Preprocessed h5ad files of Xenium spatial transcriptomics performed on atherosclerotic human carotid artery samples

Xenium_final_dataset.zip Xenium runs were performed with two panels of genes. The panels consist of a core list present in both panels (comprising 111 central genes for cell type annotations and key processes) as well as individual genes for the panels, resulting in a cell-defining (panel 1) and disease associated (panel 2) panel. In total 548 unique genes have been sequenced with both panels. Sequencing with panel 1 and panel 2 genes was performed on consecutive FFPE sections for each sample, thereby introducing a 5 µm shift in the morphology of the mounted Xenium slides across the panels. Xenium_final_dataset.zip contains the Anndata objects for count matrices obtained with panel 1 and panel 2 genes. In addition, the Anndata objects contain patient metadata variables. Description of .obs columns is provided in the Xenium_column_descriptions.md file.IMPORTANT: THE COLUMNS [x_um,y_um] IN ANNDATA.OBS, WHICH CONTAIN THE CELL CENTER COORDINATES IN MICROMETERS ARE INCORRECT IN THIS VERSION DUE TO A BUG IN THE CODE. TO CALCULATE THE CORRECT VALUES IN MICROMETERS, MULTIPLY THE COLUMNS [x_pixel, y_pixel] by 0.2125!Subregion_coordinates.zip The annotation of sample subregions is a histological analysis, using established Oxford Plaque Studies and AHA criteria and was performed by an experienced cardiovascular pathologist. The borders of the annotated subregions were initially determined on the HE stained slides by a pathology expert, then transferred to the DAPI-stained slides manually by drawing the determined subregion borders by hand in Xenium Explorer. The manually anootated subregion coordinates for individual samples are contained in the Subregion_coordinates.zip file. Note, that the "_D" suffix corresponds to plaque, whereas the "_H" suffix to control samples. subregion_area_dict.pickle Border coordinates were extracted from Xenium Explorer and converted to polygons, which then were used to assign individual cells to their respective subregions and to calculate the subregion areas. Subregion polygons and areas of individual samples, along with whole sample areas are contained in subregion_area_dict.pickle, in a Python pickled dictionary format. Detailed description of preprocessing steps can be found in our manuscript.Xenium_final_dataset.zip 本数据集的Xenium实验采用两组基因探针面板完成。两组面板均包含一组共用核心基因列表（含111个用于细胞类型注释与关键生物学过程研究的核心基因），同时各带有专属独有基因，最终分别构建出用于细胞定义的**面板1（panel 1）**与疾病关联分析的**面板2（panel 2）**。两组面板共计完成548个独特基因的测序。针对每个样本，两组面板的测序均在连续的福尔马林固定石蜡包埋（FFPE）切片上开展，因此不同面板对应的Xenium载玻片的成像形态存在5微米的偏移。 Xenium_final_dataset.zip中包含了由面板1与面板2基因测序得到的计数矩阵的Anndata对象（Anndata）。此外，这些Anndata对象中附带了患者元数据变量。.obs列的详细说明可查阅Xenium_column_descriptions.md文件。重要提示：由于代码存在漏洞，本版本Anndata对象.obs中的[x_um, y_um]列（存储以微米为单位的细胞中心坐标）存在错误。若需获取正确的微米级坐标值，请将[x_pixel, y_pixel]列乘以0.2125。 Subregion_coordinates.zip 样本亚区域的注释基于组织病理学分析，参考了已发表的牛津斑块研究（Oxford Plaque Studies）与美国心脏协会（AHA）标准，由经验丰富的心血管病理学家完成。注释亚区域的边界最初由病理专家在苏木精-伊红（HE）染色切片上确定，随后通过Xenium Explorer手动手绘亚区域边界，将其转移至4',6-二脒基-2-苯基吲哚（DAPI）染色切片上。各样本的手动注释亚区域坐标存储于Subregion_coordinates.zip文件中。请注意，文件名后缀“_D”对应斑块样本，“_H”对应对照样本。 subregion_area_dict.pickle 研究人员从Xenium Explorer中提取边界坐标并转换为多边形，以此将单个细胞分配至对应亚区域并计算亚区域面积。各样本的亚区域多边形、亚区域面积及全样本面积均以Python pickle字典格式存储于subregion_area_dict.pickle文件中。 预处理步骤的详细说明可参阅本团队的研究手稿。