: CD8+ T cells TGFB: transforming growth factor beta本数据集包含用于该论文撰写的流式细胞术所得FSC（Flow Cytometry Standard）文件，以及通过二次谐波生成显微镜、免疫组织化学或免疫荧光技术获取的图像。本数据集旨在评估生理相关氧分压在基质驱动的细胞外基质重塑中的作用，及其在高级别浆液性癌中对免疫浸润以及免疫-基质-肿瘤相互作用的影响。 数据分为两个主文件夹，即“流式细胞术”与“图像”文件夹。 每个文件夹均包含以“图号_简短实验描述”命名的子文件夹。 流式细胞术文件夹内包含流式细胞术所得原始FSC文件，文件命名格式为"Date_cell type_oxygen_treatment_PatientID或sampleID"。其中"Date"指流式细胞术实验运行日期或图像拍摄日期。 细胞类型的可选标识如下： - TME（Tumor Microenvironment，肿瘤微环境）：当使用解离的患者肿瘤组织时的标识 - MNC（Mononuclear Cells，单个核细胞）：当培养体系中包含免疫细胞时的标识 - Kura：指KURAMOCHI细胞系 - CAF(s)（Cancer-Associated Fibroblasts，癌症相关成纤维细胞）：当使用癌症相关成纤维细胞时的标识 若使用共培养或多培养体系，文件名中会以下划线分隔列出所有参与的细胞类型。 氧分压条件：分为"Physo"（代表在生理氧浓度下培养的细胞）与"Hypo"（代表在低氧条件下培养的细胞）。 样本处理方式：分为"NT"（未处理或使用溶剂对照处理的对照组）与"Gal"（经galunisertib处理的样本）；若文件名中无上述标识，则代表样本未接受任何处理。 PatientID：以"Pn"格式标注，其中"n"为随机分配的编号，用于实验当日对患者样本进行去标识化处理，且不同分析日期不会复用同一患者样本。 SampleID：代表生物学重复样本。 图像文件夹内包含通过二次谐波生成显微镜（Second Harmonic Generation microscopy, SHG）、免疫组织化学（Immunohistochemistry, IHC）或免疫荧光（Immunofluorescence, IF）采集的图像。其中免疫组织化学子文件夹以成像日期（格式为mm/dd/yy）命名，文件命名格式为"Oxygen_Cell type_treatment_PatientID或sampleID_protein detected"。 氧分压条件与上述流式细胞术部分一致，分为"Physo"（生理氧浓度培养）与"Hypo"（低氧培养）。 细胞类型可选标识如下： - HGSC（High-Grade Serous Carcinoma，高级别浆液性癌）：当使用解离的患者肿瘤组织时的标识 - MNC（Mononuclear Cells，单个核细胞）：培养体系中包含免疫细胞时的标识 - Kura：KURAMOCHI细胞系 - CAF(s)（Cancer-Associated Fibroblasts，癌症相关成纤维细胞）：癌症相关成纤维细胞的标识 样本处理方式与流式细胞术部分一致："NT"代表未处理或溶剂对照处理组，"Gal"代表经galunisertib处理的样本组，文件名无上述标识则代表样本未接受处理。 PatientID与SampleID的定义与流式细胞术部分完全相同。 ROI（Region of Interest，感兴趣区域）：指图像中的目标观测区域。 检测蛋白对应的说明如下： - COL1：Ⅰ型胶原蛋白 - HIF1a：缺氧诱导因子1α - αSMA：α-平滑肌肌动蛋白 - FN：纤连蛋白 - HE：苏木精-伊红染色 - TC：马松三色染色 - CD8：CD8+ T细胞 - TGFB：转化生长因子β